| Next changeset 1:8beb2af51dc5 (2019-02-18) |
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Commit message:
Uploaded files |
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added:
ariba_flag.xml ariba_run.xml macros.xml test-data/OUT/assembled_genes.fa.gz test-data/OUT/assembled_seqs.fa.gz test-data/OUT/assemblies.fa.gz test-data/OUT/debug.report.tsv test-data/OUT/log.clusters.gz test-data/OUT/report.tsv test-data/OUT/version_info.txt test-data/PREPAREREF/00.info.txt test-data/PREPAREREF/00.version_info.txt test-data/PREPAREREF/01.filter.check_genes.log test-data/PREPAREREF/01.filter.check_metadata.log test-data/PREPAREREF/01.filter.check_metadata.tsv test-data/PREPAREREF/02.cdhit.all.fa test-data/PREPAREREF/02.cdhit.clusters.pickle test-data/PREPAREREF/02.cdhit.clusters.tsv test-data/PREPAREREF/02.cdhit.gene.fa test-data/PREPAREREF/02.cdhit.gene.varonly.fa test-data/PREPAREREF/02.cdhit.noncoding.fa test-data/PREPAREREF/02.cdhit.noncoding.varonly.fa test-data/metadata.tsv test-data/reads_1.fq test-data/reads_2.fq test-data/ref_seqs.fa test-data/test_ariba_database.loc tool-data/ariba_databases.loc tool-data/ariba_databases.loc.sample tool-data/card.db/00.info.txt tool-data/card.db/00.rename_info tool-data/card.db/00.version_info.txt tool-data/card.db/01.filter.check_genes.log tool-data/card.db/01.filter.check_metadata.log tool-data/card.db/01.filter.check_metadata.tsv tool-data/card.db/02.cdhit.all.fa tool-data/card.db/02.cdhit.clusters.pickle tool-data/card.db/02.cdhit.clusters.tsv tool-data/card.db/02.cdhit.gene.fa tool-data/card.db/02.cdhit.gene.varonly.fa tool-data/card.db/02.cdhit.noncoding.fa tool-data/card.db/02.cdhit.noncoding.varonly.fa tool-data/plasmidfinder.db/00.info.txt tool-data/plasmidfinder.db/00.rename_info tool-data/plasmidfinder.db/00.version_info.txt tool-data/plasmidfinder.db/01.filter.check_genes.log tool-data/plasmidfinder.db/01.filter.check_metadata.log tool-data/plasmidfinder.db/01.filter.check_metadata.tsv tool-data/plasmidfinder.db/02.cdhit.all.fa tool-data/plasmidfinder.db/02.cdhit.clusters.pickle tool-data/plasmidfinder.db/02.cdhit.clusters.tsv tool-data/plasmidfinder.db/02.cdhit.gene.fa tool-data/plasmidfinder.db/02.cdhit.gene.varonly.fa tool-data/plasmidfinder.db/02.cdhit.noncoding.fa tool-data/plasmidfinder.db/02.cdhit.noncoding.varonly.fa tool-data/prepare_ref.sh tool-data/resfinder.db/00.info.txt tool-data/resfinder.db/00.rename_info tool-data/resfinder.db/00.version_info.txt tool-data/resfinder.db/01.filter.check_genes.log tool-data/resfinder.db/01.filter.check_metadata.log tool-data/resfinder.db/01.filter.check_metadata.tsv tool-data/resfinder.db/02.cdhit.all.fa tool-data/resfinder.db/02.cdhit.clusters.pickle tool-data/resfinder.db/02.cdhit.clusters.tsv tool-data/resfinder.db/02.cdhit.gene.fa tool-data/resfinder.db/02.cdhit.gene.varonly.fa tool-data/resfinder.db/02.cdhit.noncoding.fa tool-data/resfinder.db/02.cdhit.noncoding.varonly.fa tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 79b55c74fb80 ariba_flag.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ariba_flag.xml Tue Jan 08 10:26:30 2019 -0500 |
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| @@ -0,0 +1,29 @@ +<tool id="ariba_flag" name="ARIBA flag" version="@VERSION@"> + <description> + Translate the meaning of a flag + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + ariba flag $flag > flag_explain.txt + ]]> </command> + + <inputs> + <param name="flag" type="integer" value="" label="A number" help="Flag to be translated"/> + </inputs> + + <outputs> + <data name="flag_explain" format="txt" label="${tool.name} result for code: ${flag}" from_work_dir="flag_explain.txt"/> + </outputs> + + <help><![CDATA[ + usage: ariba flag <flag> + + Translate the meaning of a flag output by ARIBA, found in the report tsv file + + ]]> </help> + <expand macro="citations"/> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 79b55c74fb80 ariba_run.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ariba_run.xml Tue Jan 08 10:26:30 2019 -0500 |
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| b'@@ -0,0 +1,138 @@\n+<tool id="ariba_run" name="ARIBA run" version="@VERSION@">\n+ <description>\n+ Runs the local assembly pipeline\n+ </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="version_command" />\n+\n+ <command detect_errors="exit_code"><![CDATA[\n+ ariba run \n+ \n+ --nucmer_min_id $adv_nucmer.nucmer_min_id\n+ --nucmer_min_len $adv_nucmer.nucmer_min_len\n+ --nucmer_breaklen $adv_nucmer.nucmer_breaklen\n+\n+ --assembly_cov $adv_assembly.assembly_cov\n+ --min_scaff_depth $adv_assembly.min_scaff_depth\n+ \n+ #if str($adv_assembly.adv_assembler.assembler) == "spades"\n+ --spades_mode $adv_assembly.adv_assembler.spades_mode\n+ #if str($adv_assembly.adv_assembler.assembler) != "none"\n+ --spades_options $adv_assembly.adv_assembler.spades_options\n+ #end if\n+ #end if\n+\n+ --threads $adv_other.threads\n+ --assembled_threshold $adv_other.assembled_threshold\n+ --gene_nt_extend $adv_other.gene_nt_extend\n+ --unique_threshold $adv_other.unique_threshold\n+\n+ $adv_other.force\n+ $adv_other.noclean\n+ $adv_other.verbose\n+ \n+ \'$ariba_databases.fields.path\'\n+\n+ #if str($library.lib_type) == "paired"\n+ \'$library.R1\'\n+ \'$library.R2\'\n+ #else if str($library.lib_type) == "collection"\n+ \'$library.input1.forward\'\n+ \'$library.input1.reverse\'\n+ #end if\n+\n+ out\n+ ]]> </command>\n+ <inputs>\n+ <conditional name="library">\n+ <param name="lib_type" type="select" label="Input reads type or collection" help="Select \'paired end\' for a single library or \'collection\' for a paired end collection">\n+ <option value="paired" selected="true">Paired End</option>\n+ <option value="collection">Paired Collection</option>\n+ </param>\n+ <when value="paired">\n+ <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>\n+ <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>\n+ </when>\n+ <when value="collection">\n+ <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>\n+ </when>\n+ </conditional>\n+\n+ <!-- DATABASE INPUT-->\n+ <param label="Select a database" name="ariba_databases" type="select">\n+ <options from_data_table="ariba_databases">\n+ <validator message="No database is available" type="no_options" />\n+ </options>\n+ </param>\n+ <!-- Assembly options -->\n+ <section name="adv_assembly" title="Assembly Advanced options" expanded="False">\n+ <conditional name="adv_assembler">\n+ <param name="assembler" type="select" label="Assembler">\n+ <option value="spades" selected="true">spades</option>\n+ <option value="fermilite">fermilite</option>\n+ </param>\n+ <when value="spades">\n+ <param name="spades_mode" argument="--spades_mode" type="select" label="Spades assembler mode" help="SPAdes assembler mode either use default WGS\n+ mode, Single Cell mode (sc) or RNA mode (rna). Use SC or RNA mode if your input is from a viral sequencing with very uneven and deep coverage. Set assembly_cov to some high value if\n+ using SC or RNA mode">\n+ <option value="wgs" selected="true">WGS<'..b'cmer_min_len" type="integer" value="20" label="Minimum alignment length" help="Minimum alignment length (the delta-filter -l option). (Default: 20)" />\n+ <param name="nucmer_breaklen" argument="--nucmer_breaklen" type="integer" value="200" label="Value to use for -breaklen when running nucmer" help="Value to use for -breaklen when running nucmer. (Default: 200)" />\n+ </section>\n+ <!-- Other options -->\n+ <section name="adv_other" title="Other options" expanded="False">\n+ <param name="threads" argument="--threads" type="integer" value="1" label=" Number of threads" help=" Experimental. Number of threads. Will run clusters in parallel, but not minimap. (Default: 1)" />\n+ <param name="assembled_threshold" argument="--assembled_threshold" type="float" min="0" max="1" value="0.95" label="Assembly threshold" help="If proportion of gene assembled (regardless of into how many contigs) is at least this value then the flag gene_assembled is set. (Default: 0.95)" />\n+ <param name="gene_nt_extend" argument="--gene_nt_extend" type="integer" value="30" label="Max number of nucleotides to extend ends of gene matches to look for start/stop codons" help="Max number of nucleotides to extend ends of gene matches to look for start/stop codons. (Default: 30)" />\n+ <param name="unique_threshold" argument="--unique_threshold" type="float" min="0" max="1" value="0.03" label="Proportion of bases to set unique assembled contig" help="If proportion of bases in gene assembled more than once is smaller than this value, then the flag unique_contig is set. (Default: 0.03)" />\n+ <param name="force" argument="--force" type="boolean" truevalue="--force" falsevalue="" checked="True" label="Overwrite output directory, if it already exists" help="Overwrite output directory, if it already exists (default: ON)" />\n+ <param name="noclean" argument="--noclean" type="boolean" truevalue="--noclean" falsevalue="" checked="False" label="Do not clean up intermediate files" help="Do not clean up intermediate files (default: OFF)" />\n+ <param name="verbose" argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="False" label="Be verbose" help="Be verbose (default: OFF)" />\n+ </section>\n+ </inputs>\n+\n+ <outputs>\n+ <data format="tabular" name="report" label="${tool.name} on ${on_string} report file" from_work_dir="out/report.tsv" />\n+ <data format="fasta" name="assembled_genes" label="${tool.name} on ${on_string}: gzipped FASTA file of assembled gene sequences" from_work_dir="out/assembled_genes.fa.gz"/>\n+ <data format="fasta" name="assembled_seqs" label="${tool.name} on ${on_string}: gzipped FASTA file of assembled sequences" from_work_dir="out/assembled_seqs.fa.gz"/>\n+ <data format="fasta" name="assemblies" label="${tool.name} on ${on_string}: gzipped FASTA file of the assemblies" from_work_dir="out/assemblies.fa.gz"/>\n+ <data format="gz" name="log_cluster" label="${tool.name} on ${on_string}: Log for the progress of each cluster" from_work_dir="out/log.clusters.gz"/>\n+ <data format="txt" name="tools_version" label="${tool.name} on ${on_string}: Tools version" from_work_dir="out/version_info.txt"/>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="lib_type" value="paired"/>\n+ <param name="R1" value="reads_1.fq"/>\n+ <param name="R2" value="reads_2.fq"/>\n+ <param name="ariba_databases" value="PREPAREREF"/>\n+\n+ <output name="report" file="OUT/report.tsv" ftype="tsv"/>\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+ **Usage**: ariba run [options] <prepareref_dir><reads1.fq><reads2.fq><outdir>\n+\n+ Runs the local assembly pipeline. Input is dir made by prepareref, and paired\n+ reads\n+ \n+ ]]> </help>\n+\n+ <expand macro="citations" />\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 79b55c74fb80 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jan 08 10:26:30 2019 -0500 |
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| @@ -0,0 +1,18 @@ +<macros> + <token name="@VERSION@">0.1.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.13.2">ariba</requirement> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>ariba version | head -n 1</version_command> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1099/mgen.0.000131</citation> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r 79b55c74fb80 test-data/OUT/debug.report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT/debug.report.tsv Tue Jan 08 10:26:30 2019 -0500 |
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| @@ -0,0 +1,14 @@ +#ariba_ref_name ref_name gene var_only flag reads cluster ref_len ref_base_assembled pc_ident ctg ctg_len ctg_cov known_var var_type var_seq_type known_var_change has_known_var ref_ctg_change ref_ctg_effect ref_start ref_end ref_nt ctg_start ctg_end ctg_nt smtls_total_depth smtls_nts smtls_nts_depth var_description free_text +noncoding3 noncoding3 0 0 19 100 cluster_1 180 180 100.0 cluster_1.l6.c17.ctg.1 289 31.1 . . . . . . . . . . . . . . . . . generic description of noncoding3 +noncoding1 noncoding1 0 0 531 84 cluster_2 120 120 98.33 cluster_2.l15.c30.ctg.1 391 19.3 1 SNP n A14T 1 A14T SNP 14 14 A 128 128 T 18 T 18 noncoding1:0:0:A14T:noncoding_group1:ref has wild type, reads have variant so should report generic description of noncoding1 +noncoding1 noncoding1 0 0 531 84 cluster_2 120 120 98.33 cluster_2.l15.c30.ctg.1 391 19.3 1 SNP n A6G 1 . . 6 6 G 120 120 G 12 G 12 noncoding1:0:0:A6G:.:variant in ref and reads so should report generic description of noncoding1 +noncoding1 noncoding1 0 0 531 84 cluster_2 120 120 98.33 cluster_2.l15.c30.ctg.1 391 19.3 1 SNP n G9T 0 . . 9 9 G 123 123 G 16 G 16 noncoding1:0:0:G9T:.:wild type in ref and reads so should not report generic description of noncoding1 +noncoding2 noncoding2 0 0 19 146 cluster_3 120 120 100.0 cluster_3.l6.c30.ctg.1 468 25.5 . . . . . . . . . . . . . . . . . generic description of noncoding2 +gene1 gene1 1 0 539 110 cluster_4 96 96 98.89 cluster_4.l15.c17.ctg.1 408 24.3 1 SNP p A10V 1 A10V NONSYN 28 30 GCA 185 187 GTA 37;37;38 G;T;A 37;37;38 gene1:1:0:A10V:.:Ref has wild, reads have variant so report Generic description of presence_absence1 +gene1 gene1 1 0 539 110 cluster_4 96 96 98.89 cluster_4.l15.c17.ctg.1 408 24.3 1 SNP p R3S 0 . . 7 9 CGC 164 166 CGC 42;41;41 C;G;C 42;41;41 gene1:1:0:R3S:.:Ref and assembly have wild type, so do not report Generic description of presence_absence1 +gene1 gene1 1 0 539 110 cluster_4 96 96 98.89 cluster_4.l15.c17.ctg.1 408 24.3 1 SNP p I5A 1 . . 13 15 GCG 170 172 GCG 42;41;40 G;C;G 42;41;40 gene1:1:0:I5A:.:Ref and reads have variant so report Generic description of presence_absence1 +gene.var_only2 gene.var_only2 1 1 27 124 gene 93 93 100.0 gene.l15.c30.ctg.1 406 27.5 1 SNP p R3I 0 . . 7 9 CGC 164 166 CGC 43;43;44 C;G;C 43;43;44 gene.var_only2:1:1:R3I:.:Ref and reads have wild so do not report Generic description of variants_only2 +gene.var_only1 gene.var_only1 1 1 27 128 gene_1 90 90 100.0 gene_1.l6.c4.ctg.1 413 27.9 1 SNP p I3L 0 . . 7 9 ATT 164 166 ATT 42;41;41 A;T;T 42;41;41 gene.var_only1:1:1:I3L:.:Ref and assembly have wild type, so do not report Generic description of variants_only1 +gene.var_only1 gene.var_only1 1 1 27 128 gene_1 90 90 100.0 gene_1.l6.c4.ctg.1 413 27.9 1 SNP p S5T 1 . . 13 15 ACC 170 172 ACC 41;43;42 A;C;C 41;43;42 gene.var_only1:1:1:S5T:.:Ref and reads have variant so report Generic description of variants_only1 +noncoding.var_only1 noncoding.var_only1 0 1 19 120 noncoding 120 120 100.0 noncoding.l15.c30.ctg.1 360 30.0 1 SNP n C6T 0 . . 6 6 C 126 126 C 44 C 44 noncoding.var_only1:0:1:C6T:.:sample does not have this SNP . +noncoding.var_only2 noncoding.var_only2 0 1 531 120 noncoding_1 120 120 99.17 noncoding_1.l6.c4.ctg.1 358 30.2 1 SNP n T10A 1 T10A SNP 10 10 T 129 129 A 36 A 36 noncoding.var_only2:0:1:T10A:.:sample does have this SNP . |
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| diff -r 000000000000 -r 79b55c74fb80 test-data/OUT/report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT/report.tsv Tue Jan 08 10:26:30 2019 -0500 |
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| @@ -0,0 +1,14 @@ +#ariba_ref_name ref_name gene var_only flag reads cluster ref_len ref_base_assembled pc_ident ctg ctg_len ctg_cov known_var var_type var_seq_type known_var_change has_known_var ref_ctg_change ref_ctg_effect ref_start ref_end ref_nt ctg_start ctg_end ctg_nt smtls_total_depth smtls_nts smtls_nts_depth var_description free_text +gene.var_only1 gene.var_only1 1 1 27 128 gene_1 90 90 100.0 gene_1.l6.c4.ctg.1 413 27.9 1 SNP p I3L 0 . . 7 9 ATT 164 166 ATT 42;41;41 A;T;T 42;41;41 gene.var_only1:1:1:I3L:.:Ref and assembly have wild type, so do not report Generic description of variants_only1 +gene.var_only1 gene.var_only1 1 1 27 128 gene_1 90 90 100.0 gene_1.l6.c4.ctg.1 413 27.9 1 SNP p S5T 1 . . 13 15 ACC 170 172 ACC 41;43;42 A;C;C 41;43;42 gene.var_only1:1:1:S5T:.:Ref and reads have variant so report Generic description of variants_only1 +gene.var_only2 gene.var_only2 1 1 27 124 gene 93 93 100.0 gene.l15.c30.ctg.1 406 27.5 1 SNP p R3I 0 . . 7 9 CGC 164 166 CGC 43;43;44 C;G;C 43;43;44 gene.var_only2:1:1:R3I:.:Ref and reads have wild so do not report Generic description of variants_only2 +gene1 gene1 1 0 539 110 cluster_4 96 96 98.89 cluster_4.l15.c17.ctg.1 408 24.3 1 SNP p A10V 1 A10V NONSYN 28 30 GCA 185 187 GTA 37;37;38 G;T;A 37;37;38 gene1:1:0:A10V:.:Ref has wild, reads have variant so report Generic description of presence_absence1 +gene1 gene1 1 0 539 110 cluster_4 96 96 98.89 cluster_4.l15.c17.ctg.1 408 24.3 1 SNP p R3S 0 . . 7 9 CGC 164 166 CGC 42;41;41 C;G;C 42;41;41 gene1:1:0:R3S:.:Ref and assembly have wild type, so do not report Generic description of presence_absence1 +gene1 gene1 1 0 539 110 cluster_4 96 96 98.89 cluster_4.l15.c17.ctg.1 408 24.3 1 SNP p I5A 1 . . 13 15 GCG 170 172 GCG 42;41;40 G;C;G 42;41;40 gene1:1:0:I5A:.:Ref and reads have variant so report Generic description of presence_absence1 +noncoding.var_only1 noncoding.var_only1 0 1 19 120 noncoding 120 120 100.0 noncoding.l15.c30.ctg.1 360 30.0 1 SNP n C6T 0 . . 6 6 C 126 126 C 44 C 44 noncoding.var_only1:0:1:C6T:.:sample does not have this SNP . +noncoding.var_only2 noncoding.var_only2 0 1 531 120 noncoding_1 120 120 99.17 noncoding_1.l6.c4.ctg.1 358 30.2 1 SNP n T10A 1 T10A SNP 10 10 T 129 129 A 36 A 36 noncoding.var_only2:0:1:T10A:.:sample does have this SNP . +noncoding1 noncoding1 0 0 531 84 cluster_2 120 120 98.33 cluster_2.l15.c30.ctg.1 391 19.3 1 SNP n A14T 1 A14T SNP 14 14 A 128 128 T 18 T 18 noncoding1:0:0:A14T:noncoding_group1:ref has wild type, reads have variant so should report generic description of noncoding1 +noncoding1 noncoding1 0 0 531 84 cluster_2 120 120 98.33 cluster_2.l15.c30.ctg.1 391 19.3 1 SNP n A6G 1 . . 6 6 G 120 120 G 12 G 12 noncoding1:0:0:A6G:.:variant in ref and reads so should report generic description of noncoding1 +noncoding1 noncoding1 0 0 531 84 cluster_2 120 120 98.33 cluster_2.l15.c30.ctg.1 391 19.3 1 SNP n G9T 0 . . 9 9 G 123 123 G 16 G 16 noncoding1:0:0:G9T:.:wild type in ref and reads so should not report generic description of noncoding1 +noncoding2 noncoding2 0 0 19 146 cluster_3 120 120 100.0 cluster_3.l6.c30.ctg.1 468 25.5 . . . . . . . . . . . . . . . . . generic description of noncoding2 +noncoding3 noncoding3 0 0 19 100 cluster_1 180 180 100.0 cluster_1.l6.c17.ctg.1 289 31.1 . . . . . . . . . . . . . . . . . generic description of noncoding3 |
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| diff -r 000000000000 -r 79b55c74fb80 test-data/OUT/version_info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT/version_info.txt Tue Jan 08 10:26:30 2019 -0500 |
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| @@ -0,0 +1,28 @@ +ARIBA run with this command: +/Users/leviet/miniconda3/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT +from this directory: /Users/leviet/Documents/bioinformatics/quadram/galaxy-tools/ariba/test-ariba + +ARIBA version: 2.13.2 + +External dependencies: +bowtie2 2.3.4.3 /Users/leviet/miniconda3/bin/bowtie2 +cdhit 4.7 /Users/leviet/miniconda3/bin/cd-hit-est +nucmer 3.1 /Users/leviet/miniconda3/bin/nucmer + +External dependencies OK: True + +Python version: +3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:55:02) +[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] + +Python packages: +ariba 2.13.2 /Users/leviet/miniconda3/lib/python3.6/site-packages/ariba/__init__.py +bs4 4.6.3 /Users/leviet/miniconda3/lib/python3.6/site-packages/bs4/__init__.py +dendropy 4.4.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/dendropy/__init__.py +pyfastaq 3.17.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/pyfastaq/__init__.py +pymummer 0.10.3 /Users/leviet/miniconda3/lib/python3.6/site-packages/pymummer/__init__.py +pysam 0.15.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/pysam/__init__.py + +Python packages OK: True + +Everything looks OK: True |
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| diff -r 000000000000 -r 79b55c74fb80 test-data/PREPAREREF/00.info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PREPAREREF/00.info.txt Tue Jan 08 10:26:30 2019 -0500 |
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| @@ -0,0 +1,3 @@ +input fasta file: ref_seqs.fa +input tsv file: metadata.tsv +genetic_code 11 |
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| diff -r 000000000000 -r 79b55c74fb80 test-data/PREPAREREF/00.version_info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PREPAREREF/00.version_info.txt Tue Jan 08 10:26:30 2019 -0500 |
| [ |
| @@ -0,0 +1,28 @@ +ARIBA run with this command: +/Users/leviet/miniconda3/bin/ariba prepareref prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF +from this directory: /Users/leviet/Documents/bioinformatics/quadram/galaxy-tools/ariba/test-ariba + +ARIBA version: 2.13.2 + +External dependencies: +bowtie2 2.3.4.3 /Users/leviet/miniconda3/bin/bowtie2 +cdhit 4.7 /Users/leviet/miniconda3/bin/cd-hit-est +nucmer 3.1 /Users/leviet/miniconda3/bin/nucmer + +External dependencies OK: True + +Python version: +3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:55:02) +[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] + +Python packages: +ariba 2.13.2 /Users/leviet/miniconda3/lib/python3.6/site-packages/ariba/__init__.py +bs4 4.6.3 /Users/leviet/miniconda3/lib/python3.6/site-packages/bs4/__init__.py +dendropy 4.4.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/dendropy/__init__.py +pyfastaq 3.17.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/pyfastaq/__init__.py +pymummer 0.10.3 /Users/leviet/miniconda3/lib/python3.6/site-packages/pymummer/__init__.py +pysam 0.15.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/pysam/__init__.py + +Python packages OK: True + +Everything looks OK: True |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/PREPAREREF/01.filter.check_genes.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PREPAREREF/01.filter.check_genes.log Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +gene.var_only1 KEEP Made into gene. strand=+, frame=0 +gene.var_only2 KEEP Made into gene. strand=+, frame=0 +gene1 KEEP Made into gene. strand=+, frame=0 +gene2 KEEP Made into gene. strand=+, frame=0 |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/PREPAREREF/01.filter.check_metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PREPAREREF/01.filter.check_metadata.tsv Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,20 @@ +gene.var_only1 1 1 . . Generic description of variants_only1 +gene.var_only1 1 1 I3L . Ref and assembly have wild type, so do not report +gene.var_only1 1 1 S5T . Ref and reads have variant so report +gene.var_only2 1 1 . . Generic description of variants_only2 +gene.var_only2 1 1 R3I . Ref and reads have wild so do not report +gene1 1 0 . . Generic description of presence_absence1 +gene1 1 0 R3S . Ref and assembly have wild type, so do not report +gene1 1 0 I5A . Ref and reads have variant so report +gene1 1 0 A10V . Ref has wild, reads have variant so report +gene2 1 0 . . Generic description of presence_absence2 +noncoding.var_only1 0 1 C6T . sample does not have this SNP +noncoding.var_only2 0 1 T10A . sample does have this SNP +noncoding1 0 0 . . generic description of noncoding1 +noncoding1 0 0 A6G . variant in ref and reads so should report +noncoding1 0 0 G9T . wild type in ref and reads so should not report +noncoding1 0 0 A14T noncoding_group1 ref has wild type, reads have variant so should report +noncoding1 0 0 A40C . ref has variant, reads have wild type so should not report +noncoding2 0 0 . . generic description of noncoding2 +noncoding3 0 0 . . generic description of noncoding3 +noncoding4 0 0 . . generic description of noncoding4 |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/PREPAREREF/02.cdhit.all.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PREPAREREF/02.cdhit.all.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,32 @@ +>gene.var_only1 +ATGCTGATTAGCACCGAAAACACCACCGAAAGCAGCGAACGCGCGTGCACCGCGCTGACC +GAACGCGAAGATAGCACCGCGACCGAATAA +>gene.var_only2 +ATGTTTCGCGAAGCGAAAAAAATTACCTGCCATGAAAACATGGCGACCACCATTGCGAGC +GAAAAACTGAACGATCATTATGAAGCGCATTAA +>gene1 +ATGGATCGCGAAGCGATGACCCATGAAGCAACCGAACGCGCGAGCACCAACATTAGCCAT +ATTAACGGCATTAGCGCGTGGGAAAGCATGATTTAA +>gene2 +ATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTAA +>noncoding.var_only1 +CGTATCATCGATCATCGTACGTACGTCGTCGTAGTCAGTCACGAGCAGAGAGAGAGGAGG +CTATGCATGCATCATCTCACTGCGAGTCAGGAGAGAAGCCGTGTAGCGACGAGCGCAAAA +>noncoding.var_only2 +GGTGTCACGTACGACGGACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAA +CTGACGTAATCTACCTGATCGATCGATCATCTGACTGACTATTATATAATATCGCGACAA +>noncoding1 +CGTACGCGGGTGGAGACATGTACTCCACTCCCATACATCCCTAAGTTTGTCCCTAAGGCA +GTGCCCGCCGCCCACGAACGAACTGCGGTGAGATGCTTAGGGAACGCCATCCGAGATCAC +>noncoding2 +TCTTTAACTGTTCACGACTGTATCGCGGCTTGCAAATCTTAAGTTCTTCCCAAGCGCGCT +GCGATACAAATCCCAAGTTTAGCGGACAGTTCACGCCGGGTTCTAAGAATGTATGCGTCC +>noncoding3 +CTAACTTACTACTATGACTGACTGACTGACTGACTGATCGACTGCTGACATCTGATCGAT +CATCCTGTCGACATCATATCTCGATCGATCGATCGACTGACTGACTGACTGACTGAATCT +CACGTACTGACTCATCATCATCATACTCATCATATCATCGATCGATCATCTGATCTGATG +>noncoding4 +AGAGATGATCTCTAGCTCCTTAATTAAATCTGGCTAGCTTAACGCTATATCAGCCCGTTA +GTGTACTAGCCGTAGCATAGTCTAATTTGACCGGGTGAATAGCAATGAATTTCACCAGTC +GCAACCAGCTGCTCTTAAAAGGAATATTACCAACCTGGTGGATAAAAGGAAAATCATCGC +GCTCGGTTCGTGATAGGCACAGAACGGCGAGTTACGGAGCCCGGATGGTAGATCGGTTAA |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/PREPAREREF/02.cdhit.clusters.pickle |
| b |
| Binary file test-data/PREPAREREF/02.cdhit.clusters.pickle has changed |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/PREPAREREF/02.cdhit.clusters.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PREPAREREF/02.cdhit.clusters.tsv Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +cluster noncoding4 +cluster_1 noncoding3 +cluster_2 noncoding1 +cluster_3 noncoding2 +cluster_4 gene1 +cluster_5 gene2 +gene gene.var_only2 +gene_1 gene.var_only1 +noncoding noncoding.var_only1 +noncoding_1 noncoding.var_only2 |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/PREPAREREF/02.cdhit.gene.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PREPAREREF/02.cdhit.gene.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,5 @@ +>gene1 +ATGGATCGCGAAGCGATGACCCATGAAGCAACCGAACGCGCGAGCACCAACATTAGCCAT +ATTAACGGCATTAGCGCGTGGGAAAGCATGATTTAA +>gene2 +ATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTAA |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/PREPAREREF/02.cdhit.gene.varonly.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PREPAREREF/02.cdhit.gene.varonly.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,6 @@ +>gene.var_only1 +ATGCTGATTAGCACCGAAAACACCACCGAAAGCAGCGAACGCGCGTGCACCGCGCTGACC +GAACGCGAAGATAGCACCGCGACCGAATAA +>gene.var_only2 +ATGTTTCGCGAAGCGAAAAAAATTACCTGCCATGAAAACATGGCGACCACCATTGCGAGC +GAAAAACTGAACGATCATTATGAAGCGCATTAA |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/PREPAREREF/02.cdhit.noncoding.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PREPAREREF/02.cdhit.noncoding.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,15 @@ +>noncoding1 +CGTACGCGGGTGGAGACATGTACTCCACTCCCATACATCCCTAAGTTTGTCCCTAAGGCA +GTGCCCGCCGCCCACGAACGAACTGCGGTGAGATGCTTAGGGAACGCCATCCGAGATCAC +>noncoding2 +TCTTTAACTGTTCACGACTGTATCGCGGCTTGCAAATCTTAAGTTCTTCCCAAGCGCGCT +GCGATACAAATCCCAAGTTTAGCGGACAGTTCACGCCGGGTTCTAAGAATGTATGCGTCC +>noncoding3 +CTAACTTACTACTATGACTGACTGACTGACTGACTGATCGACTGCTGACATCTGATCGAT +CATCCTGTCGACATCATATCTCGATCGATCGATCGACTGACTGACTGACTGACTGAATCT +CACGTACTGACTCATCATCATCATACTCATCATATCATCGATCGATCATCTGATCTGATG +>noncoding4 +AGAGATGATCTCTAGCTCCTTAATTAAATCTGGCTAGCTTAACGCTATATCAGCCCGTTA +GTGTACTAGCCGTAGCATAGTCTAATTTGACCGGGTGAATAGCAATGAATTTCACCAGTC +GCAACCAGCTGCTCTTAAAAGGAATATTACCAACCTGGTGGATAAAAGGAAAATCATCGC +GCTCGGTTCGTGATAGGCACAGAACGGCGAGTTACGGAGCCCGGATGGTAGATCGGTTAA |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/PREPAREREF/02.cdhit.noncoding.varonly.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PREPAREREF/02.cdhit.noncoding.varonly.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,6 @@ +>noncoding.var_only1 +CGTATCATCGATCATCGTACGTACGTCGTCGTAGTCAGTCACGAGCAGAGAGAGAGGAGG +CTATGCATGCATCATCTCACTGCGAGTCAGGAGAGAAGCCGTGTAGCGACGAGCGCAAAA +>noncoding.var_only2 +GGTGTCACGTACGACGGACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAA +CTGACGTAATCTACCTGATCGATCGATCATCTGACTGACTATTATATAATATCGCGACAA |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata.tsv Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,20 @@ +gene1 1 0 . . Generic description of presence_absence1 +gene1 1 0 R3S . Ref and assembly have wild type, so do not report +gene1 1 0 A10V . Ref has wild, reads have variant so report +gene1 1 0 I5A . Ref and reads have variant so report +gene2 1 0 . . Generic description of presence_absence2 +gene.var_only1 1 1 . . Generic description of variants_only1 +gene.var_only1 1 1 I3L . Ref and assembly have wild type, so do not report +gene.var_only1 1 1 S5T . Ref and reads have variant so report +gene.var_only2 1 1 R3I . Ref and reads have wild so do not report +gene.var_only2 1 1 . . Generic description of variants_only2 +noncoding1 0 0 . . generic description of noncoding1 +noncoding1 0 0 A6G . variant in ref and reads so should report +noncoding1 0 0 G9T . wild type in ref and reads so should not report +noncoding1 0 0 A14T noncoding_group1 ref has wild type, reads have variant so should report +noncoding1 0 0 A40C . ref has variant, reads have wild type so should not report +noncoding2 0 0 . . generic description of noncoding2 +noncoding3 0 0 . . generic description of noncoding3 +noncoding4 0 0 . . generic description of noncoding4 +noncoding.var_only1 0 1 C6T . sample does not have this SNP +noncoding.var_only2 0 1 T10A . sample does have this SNP |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/reads_1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_1.fq Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,2092 @@\n+@gene1:1:116:235/1\n+ACTTCTTCCTTTCTTGTAGCTGTATTTGGCATAGTGTTGCGGCATATGGATCGCGAAGCGATGACCCATGAAGTAACCGAACGCGCGAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:2:147:267/1\n+TAGTGTTGCGGCATATGGATCGCGAAGCGATGACCCATGAAGTAACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:3:197:318/1\n+CGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAAGGACATACCTAGGTGCGAAGTGCAGATGGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:4:162:281/1\n+TGGATCGCGAAGCGATGACCCATGAAGTAACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:5:92:212/1\n+TCTAAACCGCGCCTAAACAGGTACACTTCTTCCTTTCTTGTAGCTGTATTTGGCATAGTGTTGCGGCATATGGATCGCGAAGCGATGACC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:6:178:296/1\n+GACCCATGAAGTAACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAAGGACATACCTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:7:85:204/1\n+TCAGCACTCTAAACCGCGCCTAAACAGGTACACTTCTTCCTTTCTTGTAGCTGTATTTGGCATAGTGTTGCGGCATATGGATCGCGAAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:8:136:255/1\n+TGTATTTGGCATAGTGTTGCGGCATATGGATCGCGAAGCGATGACCCATGAAGTAACCGAACGCGCGAGCACCAACATTAGCCATATTAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:9:128:248/1\n+CTTGTAGCTGTATTTGGCATAGTGTTGCGGCATATGGATCGCGAAGCGATGACCCATGAAGTAACCGAACGCGCGAGCACCAACATTAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:10:95:215/1\n+AAACCGCGCCTAAACAGGTACACTTCTTCCTTTCTTGTAGCTGTATTTGGCATAGTGTTGCGGCATATGGATCGCGAAGCGATGACCCAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:11:140:258/1\n+TTTGGCATAGTGTTGCGGCATATGGATCGCGAAGCGATGACCCATGAAGTAACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:12:63:181/1\n+AAGCTGCCTAACCCTATAACGTTCAGCACTCTAAACCGCGCCTAAACAGGTACACTTCTTCCTTTCTTGTAGCTGTATTTGGCATAGTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:13:148:268/1\n+AGTGTTGCGGCATATGGATCGCGAAGCGATGACCCATGAAGTAACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:14:4:123/1\n+GTAGTCAGTCATCATCATCATCGTCATGCAGTCATCTGACTGAGTACTTCATCATTATTAAGCTGCCTAACCCTATAACGTTCAGCACTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:15:160:280/1\n+TATGGATCGCGAAGCGATGACCCATGAAGTAACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:16:51:170/1\n+TTCATCATTATTAAGCTGCCTAACCCTATAACGTTCAGCACTCTAAACCGCGCCTAAACAGGTACACTTCTTCCTTTCTTGTAGCTGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:17:174:295/1\n+CGATGACCCATGAAGTAACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAAGGACATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:18:9:129/1\n+CAGTCATCATCATCATCGTCATGCAGTCATCTGACTGAGTACTTCATCATTATTAAGCTGCCTAACCCTATAACGTTCAGCACTCTAAAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:19:48:167/1\n+TACTTCATCATTATTAAGCTGCCTAACCCTATAACGTTCAGCACTCTAAACCGCGCCTAAACAGGTACACTTCTTCCTTTCTTGTAGCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:20:49:169/1\n+ACTTCATCATTATTAAGCTGCCTAAC'..b'III\n+@noncoding.var_only2:506:107:226/1\n+ATCGATCGTACTGAGGTGTCACGAACGACGGACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAACTGACGTAATCTACCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:507:6:125/1\n+GTTCTCAGTACGACGCATCACCGGGCCAGGCCACACTTTCGTCGGATCACTTTGTCTATCCATCTACTGACTGATCGATCGATCATCGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:508:35:155/1\n+GCCACACTTTCGTCGGATCACTTTGTCTATCCATCTACTGACTGATCGATCGATCATCGTACTGACTGACTGATCGATCGTACTGAGGTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:509:87:206/1\n+ATCATCGTACTGACTGACTGATCGATCGTACTGAGGTGTCACGAACGACGGACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:510:139:259/1\n+CCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAACTGACGTAATCTACCTGATCGATCGATCATCTGACTGACTATTATATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:511:94:214/1\n+TACTGACTGACTGATCGATCGTACTGAGGTGTCACGAACGACGGACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAACTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:512:108:227/1\n+TCGATCGTACTGAGGTGTCACGAACGACGGACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAACTGACGTAATCTACCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:513:30:149/1\n+GCCAGGCCACACTTTCGTCGGATCACTTTGTCTATCCATCTACTGACTGATCGATCGATCATCGTACTGACTGACTGATCGATCGTACTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:514:137:256/1\n+GACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAACTGACGTAATCTACCTGATCGATCGATCATCTGACTGACTATTATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:515:5:125/1\n+AGTTCTCAGTACGACGCATCACCGGGCCAGGCCACACTTTCGTCGGATCACTTTGTCTATCCATCTACTGACTGATCGATCGATCATCGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:516:114:234/1\n+GTACTGAGGTGTCACGAACGACGGACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAACTGACGTAATCTACCTGATCGAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:517:47:168/1\n+TCGGATCACTTTGTCTATCCATCTACTGACTGATCGATCGATCATCGTACTGACTGACTGATCGATCGTACTGAGGTGTCACGAACGACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:518:76:197/1\n+CTGATCGATCGATCATCGTACTGACTGACTGATCGATCGTACTGAGGTGTCACGAACGACGGACCAGCGTCGTACGTACGTACGTACGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:519:4:123.dup.2/1\n+TAGTTCTCAGTACGACGCATCACCGGGCCAGGCCACACTTTCGTCGGATCACTTTGTCTATCCATCTACTGACTGATCGATCGATCATCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:520:125:245/1\n+TCACGAACGACGGACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAACTGACGTAATCTACCTGATCGATCGATCATCTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:521:99:217/1\n+ACTGACTGATCGATCGTACTGAGGTGTCACGAACGACGGACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAACTGACGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:522:110:232/1\n+GATCGTACTGAGGTGTCACGAACGACGGACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAACTGACGTAATCTACCTGAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding4:1:18:130/1\n+CCTTAATTAAATCTGGCTAGCTTAACGCTATATCAGCCCGTTAGTGTACTAGCCGTAGCATAGTCTAATTTGACCGGGTGAATAGCAATG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/reads_2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_2.fq Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,2092 @@\n+@gene1:1:116:235/2\n+TTTAATCTTAAGTCTGGGTTTTCTATATCCACACCGAAACCATCTGCACTTCGCACCTAGGTATGTCCTTATTCCATGCTTTCCCACGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:2:147:267/2\n+TGAGTCATGACGTCAGTGAAGCTTTCAGAGGATTTAATCTTAAGTCTGGGTTTTCTATATCCACACCGAAACCATCTGCACTTCGCACCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:3:197:318/2\n+CATGACTGACTGACTGACGATGACTGACTGACTGTCAGTAGTAGATGTCAGTGAGTCATGACGTCAGTGAAGCTTTCAGAGGATTTAATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:4:162:281/2\n+GTAGTAGATGTCAGTGAGTCATGACGTCAGTGAAGCTTTCAGAGGATTTAATCTTAAGTCTGGGTTTTCTATATCCACACCGAAACCATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:5:92:212/2\n+TATATCCACACCGAAACCATCTGCACTTCGCACCTAGGTATGTCCTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:6:178:296/2\n+ACTGACTGACTGTCAGTAGTAGATGTCAGTGAGTCATGACGTCAGTGAAGCTTTCAGAGGATTTAATCTTAAGTCTGGGTTTTCTATATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:7:85:204/2\n+CACCGAAACCATCTGCACTTCGCACCTAGGTATGTCCTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:8:136:255/2\n+TCAGTGAAGCTTTCAGAGGATTTAATCTTAAGTCTGGGTTTTCTATATCCACACCGAAACCATCTGCACTTCGCACCTAGGTATGTCCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:9:128:248/2\n+AGCTTTCAGAGGATTTAATCTTAAGTCTGGGTTTTCTATATCCACACCGAAACCATCTGCACTTCGCACCTAGGTATGTCCTTATTCCAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:10:95:215/2\n+TTCTATATCCACACCGAAACCATCTGCACTTCGCACCTAGGTATGTCCTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:11:140:258/2\n+ACGTCAGTGAAGCTTTCAGAGGATTTAATCTTAAGTCTGGGTTTTCTATATCCACACCGAAACCATCTGCACTTCGCACCTAGGTATGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:12:63:181/2\n+ACCTAGGTATGTCCTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTTACTTCATGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:13:148:268/2\n+GTGAGTCATGACGTCAGTGAAGCTTTCAGAGGATTTAATCTTAAGTCTGGGTTTTCTATATCCACACCGAAACCATCTGCACTTCGCACC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:14:4:123/2\n+TGTTGGTGCTCGCGCGTTCGGTTACTTCATGGGTCATCGCTTCGCGATCCATATGCCGCAACACTATGCCAAATACAGCTACAAGAAAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:15:160:280/2\n+TAGTAGATGTCAGTGAGTCATGACGTCAGTGAAGCTTTCAGAGGATTTAATCTTAAGTCTGGGTTTTCTATATCCACACCGAAACCATCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:16:51:170/2\n+TCCTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTTACTTCATGGGTCATCGCTTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:17:174:295/2\n+CTGACTGACTGTCAGTAGTAGATGTCAGTGAGTCATGACGTCAGTGAAGCTTTCAGAGGATTTAATCTTAAGTCTGGGTTTTCTATATCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:18:9:129/2\n+GGCTAATGTTGGTGCTCGCGCGTTCGGTTACTTCATGGGTCATCGCTTCGCGATCCATATGCCGCAACACTATGCCAAATACAGCTACAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:19:48:167/2\n+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTTACTTCATGGGTCATCGCTTCGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@gene1:20:49:169/2\n+CCTTATTCCATGCTTTCCCACGCGCT'..b'III\n+@noncoding.var_only2:506:107:226/2\n+TTTTGGCCCCTATAACAGTACGTACGTCATGCTGCTGCTCGTAGTATATATAATTAATATATAGTATGCAGTCAGTTGTCGCGATATTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:507:6:125/2\n+TCAGATGATCGATCGATCAGGTAGATTACGTCAGTTTGCTGCTGTCTCCTACGTACGTACGTACGTACGACGCTGGTCCGTCGTTCGTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:508:35:155/2\n+TCAGTTGTCGCGATATTATATAATAGTCAGTCAGATGATCGATCGATCAGGTAGATTACGTCAGTTTGCTGCTGTCTCCTACGTACGTAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:509:87:206/2\n+CGTACGTCATGCTGCTGCTCGTAGTATATATAATTAATATATAGTATGCAGTCAGTTGTCGCGATATTATATAATAGTCAGTCAGATGAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:510:139:259/2\n+CCAAAACCATGCAGTTCGCAGCTGACAGCGGGTTTTTGGCCCCTATAACAGTACGTACGTCATGCTGCTGCTCGTAGTATATATAATTAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:511:94:214/2\n+TAACAGTACGTACGTCATGCTGCTGCTCGTAGTATATATAATTAATATATAGTATGCAGTCAGTTGTCGCGATATTATATAATAGTCAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:512:108:227/2\n+TTTTTGGCCCCTATAACAGTACGTACGTCATGCTGCTGCTCGTAGTATATATAATTAATATATAGTATGCAGTCAGTTGTCGCGATATTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:513:30:149/2\n+GTCGCGATATTATATAATAGTCAGTCAGATGATCGATCGATCAGGTAGATTACGTCAGTTTGCTGCTGTCTCCTACGTACGTACGTACGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:514:137:256/2\n+AAACCATGCAGTTCGCAGCTGACAGCGGGTTTTTGGCCCCTATAACAGTACGTACGTCATGCTGCTGCTCGTAGTATATATAATTAATAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:515:5:125/2\n+TCAGATGATCGATCGATCAGGTAGATTACGTCAGTTTGCTGCTGTCTCCTACGTACGTACGTACGTACGACGCTGGTCCGTCGTTCGTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:516:114:234/2\n+CAGCGGGTTTTTGGCCCCTATAACAGTACGTACGTCATGCTGCTGCTCGTAGTATATATAATTAATATATAGTATGCAGTCAGTTGTCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:517:47:168/2\n+ATATAGTATGCAGTCAGTTGTCGCGATATTATATAATAGTCAGTCAGATGATCGATCGATCAGGTAGATTACGTCAGTTTGCTGCTGTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:518:76:197/2\n+TGCTGCTGCTCGTAGTATATATAATTAATATATAGTATGCAGTCAGTTGTCGCGATATTATATAATAGTCAGTCAGATGATCGATCGATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:519:4:123.dup.2/2\n+AGATGATCGATCGATCAGGTAGATTACGTCAGTTTGCTGCTGTCTCCTACGTACGTACGTACGTACGACGCTGGTCCGTCGTTCGTGACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:520:125:245/2\n+TTCGCAGCTGACAGCGGGTTTTTGGCCCCTATAACAGTACGTACGTCATGCTGCTGCTCGTAGTATATATAATTAATATATAGTATGCAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:521:99:217/2\n+CTATAACAGTACGTACGTCATGCTGCTGCTCGTAGTATATATAATTAATATATAGTATGCAGTCAGTTGTCGCGATATTATATAATAGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding.var_only2:522:110:232/2\n+GCGGGTTTTTGGCCCCTATAACAGTACGTACGTCATGCTGCTGCTCGTAGTATATATAATTAATATATAGTATGCAGTCAGTTGTCGCGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@noncoding4:1:18:130/2\n+CTCCGTAACTCGCCGTTCTGTGCCTATCACGAACCGAGCGCGATGATTTTCCTTTTATCCACCAGGTTGGTAATATTCCTTTTAAGAGCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/ref_seqs.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref_seqs.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,32 @@ +>gene1 +ATGGATCGCGAAGCGATGACCCATGAAGCAACCGAACGCGCGAGCACCAACATTAGCCAT +ATTAACGGCATTAGCGCGTGGGAAAGCATGATTTAA +>gene2 +ATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTAA +>gene.var_only1 +ATGCTGATTAGCACCGAAAACACCACCGAAAGCAGCGAACGCGCGTGCACCGCGCTGACC +GAACGCGAAGATAGCACCGCGACCGAATAA +>gene.var_only2 +ATGTTTCGCGAAGCGAAAAAAATTACCTGCCATGAAAACATGGCGACCACCATTGCGAGC +GAAAAACTGAACGATCATTATGAAGCGCATTAA +>noncoding1 +CGTACGCGGGTGGAGACATGTACTCCACTCCCATACATCCCTAAGTTTGTCCCTAAGGCA +GTGCCCGCCGCCCACGAACGAACTGCGGTGAGATGCTTAGGGAACGCCATCCGAGATCAC +>noncoding2 +TCTTTAACTGTTCACGACTGTATCGCGGCTTGCAAATCTTAAGTTCTTCCCAAGCGCGCT +GCGATACAAATCCCAAGTTTAGCGGACAGTTCACGCCGGGTTCTAAGAATGTATGCGTCC +>noncoding3 +CTAACTTACTACTATGACTGACTGACTGACTGACTGATCGACTGCTGACATCTGATCGAT +CATCCTGTCGACATCATATCTCGATCGATCGATCGACTGACTGACTGACTGACTGAATCT +CACGTACTGACTCATCATCATCATACTCATCATATCATCGATCGATCATCTGATCTGATG +>noncoding4 +AGAGATGATCTCTAGCTCCTTAATTAAATCTGGCTAGCTTAACGCTATATCAGCCCGTTA +GTGTACTAGCCGTAGCATAGTCTAATTTGACCGGGTGAATAGCAATGAATTTCACCAGTC +GCAACCAGCTGCTCTTAAAAGGAATATTACCAACCTGGTGGATAAAAGGAAAATCATCGC +GCTCGGTTCGTGATAGGCACAGAACGGCGAGTTACGGAGCCCGGATGGTAGATCGGTTAA +>noncoding.var_only1 +CGTATCATCGATCATCGTACGTACGTCGTCGTAGTCAGTCACGAGCAGAGAGAGAGGAGG +CTATGCATGCATCATCTCACTGCGAGTCAGGAGAGAAGCCGTGTAGCGACGAGCGCAAAA +>noncoding.var_only2 +GGTGTCACGTACGACGGACCAGCGTCGTACGTACGTACGTACGTAGGAGACAGCAGCAAA +CTGACGTAATCTACCTGATCGATCGATCATCTGACTGACTATTATATAATATCGCGACAA |
| b |
| diff -r 000000000000 -r 79b55c74fb80 test-data/test_ariba_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_ariba_database.loc Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +PREPAREREF PREPAREREF ${__HERE__}/PREPAREREF \ No newline at end of file |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/ariba_databases.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ariba_databases.loc Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +card CARD ${__HERE__}/card.db +resfinder resfinder ${__HERE__}/resfinder.db \ No newline at end of file |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/ariba_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ariba_databases.loc.sample Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +# This file defines databases and their folder location. Each database is a line with +# three columns: value{tab}{name}{/path/to/database-folder} +# E.g. card{tab}card{tab}/home/user/ariba_databases/card +# The database folder is created by the command ariba preparef \ No newline at end of file |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/00.info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/card.db/00.info.txt Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,3 @@ +input fasta file: card.fa +input tsv file: card.tsv +genetic_code 11 |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/00.rename_info --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/card.db/00.rename_info Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b"@@ -0,0 +1,2330 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A.3002949.M97297.8016_8624.3281\n+vanXB.3002950.U35369.6004-6613.3456\tvanXB.3002950.U35369.6004_6613.3456\n+vanXD.3003070.AY082011.6937-7546.652\tvanXD.3003070.AY082011.6937_7546.652\n+vanXF.3002952.AF155139.6976-7648.685\tvanXF.3002952.AF155139.6976_7648.685\n+vanXI.3003725.NG_055644.1.100-709.4230\tvanXI.3003725.NG_055644.1.100_709.4230\n+vanXM.3002953.FJ349556.5893-6502.717\tvanXM.3002953.FJ349556.5893_6502.717\n+vanXO.3002954.KF478993.2576-3185.23\tvanXO.3002954.KF478993.2576_3185.23\n+vanXYC.3002966.AF162694.2438-3011.39\tvanXYC.3002966.AF162694.2438_3011.39\n+vanXYE.3002967.FJ872411.40765-41347.106\tvanXYE.3002967.FJ872411.40765_41347.106\n+vanXYG.3003069.DQ212986.7030-7795.123\tvanXYG.3003069.DQ212986.7030_7795.123\n+vanXYL.3002968.EU250284.1996-2578.168\tvanXYL.3002968.EU250284.1996_2578.168\n+vanXYN.3002969.JF802084.1592-2165.203\tvanXYN.3002969.JF802084.1592_2165.203\n+vanYA.3002955.M97297.9052-9963.3278\tvanYA.3002955.M97297.9052_9963.3278\n+vanYB.3002956.U35369.2358-3165.3457\tvanYB.3002956.U35369.2358_3165.3457\n+vanYD.3002957.AY082011.3848-4265.338\tvanYD.3002957.AY082011.3848_4265.338\n+vanYF.3002958.AF155139.3396-4278.380\tvanYF.3002958.AF155139.3396_4278.380\n+vanYG1.3002959.DQ212986.4222-5062.416\tvanYG1.3002959.DQ212986.4222_5062.416\n+vanYM.3002961.FJ349556.3056-3758.479\tvanYM.3002961.FJ349556.3056_3758.479\n+vanZA.3002962.M97297.10116-10601.3280\tvanZA.3002962.M97297.10116_10601.3280\n+vanZF.3002963.AF155139.4338-4959.566\tvanZF.3002963.AF155139.4338_4959.566\n+varG.3004289.AE003852.1.1674272-1675445.4194\tvarG.3004289.AE003852.1.1674272_1675445.4194\n+vatA.3002840.L07778.0-660.144\tvatA.3002840.L07778.0_660.144\n+vatB.3002841.U19459.66-705.3345\tvatB.3002841.U19459.66_705.3345\n+vatC.3002842.AF015628.1306-1945.211\tvatC.3002842.AF015628.1306_1945.211\n+vatD.3002843.AF368302.2716-3331.462\tvatD.3002843.AF368302.2716_3331.462\n+vatE.3002844.AF242872.3579-4224.507\tvatE.3002844.AF242872.3579_4224.507\n+vatF.3003744.AF170730.69-735.3514\tvatF.3003744.AF170730.69_735.3514\n+vatH.3002845.GQ205627.3036-3687.253\tvatH.3002845.GQ205627.3036_3687.253\n+vgaA.3002829.KC539823.1017-2586.376\tvgaA.3002829.KC539823.1017_2586.376\n+vgaALC.3002830.DQ823382.0-1569.412\tvgaALC.3002830.DQ823382.0_1569.412\n+vgaB.3000118.U82085.0-1659.475\tvgaB.3000118.U82085.0_1659.475\n+vgaC.3002831.KU302801.102199-102430.3686\tvgaC.3002831.KU302801.102199_102430.3686\n+vgaD.3002832.GQ205627.1393-2971.519\tvgaD.3002832.GQ205627.1393_2971.519\n+vgaE.3002833.FR772051.8740-10315.562\tvgaE.3002833.FR772051.8740_10315.562\n+vgbA.3001307.M20129.640-1540.4416\tvgbA.3001307.M20129.640_1540.4416\n+vgbB.3001308.AF015628.398-1286.4415\tvgbB.3001308.AF015628.398_1286.4415\n+vgbC.3003990.KX531055.1.0-891.3862\tvgbC.3003990.KX531055.1.0_891.3862\n+vph.3003061.X02393.96-960.62\tvph.3003061.X02393.96_960.62\n+walK.3003794.BX571856.25616-27443.3565\twalK.3003794.BX571856.25616_27443.3565\n+y56_beta-lactamase.3003558.AY954728.11-896.3318\ty56_beta_lactamase.3003558.AY954728.11_896.3318\n+ykkC.3003063.AL009126.1376516-1376855.489\tykkC.3003063.AL009126.1376516_1376855.489\n+ykkD.3003064.AL009126.1376854-1377172.536\tykkD.3003064.AL009126.1376854_1377172.536\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/00.version_info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/card.db/00.version_info.txt Tue Jan 08 10:26:30 2019 -0500 |
| [ |
| @@ -0,0 +1,28 @@ +ARIBA run with this command: +/Users/leviet/miniconda3/bin/ariba prepareref prepareref -f card.fa -m card.tsv card.db +from this directory: /Users/leviet/Documents/bioinformatics/quadram/galaxy-tools/ariba/database + +ARIBA version: 2.13.2 + +External dependencies: +bowtie2 2.3.4.3 /Users/leviet/miniconda3/bin/bowtie2 +cdhit 4.7 /Users/leviet/miniconda3/bin/cd-hit-est +nucmer 3.1 /Users/leviet/miniconda3/bin/nucmer + +External dependencies OK: True + +Python version: +3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:55:02) +[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] + +Python packages: +ariba 2.13.2 /Users/leviet/miniconda3/lib/python3.6/site-packages/ariba/__init__.py +bs4 4.6.3 /Users/leviet/miniconda3/lib/python3.6/site-packages/bs4/__init__.py +dendropy 4.4.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/dendropy/__init__.py +pyfastaq 3.17.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/pyfastaq/__init__.py +pymummer 0.10.3 /Users/leviet/miniconda3/lib/python3.6/site-packages/pymummer/__init__.py +pysam 0.15.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/pysam/__init__.py + +Python packages OK: True + +Everything looks OK: True |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/01.filter.check_genes.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/card.db/01.filter.check_genes.log Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,2253 @@\n+AAC_2___IIb.3003988.KX531051.1.0_723.3860\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_2___Ia.3002523.L06156.263_800.53\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_2___Ib.3002524.U41471.264_852.85\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_2___Ic.3002525.AL123456.3.314308_314854.4719\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_2___Id.3002526.U72743.385_1018.228\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_2___Ie.3002527.NC_002677.1.3039191_3039740.4182\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__IIIa.3002536.X55652.1123_1939.6\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__IIIb.3002537.L06160.983_1721.188\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__IIIc.3002538.L06161.105_945.9\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__IIa.3002533.X13543.1.185_1046.4266\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__IIb.3002534.M97172.655_1465.10\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__IIc.3002535.X54723.818_1679.616\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__IV.3002539.DQ241380.1.0_777.3715\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__IXa.3002543.M55427.273_1119.655\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__Ia.3002528.U12338.5055_5520.3369\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__Ib.3002530.L06157.554_1085.224\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__Ib_AAC_6___Ib__.3002600.AF355189.1434_2439.271\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__Ic.3002531.AJ511268.1294_1765.47\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__Id.3002529.AY458224.706_1183.223\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__VIIIa.3002542.M55426.465_1326.12\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__VIIa.3002541.M22999.492_1359.694\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__VIa.3002540.M88012.192_1092.659\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_3__Xa.3002544.AB028210.1.2710_3565.4702\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___30_AAC_6___Ib__fusion_protein.3002599.AJ584652.1926_2913.186\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___31.3002585.AM283489.2655_3174.267\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___32.3002586.EF614235.2246_2801.310\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___33.3002587.JN596280.1202_1757.362\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___34.3003989.KX531053.1.0_594.3861\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___I30.3002588.AY289608.1523_2078.399\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___IIa.3002594.AY123251.2950_3505.460\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___IIb.3002595.L06163.531_1074.497\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___IIc.3002596.AF162771.61_643.313\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___IId.3002548.KC543497.1.404932_405451.3392\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Ia.3002545.M18967.756_1314.547\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Iaa.3002571.NC_003197.1707357_1707795.308\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Iad.3002572.AB119105.0_435.264\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Iae.3002573.AB104852.1934_2486.583\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Iaf.3002574.AB462903.1199_1751.672\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Iai.3002575.EU886977.543_1110.708\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Iaj.3003677.AB709942.1194_1749.3379\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Iak.3003199.AB894482.1.35038_35500.4672\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Ib.3002546.JQ808129.633_1188.231\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Ib10.3002581.U59183.247_859.314\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Ib11.3002582.AY136758.377_947.366\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Ib3.3002576.FJ854362.1702_2257.141\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Ib4.3002577.AF445082.2788_3343.401\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Ib8.3002579.NC_025003.1.4171_4849.3719\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Ib9.3002580.AF043381.251_863.463\tKEEP\tMade into gene. strand=+, frame=0\n+AAC_6___Ib_.30036'..b'1.41336_43445.180\tKEEP\tMade into gene. strand=+, frame=0\n+vanTG.3002972.DQ212986.7787_9926.217\tKEEP\tMade into gene. strand=+, frame=0\n+vanTN.3002975.JF802084.2161_4264.259\tKEEP\tMade into gene. strand=+, frame=0\n+vanTmL.3002973.EU250284.2574_3564.301\tKEEP\tMade into gene. strand=+, frame=0\n+vanTrL.3002974.EU250284.3557_4658.353\tKEEP\tMade into gene. strand=+, frame=0\n+vanUG.3004253.DQ212986.2029_2257.339\tKEEP\tMade into gene. strand=+, frame=0\n+vanVB.3004254.AE016830.2211932_2212277.4564\tKEEP\tMade into gene. strand=+, frame=0\n+vanWB.3002964.U35369.3182_4010.3455\tKEEP\tMade into gene. strand=+, frame=0\n+vanWG.3002965.DQ212986.5137_5983.535\tKEEP\tMade into gene. strand=+, frame=0\n+vanWI.3003724.NC_007907.1.2195400_2196522.4648\tKEEP\tMade into gene. strand=+, frame=0\n+vanXA.3002949.M97297.8016_8624.3281\tKEEP\tMade into gene. strand=+, frame=0\n+vanXB.3002950.U35369.6004_6613.3456\tKEEP\tMade into gene. strand=+, frame=0\n+vanXD.3003070.AY082011.6937_7546.652\tKEEP\tMade into gene. strand=+, frame=0\n+vanXF.3002952.AF155139.6976_7648.685\tKEEP\tMade into gene. strand=+, frame=0\n+vanXI.3003725.NG_055644.1.100_709.4230\tKEEP\tMade into gene. strand=+, frame=0\n+vanXM.3002953.FJ349556.5893_6502.717\tKEEP\tMade into gene. strand=+, frame=0\n+vanXO.3002954.KF478993.2576_3185.23\tKEEP\tMade into gene. strand=+, frame=0\n+vanXYC.3002966.AF162694.2438_3011.39\tKEEP\tMade into gene. strand=+, frame=0\n+vanXYE.3002967.FJ872411.40765_41347.106\tKEEP\tMade into gene. strand=+, frame=0\n+vanXYG.3003069.DQ212986.7030_7795.123\tKEEP\tMade into gene. strand=+, frame=0\n+vanXYL.3002968.EU250284.1996_2578.168\tKEEP\tMade into gene. strand=+, frame=0\n+vanXYN.3002969.JF802084.1592_2165.203\tKEEP\tMade into gene. strand=+, frame=0\n+vanYA.3002955.M97297.9052_9963.3278\tKEEP\tMade into gene. strand=+, frame=0\n+vanYB.3002956.U35369.2358_3165.3457\tKEEP\tMade into gene. strand=+, frame=0\n+vanYD.3002957.AY082011.3848_4265.338\tKEEP\tMade into gene. strand=+, frame=0\n+vanYF.3002958.AF155139.3396_4278.380\tKEEP\tMade into gene. strand=+, frame=0\n+vanYG1.3002959.DQ212986.4222_5062.416\tKEEP\tMade into gene. strand=+, frame=0\n+vanYM.3002961.FJ349556.3056_3758.479\tKEEP\tMade into gene. strand=+, frame=0\n+vanZA.3002962.M97297.10116_10601.3280\tKEEP\tMade into gene. strand=+, frame=0\n+vanZF.3002963.AF155139.4338_4959.566\tKEEP\tMade into gene. strand=+, frame=0\n+varG.3004289.AE003852.1.1674272_1675445.4194\tKEEP\tMade into gene. strand=+, frame=0\n+vatA.3002840.L07778.0_660.144\tKEEP\tMade into gene. strand=+, frame=0\n+vatB.3002841.U19459.66_705.3345\tKEEP\tMade into gene. strand=+, frame=0\n+vatC.3002842.AF015628.1306_1945.211\tKEEP\tMade into gene. strand=+, frame=0\n+vatD.3002843.AF368302.2716_3331.462\tKEEP\tMade into gene. strand=+, frame=0\n+vatE.3002844.AF242872.3579_4224.507\tKEEP\tMade into gene. strand=+, frame=0\n+vatF.3003744.AF170730.69_735.3514\tKEEP\tMade into gene. strand=+, frame=0\n+vatH.3002845.GQ205627.3036_3687.253\tKEEP\tMade into gene. strand=+, frame=0\n+vgaA.3002829.KC539823.1017_2586.376\tKEEP\tMade into gene. strand=+, frame=0\n+vgaALC.3002830.DQ823382.0_1569.412\tKEEP\tMade into gene. strand=+, frame=0\n+vgaB.3000118.U82085.0_1659.475\tKEEP\tMade into gene. strand=+, frame=0\n+vgaC.3002831.KU302801.102199_102430.3686\tKEEP\tMade into gene. strand=+, frame=0\n+vgaD.3002832.GQ205627.1393_2971.519\tKEEP\tMade into gene. strand=+, frame=0\n+vgaE.3002833.FR772051.8740_10315.562\tKEEP\tMade into gene. strand=+, frame=0\n+vgbA.3001307.M20129.640_1540.4416\tKEEP\tMade into gene. strand=+, frame=0\n+vgbB.3001308.AF015628.398_1286.4415\tKEEP\tMade into gene. strand=+, frame=0\n+vgbC.3003990.KX531055.1.0_891.3862\tKEEP\tMade into gene. strand=+, frame=0\n+vph.3003061.X02393.96_960.62\tKEEP\tMade into gene. strand=+, frame=0\n+walK.3003794.BX571856.25616_27443.3565\tKEEP\tMade into gene. strand=+, frame=0\n+y56_beta_lactamase.3003558.AY954728.11_896.3318\tKEEP\tMade into gene. strand=+, frame=0\n+ykkC.3003063.AL009126.1376516_1376855.489\tKEEP\tMade into gene. strand=+, frame=0\n+ykkD.3003064.AL009126.1376854_1377172.536\tKEEP\tMade into gene. strand=+, frame=0\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/01.filter.check_metadata.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/card.db/01.filter.check_metadata.log Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,172 @@\n+Brachyspira_hyodysenteriae_23S.3004133.NZ_CP015910.2.2512812_2515808.4183 variant does not match reference. Removing. Line of file was: Brachyspira_hyodysenteriae_23S.3004133.NZ_CP015910.2.2512812_2515808.4183\t0\t0\tA2058G\t.\tb\'Point mutation in B. hyodysenteriae 23S rRNA shown to confer resistance to tylosin and erythromycin\'\n+Brachyspira_hyodysenteriae_23S.3004133.NZ_CP015910.2.2512812_2515808.4183 variant does not match reference. Removing. Line of file was: Brachyspira_hyodysenteriae_23S.3004133.NZ_CP015910.2.2512812_2515808.4183\t0\t0\tA2058U\t.\tb\'Point mutation in B. hyodysenteriae 23S rRNA shown to confer resistance to tylosin and erythromycin\'\n+Chlamydomonas_reinhardtii_23S.3004132.NC_005353.1.148590_151993.4139 variant does not match reference. Removing. Line of file was: Chlamydomonas_reinhardtii_23S.3004132.NC_005353.1.148590_151993.4139\t0\t0\tG1628G\t.\tb\'Point mutation in 23S rRNA of C. reinhardtii chloroplast shown clinically to confer resistance to Erythromycin, a macrolide antibiotic.\'\n+Chlamydomonas_reinhardtii_23S.3004132.NC_005353.1.148590_151993.4139 variant does not match reference. Removing. Line of file was: Chlamydomonas_reinhardtii_23S.3004132.NC_005353.1.148590_151993.4139\t0\t0\tG1627A\t.\tb\'Point mutation in 23S rRNA of C. reinhardtii chloroplast shown clinically to confer resistance to Erythromycin, a macrolide antibiotic.\'\n+D_Ala_D_Ala_ligase.3003970.AY168442.1.53_1109.3769 variant does not match reference. Removing. Line of file was: D_Ala_D_Ala_ligase.3003970.AY168442.1.53_1109.3769\t1\t1\tP313L\t.\tb\'Non-van ligases that synthesize D-Ala-D-Ala, the default cell wall precursor that makes a cell vulnerable to glycopeptide antibiotics. Mutations in the ddl gene can cause the production of nonfunctional/inactivated D-Ala-D-Ala ligases, which can render bacteria glycopeptide dependent depending on the presence of vancomycin resistance clusters.\'\n+D_Ala_D_Ala_ligase.3003970.AY168442.1.53_1109.3769 variant does not match reference. Removing. Line of file was: D_Ala_D_Ala_ligase.3003970.AY168442.1.53_1109.3769\t1\t1\tG99R\t.\tb\'Non-van ligases that synthesize D-Ala-D-Ala, the default cell wall precursor that makes a cell vulnerable to glycopeptide antibiotics. Mutations in the ddl gene can cause the production of nonfunctional/inactivated D-Ala-D-Ala ligases, which can render bacteria glycopeptide dependent depending on the presence of vancomycin resistance clusters.\'\n+D_Ala_D_Ala_ligase.3003970.AY168442.1.53_1109.3769 variant does not match reference. Removing. Line of file was: D_Ala_D_Ala_ligase.3003970.AY168442.1.53_1109.3769\t1\t1\tV241D\t.\tb\'Non-van ligases that synthesize D-Ala-D-Ala, the default cell wall precursor that makes a cell vulnerable to glycopeptide antibiotics. Mutations in the ddl gene can cause the production of nonfunctional/inactivated D-Ala-D-Ala ligases, which can render bacteria glycopeptide dependent depending on the presence of vancomycin resistance clusters.\'\n+D_Ala_D_Ala_ligase.3003970.AY168442.1.53_1109.3769 variant does not match reference. Removing. Line of file was: D_Ala_D_Ala_ligase.3003970.AY168442.1.53_1109.3769\t1\t1\tD295G\t.\tb\'Non-van ligases that synthesize D-Ala-D-Ala, the default cell wall precursor that makes a cell vulnerable to glycopeptide antibiotics. Mutations in the ddl gene can cause the production of nonfunctional/inactivated D-Ala-D-Ala ligases, which can render bacteria glycopeptide dependent depending on the presence of vancomycin resistance clusters.\'\n+Escherichia_coli_16S.3003223.U00096.4166659_4168200.3234 variant does not match reference. Removing. Line of file was: Escherichia_coli_16S.3003223.U00096.4166659_4168200.3234\t0\t0\tU1506A\t.\tb"Point mutations in the 3\' minor domain of the 16S rRNA in Escherichia coli can confer resistance to edeine"\n+Escherichia_coli_23S.3004131.AE014075.1.237159_240063.4149 variant does not match reference. Removing. Line of file was: Escherichia_coli_23S.3004131.AE014075.1.237159_240063.4149\t0\t0\tU754A\t.\tb\'Point mutation in the 2'..b' variant does not match reference. Removing. Line of file was: rrsB.3003399.U00096.4166659_4168200.3232\t0\t0\tU1406A\t.\tb"Point mutations in the 3\' minor domain of helix 44, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to kanamycin A"\n+rrsB.3003408.U00096.4166659_4168200.3241 variant does not match reference. Removing. Line of file was: rrsB.3003408.U00096.4166659_4168200.3241\t0\t0\tU1406A\t.\tb"Point mutations in the 3\' minor domain of the rrnB 16S rRNA gene of Escherichia coli can confer resistance to tobramycin"\n+rrsB.3003540.X52922.1.0_1454.4148 variant does not match reference. Removing. Line of file was: rrsB.3003540.X52922.1.0_1454.4148\t0\t0\tU1348C\t.\tb\'Point mutations in the highly conserved helix 44 of the 16S rrsB rRNA gene of Mycobacterium smegmatis can confer resistance to hygromycin B. Resistance against hygromycin B is the result of conformational alterations that distorts a strong hydrogen bond leading to a change in the local geometry of the hygromycin B binding site.\'\n+rrsB.3003540.X52922.1.0_1454.4148 variant does not match reference. Removing. Line of file was: rrsB.3003540.X52922.1.0_1454.4148\t0\t0\tU1441C\t.\tb\'Point mutations in the highly conserved helix 44 of the 16S rrsB rRNA gene of Mycobacterium smegmatis can confer resistance to hygromycin B. Resistance against hygromycin B is the result of conformational alterations that distorts a strong hydrogen bond leading to a change in the local geometry of the hygromycin B binding site.\'\n+rrsB.3003542.NC_008596.1.5027948_5029475.3251 variant does not match reference. Removing. Line of file was: rrsB.3003542.NC_008596.1.5027948_5029475.3251\t0\t0\tU1389A\t.\tb\'Point mutations in the helix 44 region of the 16S rRNA rrsB gene of Mycobacterium smegmatis can confer resistance to kanamycin A\'\n+rrsB.3003545.NC_008596.1.5027948_5029475.3249 variant does not match reference. Removing. Line of file was: rrsB.3003545.NC_008596.1.5027948_5029475.3249\t0\t0\tU1389A\t.\tb\'Point mutations in the helix 44 region of the 16S rRNA rrsB gene of Mycobacterium smegmatis can confer resistance to neomycin\'\n+soxR.3003381.U00096.4277468_4277933.2074 variant does not match reference. Removing. Line of file was: soxR.3003381.U00096.4277468_4277933.2074\t1\t1\tR90G\t.\tb\'SoxR is a sensory protein that upregulates soxS expression in the presence of redox-cycling drugs. This stress response leads to the expression many multidrug efflux pumps.\'\n+soxR.3003381.U00096.4277468_4277933.2074 variant does not match reference. Removing. Line of file was: soxR.3003381.U00096.4277468_4277933.2074\t1\t1\tS31A\t.\tb\'SoxR is a sensory protein that upregulates soxS expression in the presence of redox-cycling drugs. This stress response leads to the expression many multidrug efflux pumps.\'\n+soxR.3003381.U00096.4277468_4277933.2074 variant does not match reference. Removing. Line of file was: soxR.3003381.U00096.4277468_4277933.2074\t1\t1\tR71S\t.\tb\'SoxR is a sensory protein that upregulates soxS expression in the presence of redox-cycling drugs. This stress response leads to the expression many multidrug efflux pumps.\'\n+tetR.3003479.AL513383.179218_179845.2090 variant does not match reference. Removing. Line of file was: tetR.3003479.AL513383.179218_179845.2090\t1\t1\tT103I\t.\tb\'TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites. Mutations arise within tetR results in lower affinity for tetracyclin\'\n+thyA.3004153.NC_000962.3.3073679_3074471.4482 variant does not match reference. Removing. Line of file was: thyA.3004153.NC_000962.3.3073679_3074471.4482\t1\t1\tI211V\t.\tb\'Point mutations in the thymidylate synthetase thyA gene shown clinically to confer resistance to para-aminosalicylic acid. Loss-of-function mutations in thyA disrupt the catalytic activity and substrate-binding affinity, thus conferring resistance.\'\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/01.filter.check_metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/card.db/01.filter.check_metadata.tsv Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,5441 @@\n+AAC_2___IIb.3003988.KX531051.1.0_723.3860\t1\t0\t.\t.\tAAC(2\')-IIb\n+AAC_2___IIb.3003988.KX531051.1.0_723.3860\t1\t0\t.\t.\tb"AAC(2\')-IIb is an intrinsic Kasugamycin 2\' acetyltransferase protein found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to aminoglycoside antibiotics, including kasugamycin. Described by Pawlowski et al. 2016."\n+AAC_2___Ia.3002523.L06156.263_800.53\t1\t0\t.\t.\tAAC(2\')-Ia\n+AAC_2___Ia.3002523.L06156.263_800.53\t1\t0\t.\t.\tb"AAC(2\')-Ia is a chromosomal-encoded aminoglycoside acetyltransferase in P. stuartii"\n+AAC_2___Ib.3002524.U41471.264_852.85\t1\t0\t.\t.\tAAC(2\')-Ib\n+AAC_2___Ib.3002524.U41471.264_852.85\t1\t0\t.\t.\tb"AAC(2\')-Ib is a chromosomal-encoded aminoglycoside acetyltransferase in M. fortuitum and A. baumannii"\n+AAC_2___Ic.3002525.AL123456.3.314308_314854.4719\t1\t0\t.\t.\tAAC(2\')-Ic\n+AAC_2___Ic.3002525.AL123456.3.314308_314854.4719\t1\t0\t.\t.\tb"AAC(2\')-Ic is a chromosomal-encoded aminoglycoside acetyltransferase in M. tuberculosis and M. bovis"\n+AAC_2___Id.3002526.U72743.385_1018.228\t1\t0\t.\t.\tAAC(2\')-Id\n+AAC_2___Id.3002526.U72743.385_1018.228\t1\t0\t.\t.\tb"AAC(2\')-Id is a chromosomal-encoded aminoglycoside acetyltransferase in M. smegmatis"\n+AAC_2___Ie.3002527.NC_002677.1.3039191_3039740.4182\t1\t0\t.\t.\tAAC(2\')-Ie\n+AAC_2___Ie.3002527.NC_002677.1.3039191_3039740.4182\t1\t0\t.\t.\tb"AAC(2\')-Ie is a chromosomal-encoded aminoglycoside acetyltransferase in M. leprae"\n+AAC_3__IIIa.3002536.X55652.1123_1939.6\t1\t0\t.\t.\tAAC(3)-IIIa\n+AAC_3__IIIa.3002536.X55652.1123_1939.6\t1\t0\t.\t.\tb\'AAC(3)-IIIa is a chromosomal-encoded aminoglycoside acetyltransferase in P. aeruginosa\'\n+AAC_3__IIIb.3002537.L06160.983_1721.188\t1\t0\t.\t.\tAAC(3)-IIIb\n+AAC_3__IIIb.3002537.L06160.983_1721.188\t1\t0\t.\t.\tb\'AAC(3)-IIIb is an aminoglycoside acetyltransferase in P. aeruginosa\'\n+AAC_3__IIIc.3002538.L06161.105_945.9\t1\t0\t.\t.\tAAC(3)-IIIc\n+AAC_3__IIIc.3002538.L06161.105_945.9\t1\t0\t.\t.\tb\'AAC(3)-IIIc is an aminoglycoside acetyltransferase in P. aeruginosa\'\n+AAC_3__IIa.3002533.X13543.1.185_1046.4266\t1\t0\t.\t.\tAAC(3)-IIa\n+AAC_3__IIa.3002533.X13543.1.185_1046.4266\t1\t0\t.\t.\tb\'AAC(3)-IIa is a plasmid-encoded aminoglycoside acetyltransferase in K. pneumoniae, E. cloacae, Actinobacillus pleuropneumoniae, S. typhimurium, Citrobacter freundii, and P. aeruginosa.\'\n+AAC_3__IIb.3002534.M97172.655_1465.10\t1\t0\t.\t.\tAAC(3)-IIb\n+AAC_3__IIb.3002534.M97172.655_1465.10\t1\t0\t.\t.\tb\'AAC(3)-IIb is an aminoglycoside acetyltransferase in E. coli, A. faecalis and S. marcescens\'\n+AAC_3__IIc.3002535.X54723.818_1679.616\t1\t0\t.\t.\tAAC(3)-IIc\n+AAC_3__IIc.3002535.X54723.818_1679.616\t1\t0\t.\t.\tb\'AAC(3)-IIc is a plasmid-encoded aminoglycoside acetyltransferase in E. coli and P. aeruginosa\'\n+AAC_3__IV.3002539.DQ241380.1.0_777.3715\t1\t0\t.\t.\tAAC(3)-IV\n+AAC_3__IV.3002539.DQ241380.1.0_777.3715\t1\t0\t.\t.\tb\'AAC(3)-IV is a plasmid-encoded aminoglycoside acetyltransferase in E. coli, C. jejuni and P. stutzeri\'\n+AAC_3__IXa.3002543.M55427.273_1119.655\t1\t0\t.\t.\tAAC(3)-IXa\n+AAC_3__IXa.3002543.M55427.273_1119.655\t1\t0\t.\t.\tb\'AAC(3)-IXa is a chromosomal-encoded aminoglycoside acetyltransferase in Micromonospora chalcea\'\n+AAC_3__Ia.3002528.U12338.5055_5520.3369\t1\t0\t.\t.\tAAC(3)-Ia\n+AAC_3__Ia.3002528.U12338.5055_5520.3369\t1\t0\t.\t.\tb\'AAC(3)-Ia is an aminoglycoside acetyltransferase encoded by plasmids, transposons, integrons in S. marcescens, E. coli, Acinetobacter baumannii, Klebsiella pneumoniae, Klebsiella oxytoca, P. aeruginosa, Salmonella typhimurium and Proteus mirabilis\'\n+AAC_3__Ib.3002530.L06157.554_1085.224\t1\t0\t.\t.\tAAC(3)-Ib\n+AAC_3__Ib.3002530.L06157.554_1085.224\t1\t0\t.\t.\tb\'AAC(3)-Ib is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa\'\n+AAC_3__Ib_AAC_6___Ib__.3002600.AF355189.1434_2439.271\t1\t0\t.\t.\tAAC(3)-Ib/AAC(6\')-Ib\'\'\n+AAC_3__Ib_AAC_6___Ib__.3002600.AF355189.1434_2439.271\t1\t0\t.\t.\tb"AAC(3)-Ib/AAC(6\')-Ib\'\' is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa"\n+AAC_3__Ic.3002531.AJ511268.1294_1765.47\t1\t0\t.\t.\tAAC(3)-Ic\n+AAC_3__I'..b"amin A antibiotics and related compounds. It is associated with plasmid DNA.'\n+vgaALC.3002830.DQ823382.0_1569.412\t1\t0\t.\t.\tvgaALC\n+vgaB.3000118.U82085.0_1659.475\t1\t0\t.\t.\tb'Vga(B) is an ABC-F protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.'\n+vgaB.3000118.U82085.0_1659.475\t1\t0\t.\t.\tvgaB\n+vgaC.3002831.KU302801.102199_102430.3686\t1\t0\t.\t.\tb'vgaC is an ABC-F subfamily protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.'\n+vgaC.3002831.KU302801.102199_102430.3686\t1\t0\t.\t.\tvgaC\n+vgaD.3002832.GQ205627.1393_2971.519\t1\t0\t.\t.\tb'vgaD is an ABC-F subfamily protein expressed in Enterococcus faecium that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.'\n+vgaD.3002832.GQ205627.1393_2971.519\t1\t0\t.\t.\tvgaD\n+vgaE.3002833.FR772051.8740_10315.562\t1\t0\t.\t.\tb'vgaE is an ABC-F subfamily protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with transposon DNA.'\n+vgaE.3002833.FR772051.8740_10315.562\t1\t0\t.\t.\tvgaE\n+vgbA.3001307.M20129.640_1540.4416\t1\t0\t.\t.\tb'vgbA inactivates streptogramin B-type antibiotics by linearizing the lactone ring on the ester bond using an elimination mechanism, thus conferring resistance to these compounds.'\n+vgbA.3001307.M20129.640_1540.4416\t1\t0\t.\t.\tvgbA\n+vgbB.3001308.AF015628.398_1286.4415\t1\t0\t.\t.\tb'VgbB inactivates streptogramin B-type antibiotics by linearizing the lactone ring on the ester bond through an elimination mechanism, thus conferring resistance.'\n+vgbB.3001308.AF015628.398_1286.4415\t1\t0\t.\t.\tvgbB\n+vgbC.3003990.KX531055.1.0_891.3862\t1\t0\t.\t.\tb'VgbC is a streptogramin B-type lyase found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to streptogramin B-type antibiotics by linearization of the lactone ring on an ester bond, resulting in antibiotic inactivation. Described by Pawlowski et al. 2016.'\n+vgbC.3003990.KX531055.1.0_891.3862\t1\t0\t.\t.\tvgbC\n+vph.3003061.X02393.96_960.62\t1\t0\t.\t.\tb'vph is a phosphotransferase that confers resistance to viomycin in Streptomyces vinaceus'\n+vph.3003061.X02393.96_960.62\t1\t0\t.\t.\tvph\n+walK.3003794.BX571856.25616_27443.3565\t1\t1\t.\t.\tStaphylococcus aureus walK with mutation conferring resistance to daptomycin\n+walK.3003794.BX571856.25616_27443.3565\t1\t1\tL10F\t.\tb'walK is the histidine kinase sensor of a two-component regulatory system controlling peptidoglycan metabolism through regulation of the expression of most of the peptidoglycan hydrolase genes. Mutations in the gene have been found that confer daptomycin resistance.'\n+walK.3003794.BX571856.25616_27443.3565\t1\t1\tS221P\t.\tb'walK is the histidine kinase sensor of a two-component regulatory system controlling peptidoglycan metabolism through regulation of the expression of most of the peptidoglycan hydrolase genes. Mutations in the gene have been found that confer daptomycin resistance.'\n+walK.3003794.BX571856.25616_27443.3565\t1\t1\tR263C\t.\tb'walK is the histidine kinase sensor of a two-component regulatory system controlling peptidoglycan metabolism through regulation of the expression of most of the peptidoglycan hydrolase genes. Mutations in the gene have been found that confer daptomycin resistance.'\n+y56_beta_lactamase.3003558.AY954728.11_896.3318\t1\t0\t.\t.\tb'Class A beta-lactamase found in Yersinia enterocolitica biovar 1A'\n+y56_beta_lactamase.3003558.AY954728.11_896.3318\t1\t0\t.\t.\ty56 beta-lactamase\n+ykkC.3003063.AL009126.1376516_1376855.489\t1\t0\t.\t.\tb'ykkC is an SMR-type protein that is a subunit of the ykkCD efflux pump'\n+ykkC.3003063.AL009126.1376516_1376855.489\t1\t0\t.\t.\tykkC\n+ykkD.3003064.AL009126.1376854_1377172.536\t1\t0\t.\t.\tb'ykkD is an SMR-type protein that is a subunit of the ykkCD efflux pump'\n+ykkD.3003064.AL009126.1376854_1377172.536\t1\t0\t.\t.\tykkD\n" |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/02.cdhit.all.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/card.db/02.cdhit.all.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,43546 @@\n+>AAC_2___IIb.3003988.KX531051.1.0_723.3860\n+ATGAACCATAGGAAAGGTAACGAGCCAACCGCTGCGGCACTGATGGAATTGCATGTTCTG\n+GCGATGTTTACGCATGACGGGAATATGCAAATTCGCACCATCAACGAGCCTTGGCCGGGA\n+GAGGAGCTTGCCCCGAGGTTTTTCATGGGTCGAACGATAGACGGCTCTTCGATCTGCAGG\n+TTTCGTCATGATGTTCCCGAAGGAATTGCCGGGCAATTGAGGGCTTTGGTTGAAGATGAG\n+CCTATCGTTACTGAAGAGGTTCTGACGAGGCCTAAACATTTTGCAGCTTATATGAACCTC\n+CTTCGCGCTGAGCACTATACGAGCGGACCTTGTTATCGGATACCTGATCAAACAACGCAG\n+GCCAAACAGACGGTAAGGATCACACCGGGAAATATTCGCGAATATTCGCTCACCGGTTTT\n+GAATGGCTGACCACGGAAATTGATTATGACCAGCCTTGTGTTGCGCTCATTCATGAGAAT\n+AGGGTGGTGTCGGTTTGCCGCAGCGTCCGGATTACTGAACGAGCTCACGAAGCTGGGCTT\n+GAAACGTCAGAGGAATTTCGTGGAAGAGGTTATGCGGCTGCTGTTGTTGCCGGATGGGCC\n+ATAGAGGTGCAAAAAATGGGCGCGCTGGCGTTGTACAGTACTTTATGGGGAAATAGCTCT\n+TCCCGGAGAGTAGCAAATAAATTAGGGTTGTCCTATTACGGAGTTAACTTCACGATCAGT\n+TGA\n+>AAC_2___Ia.3002523.L06156.263_800.53\n+ATGGGCATAGAATACCGCAGTCTGCATACCAGCCAATTGACACTGAGTGAAAAAGAAGCG\n+CTTTACGATTTATTAATTGAAGGTTTTGAAGGCGATTTTTCGCATGACGATTTCGCGCAC\n+ACTTTAGGTGGAATGCACGTCATGGCTTTTGATCAACAAAAATTGGTTGGTCATGTTGCA\n+ATTATTCAACGCCATATGGCCCTAGATAATACGCCTATCTCTGTAGGGTATGTTGAAGCG\n+ATGGTAGTTGAACAAAGTTATCGTCGCCAAGGTATTGGGCGGCAATTGATGCTGCAAACC\n+AATAAAATTATAGCTTCGTGTTATCAATTAGGGCTGCTGTCGGCTTCAGATGATGGACAA\n+AAATTGTATCATTCGGTTGGATGGCAAATCTGGAAAGGTAAGTTGTTTGAATTGAAACAA\n+GGGAGCTATATCCGTTCTATTGAAGAAGAAGGCGGAGTCATGGGCTGGAAAGCGGATGGT\n+GAGGTTGATTTTACCGCTTCGCTTTACTGTGATTTTCGTGGCGGTGATCAGTGGTAA\n+>AAC_2___Ib.3002524.U41471.264_852.85\n+GTGCCTTTCCAGGATGTCAGCGCGCCCGTTCGAGGCGGGATCCTGCACACCGCTCGACTC\n+GTCCACACCTCCGATCTCGATCAGGAGACTCGAGAGGGCGCCCGCCGCATGGTCATCGAG\n+GCGTTCGAGGGTGATTTCAGCGACGCCGACTGGGAGCACGCGCTCGGTGGCATGCACGCC\n+TTCATCTGTCACCACGGCGCTCTGATCGCGCATGCCGCGGTGGTCCAGCGCCGGCTGCTC\n+TACCGCGACACCGCGCTGCGCTGCGGGTACGTGGAAGCCGTGGCGGTGCGCGAAGATTGG\n+CGCGGCCAAGGCCTGGCCACCGCCGTCATGGACGCGGTCGAACAGGTGCTGCGCGGCGCC\n+TACCAGCTCGGCGCCCTCAGTGCGTCCGACACAGCCAGAGGCATGTACCTCTCTCGCGGG\n+TGGCTGCCGTGGCAGGGGCCGACCTCGGTGCTGCAGCCGGCCGGCGTGACGCGTACACCC\n+GAGGACGACGAGGGACTGTTCGTGCTGCCCGTCGGTCTCCCGGCGGGAATGGAACTCGAC\n+ACCACAGCCGAGATCACCTGCGACTGGCGCGACGGGGACGTCTGGTAA\n+>AAC_2___Ic.3002525.AL123456.3.314308_314854.4719\n+GTGCACACCCAGGTACACACGGCCCGCCTGGTCCACACCGCCGATCTTGACAGCGAGACC\n+CGCCAGGACATCCGTCAGATGGTCACCGGCGCGTTTGCCGGTGACTTCACCGAGACCGAC\n+TGGGAGCACACGCTGGGTGGGATGCACGCCCTGATCTGGCATCACGGGGCGATCATCGCG\n+CATGCCGCGGTGATCCAGCGGCGACTGATCTACCGCGGCAACGCGCTGCGCTGCGGGTAC\n+GTCGAAGGCGTTGCGGTGCGGGCGGACTGGCGGGGCCAACGCCTGGTGAGCGCGCTGTTG\n+GACGCCGTCGAGCAGGTGATGCGCGGCGCTTACCAGCTCGGAGCGCTCAGTTCCTCGGCG\n+CGGGCCCGCAGACTGTACGCCTCACGCGGCTGGCTGCCCTGGCACGGCCCGACATCGGTA\n+CTGGCACCAACCGGTCCAGTCCGTACACCCGATGACGACGGAACGGTGTTCGTCCTGCCC\n+ATCGACATCAGCCTGGACACCTCGGCGGAGCTGATGTGCGATTGGCGCGCGGGCGACGTC\n+TGGTAA\n+>AAC_2___Id.3002526.U72743.385_1018.228\n+GTGCTCACCCAGCATGTCAGTGAGGCTCGCACGCGCGGTGCGATCCACACCGCGCGTCTG\n+ATCCACACCTCCGATCTGGACCAGGAAACCCGCGACGGCGCGCGCCGCATGGTGATCGAG\n+GCGTTCCGCGATCCGTCCGGAGACAGTGATTTCACCGACGATTTCACCGACGACGACTGG\n+GACCACGCGCTCGGCGGCATGCACGCGCTGATCTCTCACCACGGTGCGCTCATCGCGCAC\n+GGCGCCGTCGTCCAACGTCGGTTGATGTACCGGGGACCCGACGGTAGAGGTCACGCGCTG\n+CGCTGCGGTTACGTCGAGGCCGTCGCGGTGCGCGAGGACCGGCGGGGCGACGGTCTGGGC\n+ACCGCCGTGCTCGACGCGCTCGAGCAGGTGATCCGCGGCGCCTATCAGATCGGCGCGCTG\n+AGCGCGTCGGACATCGCCCGGCCGATGTACATTGCCAGGGGCTGGCTGTCGTGGGAGGGT\n+CCGACATCGGTGCTGACCCCCACCGAGGGCATCGTTCGCACCCCTGAGGACGACCGGTCG\n+CTGTTCGTCCTGCCGGTCGATCTCCCGGACGGCCTCGAGTTGGACACCGCGCGCGAGATC\n+ACGTGCGACTGGCGCTCCGGCGACCCCTGGTGA\n+>AAC_2___Ie.3002527.NC_002677.1.3039191_3039740.4182\n+ATGGATACCCACCACGTACATACCGCCCGCCTGGTTCATACCGCCGATCTCGACGGCGAG\n+ACTCTCCGGCGCCTCCAGCAGATGGTCACCGACGCTTTCGCCGGAGACTTCGACGAGACC\n+GACTGGGAACACGCATTGGGCGGGATGCACGCCCTGATCTGGCGGCACGGCACAATCATT\n+GCGCACGCCGCGGTCGTTCAGCGGCGACTATTCTACCACGGCAACGCGTTGCGTTGCGGT\n+TACCTCGAAGGTGTCGCGGTACGGAAGGACTGCCGGGGCCGCGGACTTGTACATGCGCTG\n+CTGGACGCTATCGAGCAAGTGATACGCGGCGCCTATCAATTCGGTGCCTTGAGTTCCTCG\n+GACCGAGCCCGTCGGGTGTATATGTCGCGCGGGTGGTTACCATGGCTCGGCCCGACGTCA\n+GTGCTGGCTCCTACCGGTGTGATCCGTACGCCCGATGATGACGGCTCGGTGTTTGTCCTT\n+CCGGTCGGCATCAACCCGGACACCTCCTCGGGGTTGATGTGCGATTGGCGCGCAGGCAAC\n+GTGTGGTAA\n+>AAC_3__'..b'CATCTCACCTCCGCGGTGGTCCACGGTGACCTCGGCGGCGAGAACGTCCTGTGGGAGACG\n+GTGGACGGAGTGCCGCGCATGAGCGGCGTCGTCGACTGGGACGAGGTCGGCATCGGCGAC\n+CCGGCTGAGGACCTGGCCGCCATCGGGGCGAGCTACGGCGAGGAACTGCTGGGCCGAGTG\n+CTCGCGCTCGGCGGCTGGGCCGACAACGGAACGGCCGAGCGGATCTCGGCGATCCGAGGC\n+ACCTTCGCACTCCAGCAGGCCCTCTACGCGCAGCGCGACGGCGACGAGGAGGAACTCGCC\n+GACGGCCTCAGCGGCTACCGGTAG\n+>walK.3003794.BX571856.25616_27443.3565\n+ATGAAGTGGCTAAAACAACTACAATCCCTTCATACTAAACTTGTAATTGTTTATGTATTA\n+CTGATTATCATTGGTATGCAAATTATCGGGCTGTATTTTACAAATAACCTTGAAAAAGAG\n+CTGCTTGATAATTTTAAGAAGAATATTACGCAGTACGCTAAGCAATTAGAAATTAGTATT\n+GAAAAAGTATATGACGAAAAGGGCTCCGTAAATGCACAAAAAGATATTCAAAATTTATTA\n+AGTGAGTATGCCAACCGTCAAGAAATTGGAGAAATTCGTTTTATAGATAAAGACCAAATT\n+ATTATTGCGACGACGAAGCAGTCTAACCGTAGTCTAATCAATCAAAAAGCGAATGATAGT\n+TCTGTCCAAAAAGCACTATCACTAGGACAATCAAACGATCATTTAATTTTAAAAGATTAT\n+GGCGGTGGTAAGGACCGTGTCTGGGTATATAATATCCCCGTTAAAGTCGATAAAAAGGTA\n+ATTGGTAATATTTATATCGAATCAAAAATTAATGACGTTTATAACCAATTAAATAATATA\n+AATCAAATATTCATTGTTGGTACAGCTATTTCATTATTAATCACAGTCATCCTAGGATTC\n+TTTATAGCGCGAACGATTACCAAACCAATCACCGATATGCGTAACCAGACGGTTGAAATG\n+TCCAGAGGTAACTATACGCAACGTGTGAAGATTTATGGTAATGATGAAATTGGCGAATTA\n+GCTTTAGCATTTAATAACTTGTCTAAACGTGTACAAGAAGCGCAGGCTAATACTGAAAGT\n+GAGAAACGTAGACTGGACTCAGTTATCACCCATATGAGTGATGGTATTATTGCAACAGAC\n+CGTCGTGGACGTATTCGTATTGTCAATGATATGGCACTTAAGATGCTTGGTATGGCGAAA\n+GAAGACATCATCGGATATTACATGTTAAGTGTATTAAGTCTTGAAGATGAATTTAAACTT\n+GAAGAAATTCAAGAGAATAATGATAGTTTCTTATTAGATTTAAATGAAGAAGAAGGTCTA\n+ATCGCACGTGTTAACTTTAGTACGATTGTGCAGGAAACAGGATTTGTAACGGGTTATATC\n+GCTGTGTTACATGACGTGACTGAACAACAACAAGTTGAACGTGAGCGTCGTGAATTTGTT\n+GCCAATGTATCACATGAGTTACGTACACCTTTAACTTCTATGAATAGTTACATTGAAGCA\n+CTTGAAGAAGGTGCATGGAAAGATGAGGAACTTGCGCCACAATTTTTATCTGTTACCCGT\n+GAAGAAACAGAACGAATGATTCGACTGGTCAATGACTTGCTACAGTTATCTAAAATGGAT\n+AATGAGTCTGATCAAATCAATAAAGAAATTATCGACTTTAACATGTTCATTAATAAAATT\n+ATTAATCGACATGAAATGTCTACGAAAGATACAACATTTATTCGAGATATTCCGAAAAAG\n+ACGATTTTCACAGAATTTGATCCTGATAAAATGACGCAAGTATTTGATAATGTCATTACA\n+AATGCGATGAAATATTCTAGAGGCGATAAACGTGTCGAGTTCCACGTGAAACAAAATCCA\n+CTTTATAATCGAATGACGATTCGTATTAAAGATAATGGCATCGGTATTCCTATCAATAAA\n+GTCGATAAGATATTCGACCGATTCTATCGTGTAGATAAGGCACGTACGCGTAAAATGGGT\n+GGTACTGGATTAGGACTAGCCATTTCGAAAGAGATCGTGGAAGCTCACAATGGTCGTATT\n+TGGGCAAACAGTGTAGAAGGTCAAGGCACATCTATCTTTATCACACTTCCATGTGAAGTC\n+ATTGAAGACGGTGATTGGGATGAATAA\n+>y56_beta_lactamase.3003558.AY954728.11_896.3318\n+ATGAAGCACTCTTCGCTACGGCGTGCGCTATTATTAGCCGGTATTACCCTGCCCTTAGTC\n+AATTTTTCGCTGCCAACCTGGGCCGCTGCGATTCCGGGGTCATTAGACAAGCAATTGGCA\n+GCACTTGAGCACAGTGCTAACGGTCGTTTAGGCATTGCGATGATTAATACCGGCAATGGC\n+ACCAAAATTCTGTATCGCGGAGCTCGACGTTTCCCATTCTGTAGTACTTTTAAGTTTATG\n+TTAGCCGCTGCTGTATTGGGTCAAAGCCAATCTCAGCCGAATTTGCTCAATAAGCATATC\n+AATTACCATGAGAGTGATTTGTTATCTTATGCCCCCATCACGCGTAAAAATCTGGCGCAT\n+GGTATGACAGTTTCTGAATTATGTGCGGCTACCATTCAATATAGCGATAACACGGCCGCG\n+AATTTATTACTTAAAGAGTTGGGTGGTTTAGCGGCTGTTAATCAGTTTGCTCGCAGTATT\n+GGCGATCAGATGTTCAGGTTAGACCGCTGGGAACCGGATTTAAACACCGCACTACCTAAT\n+GACCCACGTGATACCACCACTCCTGCGGCTATGGCAGCTAGTATAAATAAATTGGTATTG\n+GGTGATGCATTGCACCCTGCCCAACGAAGCCAACTCACGGCATGGCTGAAAGGAAACACC\n+ACCGGGGATGCCACGATTCGCGCGGGTGCCCCTACTGACTGGATTGTGGGTGACAAAACA\n+GGTAGTGGCGATTACGGAACCACCAATGATATTGCGGTACTTTGGCCGACGAAAGGTGCA\n+CCGATTGTTTTAGTGGTGTATTTCACGCAACGTGAAAAAGATGCGAAGCCACGTCGCGAT\n+GTATTGGCCTCTGCGACCAAAATAATTTTGTCGCAAATATCCTGA\n+>ykkC.3003063.AL009126.1376516_1376855.489\n+ATGAAATGGGGATTGGTCGTGCTTGCCGCTGTTTTCGAGGTTGTTTGGGTGATAGGCTTA\n+AAGCACGCTGACTCAGCCTTAACATGGAGCGGCACTGCCATCGGCATCATATTCAGCTTT\n+TACCTTCTAATGAAGGCGACTCACAGTCTGCCTGTTGGTACCGTGTATGCCGTCTTTACC\n+GGGCTCGGCACAGCGGGAACAGTACTTAGTGAAATCGTTCTTTTTCATGAACCGGTTGGA\n+TGGCCGAAGCTATTGTTAATTGGCGTGCTCTTAATCGGTGTAATCGGGTTGAAGCTTGTG\n+ACACAGGATGAGACAGAGGAAAAAGGAGGCGAGGCATAA\n+>ykkD.3003064.AL009126.1376854_1377172.536\n+ATGCTGCACTGGATCAGTTTATTGTGCGCGGGCTGTTTAGAAATGGCCGGCGTGGCCCTT\n+ATGAATCAATATGCGAAAGAAAAAAGCGTGAAATGGGTGCTGTTGATCATTGTTGGTTTT\n+GCCGCTTCATTTTCCTTGCTGTCGTACGCAATGGAAACCACTCCGATGGGAACGGCTTAC\n+GCGGTCTGGACAGGAATTGGCACCGCCGGCGGGGCGCTTATCGGCATCCTCTTTTACAAG\n+GAGCAGAAAGACGCCAAACGGATCTTCTTTATCGCGTTGATTTTATGCTCAGCAGTTGGT\n+TTAAAAATTCTGTCATAA\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/02.cdhit.clusters.pickle |
| b |
| Binary file tool-data/card.db/02.cdhit.clusters.pickle has changed |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/02.cdhit.clusters.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/card.db/02.cdhit.clusters.tsv Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,1024 @@\n+AAC_2___IIb\tAAC_2___IIb.3003988.KX531051.1.0_723.3860\n+AAC_2___Ia\tAAC_2___Ia.3002523.L06156.263_800.53\n+AAC_2___Ib\tAAC_2___Ib.3002524.U41471.264_852.85\n+AAC_2___Ic\tAAC_2___Ic.3002525.AL123456.3.314308_314854.4719\n+AAC_2___Id\tAAC_2___Id.3002526.U72743.385_1018.228\n+AAC_2___Ie\tAAC_2___Ie.3002527.NC_002677.1.3039191_3039740.4182\n+AAC_3__II-\tAAC_3__IIa.3002533.X13543.1.185_1046.4266\tAAC_3__IIc.3002535.X54723.818_1679.616\n+AAC_3__IIIa\tAAC_3__IIIa.3002536.X55652.1123_1939.6\n+AAC_3__IIIb\tAAC_3__IIIb.3002537.L06160.983_1721.188\n+AAC_3__IIIc\tAAC_3__IIIc.3002538.L06161.105_945.9\n+AAC_3__IIb\tAAC_3__IIb.3002534.M97172.655_1465.10\n+AAC_3__IV\tAAC_3__IV.3002539.DQ241380.1.0_777.3715\n+AAC_3__IXa\tAAC_3__IXa.3002543.M55427.273_1119.655\n+AAC_3__Ia\tAAC_3__Ia.3002528.U12338.5055_5520.3369\n+AAC_3__Ib\tAAC_3__Ib.3002530.L06157.554_1085.224\n+AAC_3__Ib_AAC_6___Ib__\tAAC_3__Ib_AAC_6___Ib__.3002600.AF355189.1434_2439.271\n+AAC_3__Ic\tAAC_3__Ic.3002531.AJ511268.1294_1765.47\n+AAC_3__Id\tAAC_3__Id.3002529.AY458224.706_1183.223\n+AAC_3__VIIIa\tAAC_3__VIIIa.3002542.M55426.465_1326.12\n+AAC_3__VIIa\tAAC_3__VIIa.3002541.M22999.492_1359.694\n+AAC_3__VIa\tAAC_3__VIa.3002540.M88012.192_1092.659\n+AAC_3__Xa\tAAC_3__Xa.3002544.AB028210.1.2710_3565.4702\n+AAC_6___-\tAAC_6___33.3002587.JN596280.1202_1757.362\tAAC_6___I30.3002588.AY289608.1523_2078.399\n+AAC_6___30_AAC_6___Ib__fusion_protein\tAAC_6___30_AAC_6___Ib__fusion_protein.3002599.AJ584652.1926_2913.186\n+AAC_6___31\tAAC_6___31.3002585.AM283489.2655_3174.267\n+AAC_6___32\tAAC_6___32.3002586.EF614235.2246_2801.310\n+AAC_6___34\tAAC_6___34.3003989.KX531053.1.0_594.3861\n+AAC_6___I-\tAAC_6___Iaf.3002574.AB462903.1199_1751.672\tAAC_6___Ip.3002559.NG_047307.2.100_682.4422\tAAC_6___Iq.3002560.AF047556.126_678.343\n+AAC_6___I-_1\tAAC_6___Ih.3002555.L29044.351_792.456\tAAC_6___It.3002564.AF031328.0_441.736\tAAC_6___Iv.3002566.AF031330.0_441.81\n+AAC_6___I-_2\tAAC_6___Is.3002562.AF031327.0_441.669\tAAC_6___Iu.3002565.AF031329.0_441.27\tAAC_6___Ix.3002568.AF031332.0_441.170\n+AAC_6___I-_3\tAAC_6___Iaa.3002571.NC_003197.1707357_1707795.308\tAAC_6___Iy.3002569.AF144880.3541_3979.397\n+AAC_6___IIa\tAAC_6___IIa.3002594.AY123251.2950_3505.460\n+AAC_6___IIb\tAAC_6___IIb.3002595.L06163.531_1074.497\n+AAC_6___IIc\tAAC_6___IIc.3002596.AF162771.61_643.313\n+AAC_6___IId+\tAAC_6___IId.3002548.KC543497.1.404932_405451.3392\tAAC_6___Ib.3002546.JQ808129.633_1188.231\tAAC_6___Ib10.3002581.U59183.247_859.314\tAAC_6___Ib11.3002582.AY136758.377_947.366\tAAC_6___Ib3.3002576.FJ854362.1702_2257.141\tAAC_6___Ib4.3002577.AF445082.2788_3343.401\tAAC_6___Ib8.3002579.NC_025003.1.4171_4849.3719\tAAC_6___Ib9.3002580.AF043381.251_863.463\tAAC_6___Ib_.3003676.AY660529.1.121_676.4753\tAAC_6___Ib_Hangzhou.3002592.FJ503047.0_519.29\tAAC_6___Ib_Suzhou.3002591.EU085533.0_519.83\tAAC_6___Ib_cr.3002547.DQ303918.0_600.272\tANT_3____Ii_AAC_6___IId_fusion_protein.3002598.AF453998.3554_4946.16\taadA11.3002611.AY758206.2743_3589.13\taadA6.3002606.AM087411.1611_2457.199\taadA6_aadA10.3002622.AM087405.1748_2582.409\n+AAC_6___Ia\tAAC_6___Ia.3002545.M18967.756_1314.547\n+AAC_6___Iad\tAAC_6___Iad.3002572.AB119105.0_435.264\n+AAC_6___Iae\tAAC_6___Iae.3002573.AB104852.1934_2486.583\n+AAC_6___Iai\tAAC_6___Iai.3002575.EU886977.543_1110.708\n+AAC_6___Iaj\tAAC_6___Iaj.3003677.AB709942.1194_1749.3379\n+AAC_6___Iak\tAAC_6___Iak.3003199.AB894482.1.35038_35500.4672\n+AAC_6___Ib_SK\tAAC_6___Ib_SK.3002593.AB164230.35_566.360\n+AAC_6___Ic\tAAC_6___Ic.3002549.M94066.1553_1994.306\n+AAC_6___Ie_APH_2____Ia\tAAC_6___Ie_APH_2____Ia.3002597.NC_005024.42504_43944.305\n+AAC_6___If\tAAC_6___If.3002553.X55353.278_713.358\n+AAC_6___Ig\tAAC_6___Ig.3002554.L09246.543_981.396\n+AAC_6___Ii\tAAC_6___Ii.3002556.L12710.0_549.172\n+AAC_6___Iid\tAAC_6___Iid.3002589.AJ584700.33_582.207\n+AAC_6___Iih\tAAC_6___Iih.3002590.AJ584701.10_562.250\n+AAC_6___Ij\tAAC_6___Ij.3002557.L29045.259_700.494\n+AAC_6___Ik\tAAC_6___Ik.3002558.L29510.368_806.541\n+AAC_6___Ir\tAAC_6___Ir.3002561.AF031326.0_441.581\n+AAC_6___Isa\tAAC_6___Isa.3002563.AB116646.429_903.705\n+AAC_6___Iw\tAAC_6___Iw.300256'..b'5939_6971.258\n+vanG\tvanG.3002909.DQ212986.5984_7034.300\n+vanHA\tvanHA.3002942.M97297.6018_6986.3279\n+vanHB\tvanHB.3002943.U35369.4006_4978.3452\n+vanHD\tvanHD.3002944.AY082011.4936_5908.428\n+vanHF\tvanHF.3002945.AF155139.4978_5947.487\n+vanHM\tvanHM.3002947.FJ349556.3883_4864.534\n+vanHO\tvanHO.3002948.KF478993.490_1543.576\n+vanI\tvanI.3003723.LOCK01000072.1.166343_167390.4649\n+vanJ\tvanJ.3002914.NC_003888.3968821_3969814.3441\n+vanKI\tvanKI.3003727.NC_007907.1.4204949_4206077.4647\n+vanL\tvanL.3002910.EU250284.954_2004.612\n+vanM\tvanM.3002911.FJ349556.4856_5888.651\n+vanN\tvanN.3002912.JF802084.559_1591.684\n+vanO\tvanO.3002913.KF478993.1539_2580.675\n+vanRA\tvanRA.3002919.M97297.3976_4671.3275\n+vanRB\tvanRB.3002921.U35369.177_840.3453\n+vanRC\tvanRC.3002922.AF162694.5192_5888.105\n+vanRD\tvanRD.3002923.AY082011.0_699.122\n+vanRE\tvanRE.3002924.FJ872411.43513_44203.167\n+vanRF\tvanRF.3002925.AF155139.1511_2207.202\n+vanRG\tvanRG.3002926.DQ212986.2258_2966.246\n+vanRI\tvanRI.3003728.NC_007907.1.4201992_4202691.4646\n+vanRL\tvanRL.3002927.EU250284.4730_5426.287\n+vanRM\tvanRM.3002928.FJ349556.981_1680.337\n+vanRN\tvanRN.3002929.JF802084.4337_5030.379\n+vanRO\tvanRO.3002930.KF478993.1.6002_6704.4685\n+vanSA\tvanSA.3002931.M97297.4649_5803.3276\n+vanSB\tvanSB.3002932.U35369.839_2183.3454\n+vanSC\tvanSC.3002933.AF162694.5877_6963.565\n+vanSD\tvanSD.3002934.EU999036.688_1390.3440\n+vanSE\tvanSE.3002935.FJ872411.44192_45266.649\n+vanSF\tvanSF.3002936.AF155139.2199_3297.680\n+vanSG\tvanSG.3002937.DQ212986.2979_4086.706\n+vanSL\tvanSL.3002938.EU250284.5415_6510.744\n+vanSM\tvanSM.3002939.FJ349556.1672_2785.44\n+vanSN\tvanSN.3002940.JF802084.5019_6114.78\n+vanSO\tvanSO.3002941.KF478993.4909_5947.4550\n+vanTC\tvanTC.3002970.AF162694.3007_5104.151\n+vanTE\tvanTE.3002971.FJ872411.41336_43445.180\n+vanTG\tvanTG.3002972.DQ212986.7787_9926.217\n+vanTN\tvanTN.3002975.JF802084.2161_4264.259\n+vanTmL\tvanTmL.3002973.EU250284.2574_3564.301\n+vanTrL\tvanTrL.3002974.EU250284.3557_4658.353\n+vanUG\tvanUG.3004253.DQ212986.2029_2257.339\n+vanVB\tvanVB.3004254.AE016830.2211932_2212277.4564\n+vanWB\tvanWB.3002964.U35369.3182_4010.3455\n+vanWG\tvanWG.3002965.DQ212986.5137_5983.535\n+vanWI\tvanWI.3003724.NC_007907.1.2195400_2196522.4648\n+vanXA\tvanXA.3002949.M97297.8016_8624.3281\n+vanXB\tvanXB.3002950.U35369.6004_6613.3456\n+vanXD\tvanXD.3003070.AY082011.6937_7546.652\n+vanXF\tvanXF.3002952.AF155139.6976_7648.685\n+vanXI\tvanXI.3003725.NG_055644.1.100_709.4230\n+vanXM\tvanXM.3002953.FJ349556.5893_6502.717\n+vanXO\tvanXO.3002954.KF478993.2576_3185.23\n+vanXYC\tvanXYC.3002966.AF162694.2438_3011.39\n+vanXYE\tvanXYE.3002967.FJ872411.40765_41347.106\n+vanXYG\tvanXYG.3003069.DQ212986.7030_7795.123\n+vanXYL\tvanXYL.3002968.EU250284.1996_2578.168\n+vanXYN\tvanXYN.3002969.JF802084.1592_2165.203\n+vanYA\tvanYA.3002955.M97297.9052_9963.3278\n+vanYB\tvanYB.3002956.U35369.2358_3165.3457\n+vanYD\tvanYD.3002957.AY082011.3848_4265.338\n+vanYF\tvanYF.3002958.AF155139.3396_4278.380\n+vanYG1\tvanYG1.3002959.DQ212986.4222_5062.416\n+vanYM\tvanYM.3002961.FJ349556.3056_3758.479\n+vanZA\tvanZA.3002962.M97297.10116_10601.3280\n+vanZF\tvanZF.3002963.AF155139.4338_4959.566\n+varG\tvarG.3004289.AE003852.1.1674272_1675445.4194\n+vatA\tvatA.3002840.L07778.0_660.144\n+vatB\tvatB.3002841.U19459.66_705.3345\n+vatC\tvatC.3002842.AF015628.1306_1945.211\n+vatD\tvatD.3002843.AF368302.2716_3331.462\n+vatE\tvatE.3002844.AF242872.3579_4224.507\n+vatF\tvatF.3003744.AF170730.69_735.3514\n+vatH\tvatH.3002845.GQ205627.3036_3687.253\n+vgaA-\tvgaA.3002829.KC539823.1017_2586.376\tvgaALC.3002830.DQ823382.0_1569.412\n+vgaB\tvgaB.3000118.U82085.0_1659.475\n+vgaC\tvgaC.3002831.KU302801.102199_102430.3686\n+vgaD\tvgaD.3002832.GQ205627.1393_2971.519\n+vgaE\tvgaE.3002833.FR772051.8740_10315.562\n+vgbA\tvgbA.3001307.M20129.640_1540.4416\n+vgbB\tvgbB.3001308.AF015628.398_1286.4415\n+vgbC\tvgbC.3003990.KX531055.1.0_891.3862\n+vph\tvph.3003061.X02393.96_960.62\n+walK\twalK.3003794.BX571856.25616_27443.3565\n+y56_beta_lactamase\ty56_beta_lactamase.3003558.AY954728.11_896.3318\n+ykkC\tykkC.3003063.AL009126.1376516_1376855.489\n+ykkD\tykkD.3003064.AL009126.1376854_1377172.536\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/02.cdhit.gene.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/card.db/02.cdhit.gene.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,36632 @@\n+>AAC_2___IIb.3003988.KX531051.1.0_723.3860\n+ATGAACCATAGGAAAGGTAACGAGCCAACCGCTGCGGCACTGATGGAATTGCATGTTCTG\n+GCGATGTTTACGCATGACGGGAATATGCAAATTCGCACCATCAACGAGCCTTGGCCGGGA\n+GAGGAGCTTGCCCCGAGGTTTTTCATGGGTCGAACGATAGACGGCTCTTCGATCTGCAGG\n+TTTCGTCATGATGTTCCCGAAGGAATTGCCGGGCAATTGAGGGCTTTGGTTGAAGATGAG\n+CCTATCGTTACTGAAGAGGTTCTGACGAGGCCTAAACATTTTGCAGCTTATATGAACCTC\n+CTTCGCGCTGAGCACTATACGAGCGGACCTTGTTATCGGATACCTGATCAAACAACGCAG\n+GCCAAACAGACGGTAAGGATCACACCGGGAAATATTCGCGAATATTCGCTCACCGGTTTT\n+GAATGGCTGACCACGGAAATTGATTATGACCAGCCTTGTGTTGCGCTCATTCATGAGAAT\n+AGGGTGGTGTCGGTTTGCCGCAGCGTCCGGATTACTGAACGAGCTCACGAAGCTGGGCTT\n+GAAACGTCAGAGGAATTTCGTGGAAGAGGTTATGCGGCTGCTGTTGTTGCCGGATGGGCC\n+ATAGAGGTGCAAAAAATGGGCGCGCTGGCGTTGTACAGTACTTTATGGGGAAATAGCTCT\n+TCCCGGAGAGTAGCAAATAAATTAGGGTTGTCCTATTACGGAGTTAACTTCACGATCAGT\n+TGA\n+>AAC_2___Ia.3002523.L06156.263_800.53\n+ATGGGCATAGAATACCGCAGTCTGCATACCAGCCAATTGACACTGAGTGAAAAAGAAGCG\n+CTTTACGATTTATTAATTGAAGGTTTTGAAGGCGATTTTTCGCATGACGATTTCGCGCAC\n+ACTTTAGGTGGAATGCACGTCATGGCTTTTGATCAACAAAAATTGGTTGGTCATGTTGCA\n+ATTATTCAACGCCATATGGCCCTAGATAATACGCCTATCTCTGTAGGGTATGTTGAAGCG\n+ATGGTAGTTGAACAAAGTTATCGTCGCCAAGGTATTGGGCGGCAATTGATGCTGCAAACC\n+AATAAAATTATAGCTTCGTGTTATCAATTAGGGCTGCTGTCGGCTTCAGATGATGGACAA\n+AAATTGTATCATTCGGTTGGATGGCAAATCTGGAAAGGTAAGTTGTTTGAATTGAAACAA\n+GGGAGCTATATCCGTTCTATTGAAGAAGAAGGCGGAGTCATGGGCTGGAAAGCGGATGGT\n+GAGGTTGATTTTACCGCTTCGCTTTACTGTGATTTTCGTGGCGGTGATCAGTGGTAA\n+>AAC_2___Ib.3002524.U41471.264_852.85\n+GTGCCTTTCCAGGATGTCAGCGCGCCCGTTCGAGGCGGGATCCTGCACACCGCTCGACTC\n+GTCCACACCTCCGATCTCGATCAGGAGACTCGAGAGGGCGCCCGCCGCATGGTCATCGAG\n+GCGTTCGAGGGTGATTTCAGCGACGCCGACTGGGAGCACGCGCTCGGTGGCATGCACGCC\n+TTCATCTGTCACCACGGCGCTCTGATCGCGCATGCCGCGGTGGTCCAGCGCCGGCTGCTC\n+TACCGCGACACCGCGCTGCGCTGCGGGTACGTGGAAGCCGTGGCGGTGCGCGAAGATTGG\n+CGCGGCCAAGGCCTGGCCACCGCCGTCATGGACGCGGTCGAACAGGTGCTGCGCGGCGCC\n+TACCAGCTCGGCGCCCTCAGTGCGTCCGACACAGCCAGAGGCATGTACCTCTCTCGCGGG\n+TGGCTGCCGTGGCAGGGGCCGACCTCGGTGCTGCAGCCGGCCGGCGTGACGCGTACACCC\n+GAGGACGACGAGGGACTGTTCGTGCTGCCCGTCGGTCTCCCGGCGGGAATGGAACTCGAC\n+ACCACAGCCGAGATCACCTGCGACTGGCGCGACGGGGACGTCTGGTAA\n+>AAC_2___Ic.3002525.AL123456.3.314308_314854.4719\n+GTGCACACCCAGGTACACACGGCCCGCCTGGTCCACACCGCCGATCTTGACAGCGAGACC\n+CGCCAGGACATCCGTCAGATGGTCACCGGCGCGTTTGCCGGTGACTTCACCGAGACCGAC\n+TGGGAGCACACGCTGGGTGGGATGCACGCCCTGATCTGGCATCACGGGGCGATCATCGCG\n+CATGCCGCGGTGATCCAGCGGCGACTGATCTACCGCGGCAACGCGCTGCGCTGCGGGTAC\n+GTCGAAGGCGTTGCGGTGCGGGCGGACTGGCGGGGCCAACGCCTGGTGAGCGCGCTGTTG\n+GACGCCGTCGAGCAGGTGATGCGCGGCGCTTACCAGCTCGGAGCGCTCAGTTCCTCGGCG\n+CGGGCCCGCAGACTGTACGCCTCACGCGGCTGGCTGCCCTGGCACGGCCCGACATCGGTA\n+CTGGCACCAACCGGTCCAGTCCGTACACCCGATGACGACGGAACGGTGTTCGTCCTGCCC\n+ATCGACATCAGCCTGGACACCTCGGCGGAGCTGATGTGCGATTGGCGCGCGGGCGACGTC\n+TGGTAA\n+>AAC_2___Id.3002526.U72743.385_1018.228\n+GTGCTCACCCAGCATGTCAGTGAGGCTCGCACGCGCGGTGCGATCCACACCGCGCGTCTG\n+ATCCACACCTCCGATCTGGACCAGGAAACCCGCGACGGCGCGCGCCGCATGGTGATCGAG\n+GCGTTCCGCGATCCGTCCGGAGACAGTGATTTCACCGACGATTTCACCGACGACGACTGG\n+GACCACGCGCTCGGCGGCATGCACGCGCTGATCTCTCACCACGGTGCGCTCATCGCGCAC\n+GGCGCCGTCGTCCAACGTCGGTTGATGTACCGGGGACCCGACGGTAGAGGTCACGCGCTG\n+CGCTGCGGTTACGTCGAGGCCGTCGCGGTGCGCGAGGACCGGCGGGGCGACGGTCTGGGC\n+ACCGCCGTGCTCGACGCGCTCGAGCAGGTGATCCGCGGCGCCTATCAGATCGGCGCGCTG\n+AGCGCGTCGGACATCGCCCGGCCGATGTACATTGCCAGGGGCTGGCTGTCGTGGGAGGGT\n+CCGACATCGGTGCTGACCCCCACCGAGGGCATCGTTCGCACCCCTGAGGACGACCGGTCG\n+CTGTTCGTCCTGCCGGTCGATCTCCCGGACGGCCTCGAGTTGGACACCGCGCGCGAGATC\n+ACGTGCGACTGGCGCTCCGGCGACCCCTGGTGA\n+>AAC_2___Ie.3002527.NC_002677.1.3039191_3039740.4182\n+ATGGATACCCACCACGTACATACCGCCCGCCTGGTTCATACCGCCGATCTCGACGGCGAG\n+ACTCTCCGGCGCCTCCAGCAGATGGTCACCGACGCTTTCGCCGGAGACTTCGACGAGACC\n+GACTGGGAACACGCATTGGGCGGGATGCACGCCCTGATCTGGCGGCACGGCACAATCATT\n+GCGCACGCCGCGGTCGTTCAGCGGCGACTATTCTACCACGGCAACGCGTTGCGTTGCGGT\n+TACCTCGAAGGTGTCGCGGTACGGAAGGACTGCCGGGGCCGCGGACTTGTACATGCGCTG\n+CTGGACGCTATCGAGCAAGTGATACGCGGCGCCTATCAATTCGGTGCCTTGAGTTCCTCG\n+GACCGAGCCCGTCGGGTGTATATGTCGCGCGGGTGGTTACCATGGCTCGGCCCGACGTCA\n+GTGCTGGCTCCTACCGGTGTGATCCGTACGCCCGATGATGACGGCTCGGTGTTTGTCCTT\n+CCGGTCGGCATCAACCCGGACACCTCCTCGGGGTTGATGTGCGATTGGCGCGCAGGCAAC\n+GTGTGGTAA\n+>AAC_3__'..b'GAAGAATATCCTCTACCAACA\n+AATGCAGCGGCTCCAGTGGGTATCACTAGTGGTAACGATGGTGCACTCTGGTTTGTCGAA\n+ATTATGGGCAACAAAATAGGTCGAATCACTACAACTGGTGAGATTAGCGAATATGATATT\n+CCAACTCCAAACGCACGTCCACACGCTATAACCGCGGGGAAAAATAGCGAAATATGGTTT\n+ACTGAATGGGGGGCAAATCAAATCGGCAGAATTACAAACGACAAAACAATTCAAGAATAT\n+CAACTTCAAACAGAAAATGCGGAACCTCATGGTATTACCTTTGGAAAAGATGGATCCGTA\n+TGGTTTGCATTAAAATGTAAAATTGGGAAGCTGAATTTGAACGAATGA\n+>vgbC.3003990.KX531055.1.0_891.3862\n+ATGCAGATCGCCGCACAGGAGTACAAGACAGCGAATCGGGAATCGGGACCTTATGGTATT\n+ACGGCAAGACAAGATCGGACCATATGGTTCACGGAACAAAAAGGAAACCGGATCGGACGG\n+CTCACCAAGGATGGGGATATGCGCACGTTCGAAGTGCCGACTCCAGATGCCGGGGTCATG\n+TCTATCCTCTCTGCCCATACCGGTGACCTCTGGTTTACGGAGTACAAAGCAAATAAAATC\n+GGAAGGATGACAATGGAAGGAACATTTGCGGAATTCGAGCTGCCTGAAGCCAATTCGTCT\n+CCCTACGGCTTGGCTGAGGGTCCGGATGGAGCCATATGGTTCACCGAGCTAAGCGGCAAC\n+CGAATCGGAAGGATAACGCCGGCAGGCATTATCACGGAATATGACTTACCATGCGAAGGA\n+TCGTACCCTTCCTATATTACAGCCGGTCCGGACGGCGCGTTGTGGTTTACGGAAAACCAG\n+AACAACTGCATCGGCCGAATTACGGTGGACGGGGAGATTACCGAGTACCGGATTCCAACA\n+GAGCAATCCGGGCCGGTCGGCATCACGACAGGTGCCGATGGCGCTCTATGGTTTGTTCAA\n+ATCAACGGCAATCAAATCGGCCGGATCACAACGGCCGGGGAAATTACGGAATTCAAGCTC\n+CCGTCCGGGAATGCCAGACCCCATGCCATCACGGCGGGCGTTTCCGGGGATCTATGGTTT\n+ACCGAATGGGGAGCCAATCAAATCGGACGAATTACCTGCACCGGGGACATTACCGAGTAT\n+CCAATCCCTACCCCCTCCGCAGAACCTCATGGCATAACCGTGGATTCGGGCGGCGAGGTC\n+TGGTTCGCCGAGGAATGCGATCAGATCGGCCGGTTTACGATTCAGTATTAG\n+>vph.3003061.X02393.96_960.62\n+ATGAGAATCATTGAGACGCACCGCGATCTGCTGAGCCGGCTCCTGCCCGGGGACACCGTG\n+GGCGGACTCGCCGTCCACGAGGGGCAGTTCCACCATGTGGTGATCGGATCGCACCGGGTG\n+GTCTGCTTCGCCCGCACCCGGGCGGCCGCCGACCGTCTGCCCGGCAGGGCGGACGTCCTG\n+CGCGCTCTTGCCGGGATCGACCTCGGGTTTCGCACGCCGCAGCCGCTGTCCGAGGGCGGC\n+GCCCAGGGCACGGACGAGCCGCCGTACCTGGTGCTGAGCCGCATTCCCGGAGCACCGTTG\n+GAGGACGATGTGCTCACCAGCCCGGAGGTGGCGGAGGCCGTCGCCCGACAGTACGCGACC\n+CTGCTGTCCGGGCTCGCGGCGGCGGGCGACGAGGAGAAGGTGCGCGCCGCGCTGCCGGAG\n+GCTCCCGCGAACGAGTGGCAGGAGTTCGCCACGGGGGTGCGTACCGAACTGTTCCCGCTG\n+ATGTCCGACGGCGGCCGGGAGCGTGCCGAGCGCGAGCTCGCCGCGCTCGACGCCCTGCCC\n+CATCTCACCTCCGCGGTGGTCCACGGTGACCTCGGCGGCGAGAACGTCCTGTGGGAGACG\n+GTGGACGGAGTGCCGCGCATGAGCGGCGTCGTCGACTGGGACGAGGTCGGCATCGGCGAC\n+CCGGCTGAGGACCTGGCCGCCATCGGGGCGAGCTACGGCGAGGAACTGCTGGGCCGAGTG\n+CTCGCGCTCGGCGGCTGGGCCGACAACGGAACGGCCGAGCGGATCTCGGCGATCCGAGGC\n+ACCTTCGCACTCCAGCAGGCCCTCTACGCGCAGCGCGACGGCGACGAGGAGGAACTCGCC\n+GACGGCCTCAGCGGCTACCGGTAG\n+>y56_beta_lactamase.3003558.AY954728.11_896.3318\n+ATGAAGCACTCTTCGCTACGGCGTGCGCTATTATTAGCCGGTATTACCCTGCCCTTAGTC\n+AATTTTTCGCTGCCAACCTGGGCCGCTGCGATTCCGGGGTCATTAGACAAGCAATTGGCA\n+GCACTTGAGCACAGTGCTAACGGTCGTTTAGGCATTGCGATGATTAATACCGGCAATGGC\n+ACCAAAATTCTGTATCGCGGAGCTCGACGTTTCCCATTCTGTAGTACTTTTAAGTTTATG\n+TTAGCCGCTGCTGTATTGGGTCAAAGCCAATCTCAGCCGAATTTGCTCAATAAGCATATC\n+AATTACCATGAGAGTGATTTGTTATCTTATGCCCCCATCACGCGTAAAAATCTGGCGCAT\n+GGTATGACAGTTTCTGAATTATGTGCGGCTACCATTCAATATAGCGATAACACGGCCGCG\n+AATTTATTACTTAAAGAGTTGGGTGGTTTAGCGGCTGTTAATCAGTTTGCTCGCAGTATT\n+GGCGATCAGATGTTCAGGTTAGACCGCTGGGAACCGGATTTAAACACCGCACTACCTAAT\n+GACCCACGTGATACCACCACTCCTGCGGCTATGGCAGCTAGTATAAATAAATTGGTATTG\n+GGTGATGCATTGCACCCTGCCCAACGAAGCCAACTCACGGCATGGCTGAAAGGAAACACC\n+ACCGGGGATGCCACGATTCGCGCGGGTGCCCCTACTGACTGGATTGTGGGTGACAAAACA\n+GGTAGTGGCGATTACGGAACCACCAATGATATTGCGGTACTTTGGCCGACGAAAGGTGCA\n+CCGATTGTTTTAGTGGTGTATTTCACGCAACGTGAAAAAGATGCGAAGCCACGTCGCGAT\n+GTATTGGCCTCTGCGACCAAAATAATTTTGTCGCAAATATCCTGA\n+>ykkC.3003063.AL009126.1376516_1376855.489\n+ATGAAATGGGGATTGGTCGTGCTTGCCGCTGTTTTCGAGGTTGTTTGGGTGATAGGCTTA\n+AAGCACGCTGACTCAGCCTTAACATGGAGCGGCACTGCCATCGGCATCATATTCAGCTTT\n+TACCTTCTAATGAAGGCGACTCACAGTCTGCCTGTTGGTACCGTGTATGCCGTCTTTACC\n+GGGCTCGGCACAGCGGGAACAGTACTTAGTGAAATCGTTCTTTTTCATGAACCGGTTGGA\n+TGGCCGAAGCTATTGTTAATTGGCGTGCTCTTAATCGGTGTAATCGGGTTGAAGCTTGTG\n+ACACAGGATGAGACAGAGGAAAAAGGAGGCGAGGCATAA\n+>ykkD.3003064.AL009126.1376854_1377172.536\n+ATGCTGCACTGGATCAGTTTATTGTGCGCGGGCTGTTTAGAAATGGCCGGCGTGGCCCTT\n+ATGAATCAATATGCGAAAGAAAAAAGCGTGAAATGGGTGCTGTTGATCATTGTTGGTTTT\n+GCCGCTTCATTTTCCTTGCTGTCGTACGCAATGGAAACCACTCCGATGGGAACGGCTTAC\n+GCGGTCTGGACAGGAATTGGCACCGCCGGCGGGGCGCTTATCGGCATCCTCTTTTACAAG\n+GAGCAGAAAGACGCCAAACGGATCTTCTTTATCGCGTTGATTTTATGCTCAGCAGTTGGT\n+TTAAAAATTCTGTCATAA\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/02.cdhit.gene.varonly.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/card.db/02.cdhit.gene.varonly.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,4182 @@\n+>AxyZ.3004145.AFRQ01000061.1.28538_29177.4134\n+ATGGCCCGCAAGACGAAAGAAGAATCCCAACGCACCCGCGACCGCATCCTGGACGCCGCC\n+GAACACGTGTTCCTGTCCAAGGGCGTGGCCAGCACCACCATGAGCGATATCGCTGATTTC\n+GCGGGCGTGTCCCGGGGCGCCGTCTACGGCCATTACAAGAACAAGATCGATGTCTGCATC\n+GCCATGTGCGACCGGGCCCTGGGGGAAGCGGTGTCGCTGACCCGCGTGTCGACCGACGGC\n+GAGGCGCTGGAAGCGCTCTACGCGTCGATGCGCCAGTACGTGCAGATCTACGCCGAGGAA\n+GGCTCGGTGCAGCGTGTGCTGGAAATCCTCTACCTGAAATGCGAGCGCAGCGACGAGAAC\n+GCGCCGCTCCTGCGCCGCCGCGACCTGTGGGAGCGCCACGCCCTGCGCACTTCCGAAAAG\n+TTGCTGCGCGCCGCCGTCAGCCGCGAGGACCTGCCGCCCGCGCTGGACGTGCGTCTGTCC\n+AATGTCTACCTGCACTCCCTGGTCGAGGGCGTGTTTGGCACCATCTGCTGGTCCGATCGC\n+CTCAAGGGCGATATCTGGCCGCGCGTCGAGCGCATGCTCCGCGCCGCCATCGACACGCTG\n+CGCCTGTCGCCGCAACTGCGGTTGCCACAGGCCGCCTGA\n+>Clostridium_difficile_EF_Tu.3003357.NC_017174.109609_110803.3358\n+ATGGCTAAAGCTAAATACGAAAGAACAAAACCTCATGTTAATATAGGGACAATAGGACAC\n+GTAGACCACGGTAAAACTACATTAACAGCAGCAATAACAAAAACATTATATGACAGATAT\n+CAATTAGGAGAAGCAGTAGATTTCGCAAACATAGATAAAGCTCCAGAAGAAAGAGAAAGA\n+GGAATCACAATATCAACAGCACACGTTGAGTATGAAACACCAAATAGACACTATGCACAC\n+GTTGACTGCCCAGGGCATGCTGACTACGTTAAGAACATGATAACAGGAGCAGCACAAATG\n+GACGGAGCAATATTAGTTTGTTCAGCAACAGATGGACCAATGCCACAAACAAGAGAGCAT\n+ATACTATTATCAAGACAAGTTGGAGTACCATATATAGTAGTATTCTTAAATAAATGTGAC\n+ATGGTAGATGATGAAGAGTTATTAGAGTTAGTAGAGATGGAAGTAAGAGATTTATTAACA\n+GAGTATGATTTCCCAGGAGATGACACTCCAATAGTAAGAGGATCAGCGTTAATGGCATTA\n+GAAGATCCAAAGAGTGAGTGGGGAGATAAGATAGTAGAATTATTCGAGCAAATAGATGAA\n+TATATACCAGCACCAGAGAGAGATACAGATAAGCCATTCTTAATGCCAGTAGAGGACGTA\n+TTCTCAATCACAGGAAGAGGAACAGTTGCAACAGGAAGAGTGGAAAGAGGAGTACTAAAA\n+GTACAAGACGAAGTAGAATTAGTAGGATTAACAGAAGCACCAAGAAAAGTAGTAGTAACA\n+GGAGTAGAGATGTTCAGAAAATTATTAGACCAAGCACAAGCAGGGGATAATATAGGAGCA\n+TTATTAAGAGGAGTACAAAGAAACGAGATAGAAAGAGGACAAGTACTAGCAAAGACTGGA\n+TCAGTAAAGGCACACACAAAGTTTACAGCAGAAGTATATGTACTTAAAAAAGAAGAAGGT\n+GGAAGACATACACCATTCTTTGATGGATATAGACCACAATTTTACTTCAGAACAACAGAC\n+GTAACAGGAGCTTGTAAGTTACCAGAAGGAATAGAGATGGTAATGCCTGGAGATAACGTA\n+ACAATGGAAGTAGACTTAATAAACTCAATAGTTGTAGAAGAGGGATTAAGATTCTCAATA\n+AGAGAAGGTGGAAGAACAGTAGCTTCAGGAGTTGTTGCTACAATAATAGAGTAA\n+>D_Ala_D_Ala_ligase.3003970.AY168442.1.53_1109.3769\n+TTGAAAATTATTTTATTATATGGCGGACGCAGTGCAGAGCATGATGTATCGCTTCTATCC\n+GCTTTTTCAGTAGTCAATGCTGTATATTATAATTACTACCAAGTACAATTAGTAATGATC\n+ACGAGAGATGGCCAGTGGCTAAAAGGCTCTTTATTGACTGAAGCCCCTACATCCAAAGAA\n+GTGTTGAATCTGACGGATTCGGCTTACCAAGGGACGCCGATCCAACCTGGTGAGATCAAG\n+GAAGAGGATGCGATTGTTTTTCCGCTGCTCCACGGACCAAATGGAGAAGATGGAACGATC\n+CAAGGTTTTCTAGAGACCATCGGCATGCCTTATGTAGGCGCAGGGGTTTTAACTAGTGCC\n+TGTGGCATGGATAAGATTATGACCAAATATATCTTGCAGGCGGCGGGGATTCCGCAAGTT\n+CCTTATGTACCCGTTCTTAAAAACTATTGGAAAGAAAATCCTAAAAAAGTATTTGAACAA\n+TGTGAAGGCAGTCTTTTGTATCCAATGTTTATCAAACCTGCCAATATGGGTTCAAGTGTT\n+GGGATCACAAAAGCTGAAAATCGGGAAGAATTGCAAAATGCACTTCAAGAAGCCTACCGT\n+TATGATACACGAGCGATCGTAGAACAAGGGATCGAAGCTCGCGAAATCGAAGTCGCTGTT\n+CTTGGAAATGAAGATGTGCGTACAACAATGCCCGGCGAGATCGTTAAAGATGTAGCTTTT\n+TATGATTACAATTCGAAGTATCTTGACAATAAGATTGAGATGCAGATCCCAGCTCAAATT\n+CCTGAGGAGACACAAGCGAAAGCGCAAGAGTTTGCCAAAAAAGCTTATACGATGCTTGGA\n+GGAAGCGGCCTCAGCCGCTGCGACTTTTTCTTGACGAACAAAAACGAATTATTCCTGAAT\n+GAATTGAACACGATGCCTGGTTTTACCGAGTTTAGTATGTACCCGCTGTTGTGGGAAAAA\n+ACCGGTCTGCCATATGGTGATTTGATTGAGGAATTGATTCAATTAGGAGTCAACCGTTTT\n+AAACAGCGTCAAGCCTTTTTAACCGATGTCGAATAA\n+>Enterobacter_aerogenes_Omp36.3003385.AF335467.36_1164.2109\n+ATGAAAGTTAAAGTACTGTCCCTCCTGGTACCAGCACTGCTGGTAGCGGGCGCAGCAAAT\n+GCGGCTGAAATTTATAACAAAGACGGCAACAAATTAGACCTGTACGGTAAAATCGACGGT\n+CTGCACTACTTCTCTTCCGACGACAGCGTCGACGGCGACCAGACCTACATGCGTATCGGC\n+GTGAAAGGCGAAACCCAGATCAACGACCAGCTGACCGGTTACGGCCAGTGGGAATACAAC\n+GTTCAGGCGAACAACACTGAAAGCTCCAGCGACCAGGCATGGACTCGTCTGGCCTTCGCG\n+GGTCTGAAATTCGGCGACGCGGGTTCTTTCGACTACGGTCGTAACTACGGCGTTGTTTAC\n+GACGTAACTTCCTGGACCGACGTTCTGCCGGAATTCGGCGGCGACACCTACGGTTCCGAC\n+AACTTCCTGCAGTCCCGTGCTAACGGTGTTGCCACCTACCGTAACTCTGACTTCTTCGGT\n+CTGGTTGACGGCCTGAACTTTGCTCTGCAGTACCAGGGTAAAAACGGCAGCGTGAGCGGC\n+GAAGATCAGACCAACAACGGTCGTGACTTCCAGAAACAGAACGGCGAAGGCTTCGGCACC\n+TCCGTAACTTATGATATCTGGGACGGCATCAGCGCTGGTTTCGCGTACTCCAGCTCTAAA\n+CGTACCGACGAGCAGAACAACTCTACCTTCGTGTCTAAGACCGATGGTGGTCGTTACGGT\n+GTTCTGGGTGAAGGCGATCA'..b'TACAGAAAAACAGTATGAAACTCTCGAAAATCAATTAGCCTTT\n+TTATGCCAACAAGGTTTTTCACTAGAGAATGCATTATATGCACTCAGCGCTGTGGGGCAT\n+TTTACTTTAGGTTGCGTATTGGAAGATCAAGAGCATCAAGTCGCTAAAGAAGAAAGGGAA\n+ACACCTACTACTGATAGTATGCCGCCATTATTACGACAAGCTATCGAATTATTTGATCAC\n+CAAGGTGCAGAGCCAGCCTTCTTATTCGGCCTTGAATTGATCATATGCGGATTAGAAAAA\n+CAACTTAAATGTGAAAGTGGGTCTTAA\n+>thyA.3004153.NC_000962.3.3073679_3074471.4482\n+GTGACGCCATACGAGGACCTGCTGCGCTTCGTGCTCGAAACGGGTACGCCCAAATCCGAC\n+CGCACCGGCACCGGAACCCGCAGCCTGTTCGGCCAGCAGATGCGCTATGATTTGTCGGCC\n+GGTTTCCCGCTGCTCACTACCAAGAAAGTCCATTTCAAATCGGTAGCCTACGAGCTGCTG\n+TGGTTTTTGCGCGGCGATTCCAATATCGGTTGGCTGCACGAGCACGGAGTCACCATCTGG\n+GACGAATGGGCAAGTGATACAGGCGAACTCGGGCCGATCTACGGTGTACAATGGCGATCG\n+TGGCCGGCTCCATCCGGTGAGCACATCGACCAGATCAGCGCGGCGCTGGATTTGCTGCGC\n+ACCGATCCCGATTCCCGGCGCATCATCGTGTCGGCCTGGAACGTCGGCGAAATCGAGCGG\n+ATGGCGCTGCCGCCCTGTCATGCGTTCTTCCAGTTCTACGTCGCCGATGGCCGGCTGAGC\n+TGTCAGCTCTACCAACGCAGCGCCGACCTGTTTCTGGGTGTGCCGTTCAACATCGCCAGC\n+TATGCGTTGCTCACCCACATGATGGCCGCCCAGGCCGGCTTGTCGGTCGGCGAGTTCATC\n+TGGACCGGTGGCGACTGCCACATCTACGACAATCACGTCGAGCAAGTACGGCTGCAGCTC\n+AGCCGCGAGCCGCGGCCATATCCGAAACTACTTCTAGCCGACCGGGATTCAATCTTCGAG\n+TACACCTATGAAGACATCGTTGTGAAGAACTACGATCCGCATCCGGCGATCAAAGCTCCA\n+GTCGCGGTATGA\n+>tlyA.3003445.AE000516.1908741_1909548.2076\n+GTGGCACGACGTGCCCGCGTTGACGCCGAGCTGGTCCGGCGGGGCCTGGCGCGATCACGT\n+CAACAGGCCGCGGAGTTGATCGGCGCCGGCAAGGTGCGCATCGACGGGCTGCCGGCGGTC\n+AAGCCGGCCACCGCCGTGTCCGACACCACCGCGCTGACCGTGGTGACCGACAGTGAACGC\n+GCCTGGGTATCGCGCGGAGCGCACAAACTAGTCGGTGCGCTGGAGGCGTTCGCGATCGCG\n+GTGGCGGGCCGGCGCTGTCTGGACGCGGGCGCATCGACCGGTGGGTTCACCGAAGTACTG\n+CTGGACCGTGGTGCCGCCCACGTGGTGGCCGCCGATGTCGGATACGGCCAGCTGGCGTGG\n+TCGCTGCGCAACGATCCTCGGGTGGTGGTCCTCGAGCGGACCAACGCACGTGGCCTCACA\n+CCGGAGGCGATCGGCGGTCGCGTCGACCTGGTAGTGGCCGACCTGTCGTTCATCTCGTTG\n+GCTACCGTGTTGCCCGCGCTGGTTGGATGCGCTTCGCGCGACGCCGATATCGTTCCACTG\n+GTGAAGCCGCAGTTTGAGGTGGGGAAAGGTCAGGTCGGCCCCGGTGGGGTGGTCCATGAC\n+CCGCAGTTGCGTGCGCGGTCGGTGCTCGCGGTCGCGCGGCGGGCACAGGAGCTGGGCTGG\n+CACAGCGTCGGCGTCAAGGCCAGCCCGCTGCCGGGCCCATCGGGCAATGTCGAGTACTTC\n+CTGTGGTTGCGCACGCAGACCGACCGGGCATTGTCGGCCAAGGGATTGGAGGATGCGGTG\n+CACCGTGCGATTAGCGAGGGCCCGTAG\n+>walK.3003794.BX571856.25616_27443.3565\n+ATGAAGTGGCTAAAACAACTACAATCCCTTCATACTAAACTTGTAATTGTTTATGTATTA\n+CTGATTATCATTGGTATGCAAATTATCGGGCTGTATTTTACAAATAACCTTGAAAAAGAG\n+CTGCTTGATAATTTTAAGAAGAATATTACGCAGTACGCTAAGCAATTAGAAATTAGTATT\n+GAAAAAGTATATGACGAAAAGGGCTCCGTAAATGCACAAAAAGATATTCAAAATTTATTA\n+AGTGAGTATGCCAACCGTCAAGAAATTGGAGAAATTCGTTTTATAGATAAAGACCAAATT\n+ATTATTGCGACGACGAAGCAGTCTAACCGTAGTCTAATCAATCAAAAAGCGAATGATAGT\n+TCTGTCCAAAAAGCACTATCACTAGGACAATCAAACGATCATTTAATTTTAAAAGATTAT\n+GGCGGTGGTAAGGACCGTGTCTGGGTATATAATATCCCCGTTAAAGTCGATAAAAAGGTA\n+ATTGGTAATATTTATATCGAATCAAAAATTAATGACGTTTATAACCAATTAAATAATATA\n+AATCAAATATTCATTGTTGGTACAGCTATTTCATTATTAATCACAGTCATCCTAGGATTC\n+TTTATAGCGCGAACGATTACCAAACCAATCACCGATATGCGTAACCAGACGGTTGAAATG\n+TCCAGAGGTAACTATACGCAACGTGTGAAGATTTATGGTAATGATGAAATTGGCGAATTA\n+GCTTTAGCATTTAATAACTTGTCTAAACGTGTACAAGAAGCGCAGGCTAATACTGAAAGT\n+GAGAAACGTAGACTGGACTCAGTTATCACCCATATGAGTGATGGTATTATTGCAACAGAC\n+CGTCGTGGACGTATTCGTATTGTCAATGATATGGCACTTAAGATGCTTGGTATGGCGAAA\n+GAAGACATCATCGGATATTACATGTTAAGTGTATTAAGTCTTGAAGATGAATTTAAACTT\n+GAAGAAATTCAAGAGAATAATGATAGTTTCTTATTAGATTTAAATGAAGAAGAAGGTCTA\n+ATCGCACGTGTTAACTTTAGTACGATTGTGCAGGAAACAGGATTTGTAACGGGTTATATC\n+GCTGTGTTACATGACGTGACTGAACAACAACAAGTTGAACGTGAGCGTCGTGAATTTGTT\n+GCCAATGTATCACATGAGTTACGTACACCTTTAACTTCTATGAATAGTTACATTGAAGCA\n+CTTGAAGAAGGTGCATGGAAAGATGAGGAACTTGCGCCACAATTTTTATCTGTTACCCGT\n+GAAGAAACAGAACGAATGATTCGACTGGTCAATGACTTGCTACAGTTATCTAAAATGGAT\n+AATGAGTCTGATCAAATCAATAAAGAAATTATCGACTTTAACATGTTCATTAATAAAATT\n+ATTAATCGACATGAAATGTCTACGAAAGATACAACATTTATTCGAGATATTCCGAAAAAG\n+ACGATTTTCACAGAATTTGATCCTGATAAAATGACGCAAGTATTTGATAATGTCATTACA\n+AATGCGATGAAATATTCTAGAGGCGATAAACGTGTCGAGTTCCACGTGAAACAAAATCCA\n+CTTTATAATCGAATGACGATTCGTATTAAAGATAATGGCATCGGTATTCCTATCAATAAA\n+GTCGATAAGATATTCGACCGATTCTATCGTGTAGATAAGGCACGTACGCGTAAAATGGGT\n+GGTACTGGATTAGGACTAGCCATTTCGAAAGAGATCGTGGAAGCTCACAATGGTCGTATT\n+TGGGCAAACAGTGTAGAAGGTCAAGGCACATCTATCTTTATCACACTTCCATGTGAAGTC\n+ATTGAAGACGGTGATTGGGATGAATAA\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/card.db/02.cdhit.noncoding.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/card.db/02.cdhit.noncoding.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,2732 @@\n+>Borrelia_burgdorferi_16S.3003502.NR_044732.2.0_1477.3267\n+AATAACGAAGAGTTTGATCCTGGCTTAGAACTAACGCTGGCAGTGCGTCTTAAGCATGCA\n+AGTCAAACGGGATGTAGCAATACATTCAGTGGCGAACGGGTGAGTAACGCGTGGATGATC\n+TACCTATGAGATGGGGATAACTATTAGAAATAGTAGCTAATACCGAATAAGGTCAGTTAA\n+TTTGTTAATTGATGAAAGGAAGCCTTTAAACGTTCGCTTGTAGATGAGTCTGCGTCTTAT\n+TAGCTAGTTGGTAGGGTAAATGCCTACCAAGGCAATGATAAGTAACCGGCCTGAGAGGGT\n+GAACGGTCACACTGGAACTGAGATACGGTCCAGNCTCCTACGGGAGGCAGCAGCTAAGAA\n+TCTTCCGCAATGGGCGAAAGCCTGACGGAGCGACACTGCGTGAATGAAGAAGGTCGAAAG\n+ATTGTAAAATTCTTTTATAAATGAGGAATAAGCTTTGTAGGAAATGACAAAGTGATGACG\n+TTAATTTATGAATAAGCCCCGGCTAATTACGTGCCAGNAGCCGCGGTAATACGTAAGGGN\n+NNAGCGTTGTTCGGGATTATTGGGCGTAAAGGGTGAGTAGGCGGATATATAAGTCTATGC\n+ATAAAATACCACAGCTCAACTGTGGACCTATGTTGGAAACTATATGTCTAGAGTCTGATA\n+GAGGAAGTTAGAATTTCTGGTGTAAGGGTGGAATCTGTTGATATCAGAAAGAATACCGGA\n+GGCGAAGGCGAACTTCTGGGTCAAGACTGACGCTGAGTCACGAAAGCGTAGGGAGCAAAC\n+AGGATTAGATACCCTGGTAGTCTACGCTGTAAACGATGCACACTTGGTGTTAACTAAAAG\n+TTAGTACCGAAGCTAACGTGTTAAGTGTGCAGCCTGGGGAGTATGCTCGCAAGAGNGAAA\n+CTCAAAGGNATTNANNNGNGCCNGCACAAGNNGTGGAGCATGTGGTTTNNNNNNANNNTA\n+CGCGAGGAACCTTACCAGGGCTTGACATATATAGGATATAGTTAGAGATAATTATTCCCC\n+GTTTGGGGTCTATATACAGGTGCTGCATGGTTGTCGTCAGCTCGTGCTGTGAGGTGTTGG\n+GTTAAGTCCCGCAACGAGCGCAACCCTTGTTATCTGTTACCAGCATGTAATGGTGGGGAC\n+TCAGATAAGACTGCCGGTGATAAGTCGGAGGAAGGTGAGGATGACGTCAAATCATCATGG\n+CCCTTATGTCCTGGGCTACACACGTGCTACAATGGCCTGTACAAAGCGAAGCGAAACAGT\n+GATGTGAAGCAAAACGCATAAAGCAGGTCTCAGTCCGGATTGAAGTCTGAAACTCGACTT\n+CATGAAGTTGGAATCGCTAGTAATCGTATATCAGAATGATACGGTGAATACGTTCTCGGG\n+CNTTGTACACACCGCCCGTCACACCACCCGAGTTGAGGATACCCGAAGCTATTATTCTAA\n+CCCGTAAGGGAGGAAGGTATTTAAGGTATGTTTAGCA\n+>Borrelia_burgdorferi_16S.3003503.NR_044732.2.0_1477.3266\n+AATAACGAAGAGTTTGATCCTGGCTTAGAACTAACGCTGGCAGTGCGTCTTAAGCATGCA\n+AGTCAAACGGGATGTAGCAATACATTCAGTGGCGAACGGGTGAGTAACGCGTGGATGATC\n+TACCTATGAGATGGGGATAACTATTAGAAATAGTAGCTAATACCGAATAAGGTCAGTTAA\n+TTTGTTAATTGATGAAAGGAAGCCTTTAAACGTTCGCTTGTAGATGAGTCTGCGTCTTAT\n+TAGCTAGTTGGTAGGGTAAATGCCTACCAAGGCAATGATAAGTAACCGGCCTGAGAGGGT\n+GAACGGTCACACTGGAACTGAGATACGGTCCAGNCTCCTACGGGAGGCAGCAGCTAAGAA\n+TCTTCCGCAATGGGCGAAAGCCTGACGGAGCGACACTGCGTGAATGAAGAAGGTCGAAAG\n+ATTGTAAAATTCTTTTATAAATGAGGAATAAGCTTTGTAGGAAATGACAAAGTGATGACG\n+TTAATTTATGAATAAGCCCCGGCTAATTACGTGCCAGNAGCCGCGGTAATACGTAAGGGN\n+NNAGCGTTGTTCGGGATTATTGGGCGTAAAGGGTGAGTAGGCGGATATATAAGTCTATGC\n+ATAAAATACCACAGCTCAACTGTGGACCTATGTTGGAAACTATATGTCTAGAGTCTGATA\n+GAGGAAGTTAGAATTTCTGGTGTAAGGGTGGAATCTGTTGATATCAGAAAGAATACCGGA\n+GGCGAAGGCGAACTTCTGGGTCAAGACTGACGCTGAGTCACGAAAGCGTAGGGAGCAAAC\n+AGGATTAGATACCCTGGTAGTCTACGCTGTAAACGATGCACACTTGGTGTTAACTAAAAG\n+TTAGTACCGAAGCTAACGTGTTAAGTGTGCAGCCTGGGGAGTATGCTCGCAAGAGNGAAA\n+CTCAAAGGNATTNANNNGNGCCNGCACAAGNNGTGGAGCATGTGGTTTNNNNNNANNNTA\n+CGCGAGGAACCTTACCAGGGCTTGACATATATAGGATATAGTTAGAGATAATTATTCCCC\n+GTTTGGGGTCTATATACAGGTGCTGCATGGTTGTCGTCAGCTCGTGCTGTGAGGTGTTGG\n+GTTAAGTCCCGCAACGAGCGCAACCCTTGTTATCTGTTACCAGCATGTAATGGTGGGGAC\n+TCAGATAAGACTGCCGGTGATAAGTCGGAGGAAGGTGAGGATGACGTCAAATCATCATGG\n+CCCTTATGTCCTGGGCTACACACGTGCTACAATGGCCTGTACAAAGCGAAGCGAAACAGT\n+GATGTGAAGCAAAACGCATAAAGCAGGTCTCAGTCCGGATTGAAGTCTGAAACTCGACTT\n+CATGAAGTTGGAATCGCTAGTAATCGTATATCAGAATGATACGGTGAATACGTTCTCGGG\n+CNTTGTACACACCGCCCGTCACACCACCCGAGTTGAGGATACCCGAAGCTATTATTCTAA\n+CCCGTAAGGGAGGAAGGTATTTAAGGTATGTTTAGCA\n+>Borrelia_burgdorferi_16S.3003504.NR_044732.2.0_1477.3268\n+AATAACGAAGAGTTTGATCCTGGCTTAGAACTAACGCTGGCAGTGCGTCTTAAGCATGCA\n+AGTCAAACGGGATGTAGCAATACATTCAGTGGCGAACGGGTGAGTAACGCGTGGATGATC\n+TACCTATGAGATGGGGATAACTATTAGAAATAGTAGCTAATACCGAATAAGGTCAGTTAA\n+TTTGTTAATTGATGAAAGGAAGCCTTTAAACGTTCGCTTGTAGATGAGTCTGCGTCTTAT\n+TAGCTAGTTGGTAGGGTAAATGCCTACCAAGGCAATGATAAGTAACCGGCCTGAGAGGGT\n+GAACGGTCACACTGGAACTGAGATACGGTCCAGNCTCCTACGGGAGGCAGCAGCTAAGAA\n+TCTTCCGCAATGGGCGAAAGCCTGACGGAGCGACACTGCGTGAATGAAGAAGGTCGAAAG\n+ATTGTAAAATTCTTTTATAAATGAGGAATAAGCTTTGTAGGAAATGACAAAGTGATGACG\n+TTAATTTATGAATAAGCCCCGGCTAATTACGTGCCAGNAGCCGCGGTAATACGTAAGGGN\n+NNAGCGTTGTTCGGGATTATTGGGCGTAAAGGGTGAGTAGGCGGATATATAAGTCTATGC\n+ATAAAATACCACAGCTCAACTGTGGACCTATGTTGGAAACTATATGTCTAGAGTCTGATA\n+GAGGAAGTTAGAATTTCTGGTGTAAGGGTGGAATCTGTTGATATCAGAAAGAATACCGGA\n+GGCG'..b'TGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCA\n+AGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAAT\n+TCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAG\n+AATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGA\n+AATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGC\n+CGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTC\n+ATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCG\n+ACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAAC\n+TCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGT\n+TCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGT\n+AGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAA\n+CAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA\n+>rrsD.3003512.AE006468.3570463_3572006.3227\n+AGGTAAGGAGGTGATCCAACCGCAGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCC\n+AGTCATGAATCACAAAGTGGTAAGCGCCCTCCCGAAGGTTAAGCTACCTACTTCTTTTGC\n+AACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGTGG\n+CATTCTGATCCACGATTACTAGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAAT\n+CCGGACTACGACGCACTTTATGAGGTCCGCTTGCTCTCGCGAGGTCGCTTCTCTTTGTAT\n+GCGCCATTGTAGCACGTGTGTAGCCCTGGTCGTAAGGGCCATGATGACTTGACGTCATCC\n+CCACCTTCCTCCAGTTTATCACTGGCAGTCTCCTTTGAGTTCCCGACCTAATCGCTGGCA\n+ACAAAGGATAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTG\n+ACGACAGCCATGCAGCACCTGTCTCACAGTTCCCGAAGGCACCAATCCATCTCTGGAAAG\n+TTCTGTGGATGTCAAGACCAGGTAAGGTTCTTCGCGTTGCATCGAATTAAACCACATGCT\n+CCACCGCTTGTGCGGGCCCCCGTCAATTCATTTGAGTTTTAACCTTGCGGCCGTACTCCC\n+CAGGCGGTCTACTTAACGCGTTAGCTCCGGAAGCCACGCCTCAAGGGCACAACCTCCAAG\n+TAGACATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTT\n+CGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGAT\n+CTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGC\n+CAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCG\n+CCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTCCGTATTACCGCG\n+GCTGCTGGCACGGAGTTAGCCGGTGCTTCTTCTGCGGGTAACGTCAATTGCTGCGGTTAT\n+TAACCACAACACCTTCCTCCCCGCTGAAAGTACTTTACAACCCGAAGGCCTTCTTCATAC\n+ACGCGGCATGGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCC\n+GTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAG\n+GGATCGTCGCCTTGGTGAGCCGTTACCTCACCAACAAGCTAATCCCATCTGGGCACATCT\n+GATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCCA\n+CCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGTTTCCCAGACATTACTCACCCGTCCG\n+CCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTGTTACCGTTCGACTTGCATGTGTTAGGC\n+CTGCCGCCAGCGTTCAATCTGAGCCATGATCAAACTCTTCAATT\n+>rrsH.3003372.U00096.223771_225312.3228\n+AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA\n+GTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAA\n+TGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCAT\n+AACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATG\n+GGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGA\n+GGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGG\n+GGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCT\n+TCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATT\n+GACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAG\n+GGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCA\n+GATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTC\n+GTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACC\n+GGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCA\n+AACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCC\n+CTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCA\n+AGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAAT\n+TCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGA\n+TTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGA\n+AATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCTTTTGTTGCCAGCGGTCCGGC\n+CGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTC\n+ATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCG\n+ACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAAC\n+TCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGT\n+TCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGT\n+AGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAA\n+CAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/plasmidfinder.db/00.info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder.db/00.info.txt Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,3 @@ +input fasta file: plasmidfinder.fa +input tsv file: plasmidfinder.tsv +genetic_code 11 |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/plasmidfinder.db/00.rename_info --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder.db/00.rename_info Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,211 @@\n+Col(BS512).1__NC_010656\tCol_BS512_.1__NC_010656\n+Col(IMGS31).1__NC_011406\tCol_IMGS31_.1__NC_011406\n+Col(IRGK).1__AY543071\tCol_IRGK_.1__AY543071\n+Col(KPHS6).1__NC_016841\tCol_KPHS6_.1__NC_016841\n+Col(MG828).1__NC_008486\tCol_MG828_.1__NC_008486\n+Col(MGD2).1__NC_003789\tCol_MGD2_.1__NC_003789\n+Col(MP18).1__NC_013652\tCol_MP18_.1__NC_013652\n+Col(SD853).1__NC_015392\tCol_SD853_.1__NC_015392\n+Col(VCM04).1__HM231165\tCol_VCM04_.1__HM231165\n+Col(YC).1__NC_002144\tCol_YC_.1__NC_002144\n+Col(YF27601).1__JF937655\tCol_YF27601_.1__JF937655\n+Col(Ye4449).1__FJ696405\tCol_Ye4449_.1__FJ696405\n+Col(pWES).1__DQ268764\tCol_pWES_.1__DQ268764\n+FIA(pBK30683).1__KF954760\tFIA_pBK30683_.1__KF954760\n+FII(pBK30683).1__KF954760\tFII_pBK30683_.1__KF954760\n+IncA/C.1__FJ705807\tIncA_C.1__FJ705807\n+IncA/C2.1__JN157804\tIncA_C2.1__JN157804\n+IncB/O/K/Z.1__CU928147\tIncB_O_K_Z.1__CU928147\n+IncB/O/K/Z.2__GU256641\tIncB_O_K_Z.2__GU256641\n+IncB/O/K/Z.3__GQ259888\tIncB_O_K_Z.3__GQ259888\n+IncB/O/K/Z.4__FN868832\tIncB_O_K_Z.4__FN868832\n+IncFIA(HI1).1_HI1_AF250878\tIncFIA_HI1_.1_HI1_AF250878\n+IncFIB(AP001918).1__AP001918\tIncFIB_AP001918_.1__AP001918\n+IncFIB(K).1_Kpn3_JN233704\tIncFIB_K_.1_Kpn3_JN233704\n+IncFIB(Mar).1_pNDM-Mar_JN420336\tIncFIB_Mar_.1_pNDM_Mar_JN420336\n+IncFIB(S).1__FN432031\tIncFIB_S_.1__FN432031\n+IncFIB(pB171).1_pB171_AB024946\tIncFIB_pB171_.1_pB171_AB024946\n+IncFIB(pCTU1).1_pCTU1_FN543094\tIncFIB_pCTU1_.1_pCTU1_FN543094\n+IncFIB(pCTU3).1_pCTU3_FN543096\tIncFIB_pCTU3_.1_pCTU3_FN543096\n+IncFIB(pECLA).1_pECLA_CP001919\tIncFIB_pECLA_.1_pECLA_CP001919\n+IncFIB(pENTAS01).1_pENTAS01_CP003027\tIncFIB_pENTAS01_.1_pENTAS01_CP003027\n+IncFIB(pENTE01).1_pENTE01_CP000654\tIncFIB_pENTE01_.1_pENTE01_CP000654\n+IncFIB(pHCM2).1_pHCM2_AL513384\tIncFIB_pHCM2_.1_pHCM2_AL513384\n+IncFIB(pKPHS1).1_pKPHS1_CP003223\tIncFIB_pKPHS1_.1_pKPHS1_CP003223\n+IncFIB(pLF82).1_pLF82_CU638872\tIncFIB_pLF82_.1_pLF82_CU638872\n+IncFIB(pQil).1_pQil_JN233705\tIncFIB_pQil_.1_pQil_JN233705\n+IncFIC(FII).1__AP001918\tIncFIC_FII_.1__AP001918\n+IncFII(29).1_pUTI89_CP003035\tIncFII_29_.1_pUTI89_CP003035\n+IncFII(K).1__CP000648\tIncFII_K_.1__CP000648\n+IncFII(S).1__CP000858\tIncFII_S_.1__CP000858\n+IncFII(SARC14).1_SARC14_JQ418540\tIncFII_SARC14_.1_SARC14_JQ418540\n+IncFII(Serratia).1_Serratia_NC_009829\tIncFII_Serratia_.1_Serratia_NC_009829\n+IncFII(Y).1_ps_CP001049\tIncFII_Y_.1_ps_CP001049\n+IncFII(Yp).1_Yersenia_CP000670\tIncFII_Yp_.1_Yersenia_CP000670\n+IncFII(p14).1_p14_JQ418538\tIncFII_p14_.1_p14_JQ418538\n+IncFII(p96A).1_p96A_JQ418521\tIncFII_p96A_.1_p96A_JQ418521\n+IncFII(pAMA1167-NDM-5).1_pAMA1167-NDM-5_CP024805.1\tIncFII_pAMA1167_NDM_5_.1_pAMA1167_NDM_5_CP024805.1\n+IncFII(pCRY).1_pCRY_NC_005814\tIncFII_pCRY_.1_pCRY_NC_005814\n+IncFII(pCTU2).1_pCTU2_FN543095\tIncFII_pCTU2_.1_pCTU2_FN543095\n+IncFII(pCoo).1_pCoo_CR942285\tIncFII_pCoo_.1_pCoo_CR942285\n+IncFII(pECLA).1_pECLA_CP001919\tIncFII_pECLA_.1_pECLA_CP001919\n+IncFII(pENTA).1_pENTA_CP003027\tIncFII_pENTA_.1_pENTA_CP003027\n+IncFII(pHN7A8).1_pHN7A8_JN232517\tIncFII_pHN7A8_.1_pHN7A8_JN232517\n+IncFII(pKPX1)._AP012055\tIncFII_pKPX1_._AP012055\n+IncFII(pMET).1_pMET1_EU383016\tIncFII_pMET_.1_pMET1_EU383016\n+IncFII(pRSB107).1_pRSB107_AJ851089\tIncFII_pRSB107_.1_pRSB107_AJ851089\n+IncFII(pSE11).1_pSE11_AP009242\tIncFII_pSE11_.1_pSE11_AP009242\n+IncFII(pYVa12790).1_pYVa12790_AY150843\tIncFII_pYVa12790_.1_pYVa12790_AY150843\n+IncFII(pseudo).1_pseudo_NC_011759\tIncFII_pseudo_.1_pseudo_NC_011759\n+IncHI1A(CIT).1_pNDM-CIT_JX182975\tIncHI1A_CIT_.1_pNDM_CIT_JX182975\n+IncHI1B(CIT).1_pNDM-CIT_JX182975\tIncHI1B_CIT_.1_pNDM_CIT_JX182975\n+IncHI1B(R27).1_R27_AF250878\tIncHI1B_R27_.1_R27_AF250878\n+IncHI1B.1_pNDM-MAR_JN420336\tIncHI1B.1_pNDM_MAR_JN420336\n+IncL/M(pMU407).1_pMU407_U27345\tIncL_M_pMU407_.1_pMU407_U27345\n+IncL/M(pOXA-48).1_pOXA-48_JN626286\tIncL_M_pOXA_48_.1_pOXA_48_JN626286\n+IncL/M.1__AF550415\tIncL_M.1__AF550415\n+IncX3(pEC14).1_pEC14_JN935899\tIncX3_pEC14_.1_pEC14_JN935899\n+Rep.1_pKPC-2_CP011573\tRep.1_pKPC_2_CP011573\n+RepA.1_pKPC-CAV1321_CP011611\tRepA.1_pKPC_CAV1321_CP011611\n+pIP31758(p153).1_p153_CP000719\tpI'..b'GU237136.1\trep23.1_rep_pPR9__GU237136.1\n+rep23.2_rep(pV030-8)_EU366902.1\trep23.2_rep_pV030_8__EU366902.1\n+rep24.1_rep(pWBG745)_GQ900389.1\trep24.1_rep_pWBG745__GQ900389.1\n+rep24.2_rep(pWBG749)_GQ900391.1\trep24.2_rep_pWBG749__GQ900391.1\n+rep3.1_rep63A(pAW63)_BTH011655\trep3.1_rep63A_pAW63__BTH011655\n+rep3.2_rep165(pBMB165)_DQ242517\trep3.2_rep165_pBMB165__DQ242517\n+rep3.3_rep(pBT9727)_CP000047\trep3.3_rep_pBT9727__CP000047\n+rep3.4_CDS38(pOX2)_NC002146\trep3.4_CDS38_pOX2__NC002146\n+rep4.1_CDS2(pCRL291.1)_NC002799\trep4.1_CDS2_pCRL291.1__NC002799\n+rep4.2_CDS3(pKC5b)_AF378372\trep4.2_CDS3_pKC5b__AF378372\n+rep4.3_ORF(pMBB1)_EFU26268\trep4.3_ORF_pMBB1__EFU26268\n+rep5.1_rep(pMW2)_NC005011\trep5.1_rep_pMW2__NC005011\n+rep5.2_rep(pN315)_AP003139\trep5.2_rep_pN315__AP003139\n+rep5.3_rep(pWBG752)_GQ900394.1\trep5.3_rep_pWBG752__GQ900394.1\n+rep5.4_rep(SAP047A)_GQ900405.1\trep5.4_rep_SAP047A__GQ900405.1\n+rep5.5_rep(pRJ6)_AF241888.2\trep5.5_rep_pRJ6__AF241888.2\n+rep5.6_rep(pRJ9)_AF447813.1\trep5.6_rep_pRJ9__AF447813.1\n+rep5.7_rep(pJE1)_AF051916.1\trep5.7_rep_pJE1__AF051916.1\n+rep6.1_repA(p703/5)_AF109375\trep6.1_repA_p703_5__AF109375\n+rep7.10_repC(pKH17)_NC_010284.1\trep7.10_repC_pKH17__NC_010284.1\n+rep7.11_repD(pTZ4)_NC010111.1\trep7.11_repD_pTZ4__NC010111.1\n+rep7.12_rep(SAP060B)_GQ900417.1\trep7.12_rep_SAP060B__GQ900417.1\n+rep7.13_rep(pSBK203)_U35036.1\trep7.13_rep_pSBK203__U35036.1\n+rep7.14_rep(MSSA476)_BX571857.1\trep7.14_rep_MSSA476__BX571857.1\n+rep7.15_rep(pS0385-2)_AM990994.1\trep7.15_rep_pS0385_2__AM990994.1\n+rep7.17_repC(pS0385-1)_AM990993.1\trep7.17_repC_pS0385_1__AM990993.1\n+rep7.1_repC(Cassette)_AB037671\trep7.1_repC_Cassette__AB037671\n+rep7.3_CDS1(pCW7)_J03323\trep7.3_CDS1_pCW7__J03323\n+rep7.4_repD(pK214)_NC009751\trep7.4_repD_pK214__NC009751\n+rep7.5_CDS1(pKC5b)_AF378372\trep7.5_CDS1_pKC5b__AF378372\n+rep7.6_ORF(pKH1)_SAU38656\trep7.6_ORF_pKH1__SAU38656\n+rep7.7_rep(pKH7)_NC002096\trep7.7_rep_pKH7__NC002096\n+rep7.8_CDS4(pS194)_NC005564\trep7.8_CDS4_pS194__NC005564\n+rep7.9_CDS3(pUSA02)_NC007791\trep7.9_CDS3_pUSA02__NC007791\n+rep7b.1_repJ(pC223)_NC_005243.1\trep7b.1_repJ_pC223__NC_005243.1\n+rep8.1_EP002*(pAM373)_NC002630\trep8.1_EP002__pAM373__NC002630\n+rep8.2_repA(pEJ97-1)_AJ49170\trep8.2_repA_pEJ97_1__AJ49170\n+rep9.1_repA(pAD1)_L01794\trep9.1_repA_pAD1__L01794\n+rep9.2_prgW(pCF10)_AY855841\trep9.2_prgW_pCF10__AY855841\n+rep9.3_repA(pPD1)_D78016\trep9.3_repA_pPD1__D78016\n+rep9.4_repA2(pTEF2)_AE016831\trep9.4_repA2_pTEF2__AE016831\n+repA.1_pKPC-2_CP013325\trepA.1_pKPC_2_CP013325\n+repA.2_pKPC-2_JX397875\trepA.2_pKPC_2_JX397875\n+repUS1._ORF(E.faeciumContig1258)_JDOE\trepUS1._ORF_E.faeciumContig1258__JDOE\n+repUS10._CDS25(pSSP1)_AP008935\trepUS10._CDS25_pSSP1__AP008935\n+repUS11._CDS16(pTEF3)_AE016832\trepUS11._CDS16_pTEF3__AE016832\n+repUS12._rep(pUB110)_AF181950\trepUS12._rep_pUB110__AF181950\n+repUS13._CDS1(pUSA01)_NC007790\trepUS13._CDS1_pUSA01__NC007790\n+repUS14._repA(VRSAp)_AP003367\trepUS14._repA_VRSAp__AP003367\n+repUS15._ORF(E.faecium287)_NZAAAK010000287\trepUS15._ORF_E.faecium287__NZAAAK010000287\n+repUS16._repF(pE194)_M17811.1\trepUS16._repF_pE194__M17811.1\n+repUS17._rep(pKKS825)_FN377602.2\trepUS17._rep_pKKS825__FN377602.2\n+repUS18._rep(pKKS825)_FN377602.2\trepUS18._rep_pKKS825__FN377602.2\n+repUS19._rep(pDLK3)_GU562626.1\trepUS19._rep_pDLK3__GU562626.1\n+repUS2._repA(pBI143)_BFU30316\trepUS2._repA_pBI143__BFU30316\n+repUS20._rep(pAVX)_CP001784.1\trepUS20._rep_pAVX__CP001784.1\n+repUS21._rep(pWBG764)_GQ900468.1\trepUS21._rep_pWBG764__GQ900468.1\n+repUS22._rep(SAP015B)_GQ900502.1\trepUS22._rep_SAP015B__GQ900502.1\n+repUS23._repA(SAP099B)_GQ900449.1\trepUS23._repA_SAP099B__GQ900449.1\n+repUS3._repM200(pBM200)_DQ437521\trepUS3._repM200_pBM200__DQ437521\n+repUS4._repA(pCI2000)_AF178424\trepUS4._repA_pCI2000__AF178424\n+repUS5._CDS20(pETB)_NC003265\trepUS5._CDS20_pETB__NC003265\n+repUS6._rep(pFL1)_NC002132\trepUS6._rep_pFL1__NC002132\n+repUS7._rep(pHTbeta)_AB183714\trepUS7._rep_pHTbeta__AB183714\n+repUS8._ORF1(pOg32)_LOPPOG32\trepUS8._ORF1_pOg32__LOPPOG32\n+repUS9._rep(pSK1)_AF203376\trepUS9._rep_pSK1__AF203376\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/plasmidfinder.db/00.version_info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder.db/00.version_info.txt Tue Jan 08 10:26:30 2019 -0500 |
| [ |
| @@ -0,0 +1,28 @@ +ARIBA run with this command: +/Users/leviet/miniconda3/bin/ariba prepareref prepareref -f plasmidfinder.fa -m plasmidfinder.tsv plasmidfinder.db +from this directory: /Users/leviet/Documents/bioinformatics/quadram/galaxy-tools/ariba/database + +ARIBA version: 2.13.2 + +External dependencies: +bowtie2 2.3.4.3 /Users/leviet/miniconda3/bin/bowtie2 +cdhit 4.7 /Users/leviet/miniconda3/bin/cd-hit-est +nucmer 3.1 /Users/leviet/miniconda3/bin/nucmer + +External dependencies OK: True + +Python version: +3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:55:02) +[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] + +Python packages: +ariba 2.13.2 /Users/leviet/miniconda3/lib/python3.6/site-packages/ariba/__init__.py +bs4 4.6.3 /Users/leviet/miniconda3/lib/python3.6/site-packages/bs4/__init__.py +dendropy 4.4.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/dendropy/__init__.py +pyfastaq 3.17.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/pyfastaq/__init__.py +pymummer 0.10.3 /Users/leviet/miniconda3/lib/python3.6/site-packages/pymummer/__init__.py +pysam 0.15.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/pysam/__init__.py + +Python packages OK: True + +Everything looks OK: True |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/plasmidfinder.db/01.filter.check_metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder.db/01.filter.check_metadata.tsv Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,273 @@\n+Col156.1__NC_009781\t0\t0\t.\t.\tOriginal name was Col156_1__NC_009781\n+Col3M.1__JX514065\t0\t0\t.\t.\tOriginal name was Col3M_1__JX514065\n+Col440I.1__CP023920.1\t0\t0\t.\t.\tOriginal name was Col440I_1__CP023920.1\n+Col440II.1__CP023921.1\t0\t0\t.\t.\tOriginal name was Col440II_1__CP023921.1\n+Col8282.1__DQ995352\t0\t0\t.\t.\tOriginal name was Col8282_1__DQ995352\n+ColE10.1__X01654\t0\t0\t.\t.\tOriginal name was ColE10_1__X01654\n+ColKP3.1__JN205800\t0\t0\t.\t.\tOriginal name was ColKP3_1__JN205800\n+ColRNAI.1__DQ298019\t0\t0\t.\t.\tOriginal name was ColRNAI_1__DQ298019\n+Col_BS512_.1__NC_010656\t0\t0\t.\t.\tOriginal name was Col(BS512)_1__NC_010656\n+Col_IMGS31_.1__NC_011406\t0\t0\t.\t.\tOriginal name was Col(IMGS31)_1__NC_011406\n+Col_IRGK_.1__AY543071\t0\t0\t.\t.\tOriginal name was Col(IRGK)_1__AY543071\n+Col_KPHS6_.1__NC_016841\t0\t0\t.\t.\tOriginal name was Col(KPHS6)_1__NC_016841\n+Col_MG828_.1__NC_008486\t0\t0\t.\t.\tOriginal name was Col(MG828)_1__NC_008486\n+Col_MGD2_.1__NC_003789\t0\t0\t.\t.\tOriginal name was Col(MGD2)_1__NC_003789\n+Col_MP18_.1__NC_013652\t0\t0\t.\t.\tOriginal name was Col(MP18)_1__NC_013652\n+Col_SD853_.1__NC_015392\t0\t0\t.\t.\tOriginal name was Col(SD853)_1__NC_015392\n+Col_VCM04_.1__HM231165\t0\t0\t.\t.\tOriginal name was Col(VCM04)_1__HM231165\n+Col_YC_.1__NC_002144\t0\t0\t.\t.\tOriginal name was Col(YC)_1__NC_002144\n+Col_YF27601_.1__JF937655\t0\t0\t.\t.\tOriginal name was Col(YF27601)_1__JF937655\n+Col_Ye4449_.1__FJ696405\t0\t0\t.\t.\tOriginal name was Col(Ye4449)_1__FJ696405\n+Col_pWES_.1__DQ268764\t0\t0\t.\t.\tOriginal name was Col(pWES)_1__DQ268764\n+ColpVC.1__JX133088\t0\t0\t.\t.\tOriginal name was ColpVC_1__JX133088\n+FIA_pBK30683_.1__KF954760\t0\t0\t.\t.\tOriginal name was FIA(pBK30683)_1__KF954760\n+FII_pBK30683_.1__KF954760\t0\t0\t.\t.\tOriginal name was FII(pBK30683)_1__KF954760\n+IncA_C.1__FJ705807\t0\t0\t.\t.\tOriginal name was IncA/C_1__FJ705807\n+IncA_C2.1__JN157804\t0\t0\t.\t.\tOriginal name was IncA/C2_1__JN157804\n+IncB_O_K_Z.1__CU928147\t0\t0\t.\t.\tOriginal name was IncB/O/K/Z_1__CU928147\n+IncB_O_K_Z.2__GU256641\t0\t0\t.\t.\tOriginal name was IncB/O/K/Z_2__GU256641\n+IncB_O_K_Z.3__GQ259888\t0\t0\t.\t.\tOriginal name was IncB/O/K/Z_3__GQ259888\n+IncB_O_K_Z.4__FN868832\t0\t0\t.\t.\tOriginal name was IncB/O/K/Z_4__FN868832\n+IncFIA.1__AP001918\t0\t0\t.\t.\tOriginal name was IncFIA_1__AP001918\n+IncFIA_HI1_.1_HI1_AF250878\t0\t0\t.\t.\tOriginal name was IncFIA(HI1)_1_HI1_AF250878\n+IncFIB_AP001918_.1__AP001918\t0\t0\t.\t.\tOriginal name was IncFIB(AP001918)_1__AP001918\n+IncFIB_K_.1_Kpn3_JN233704\t0\t0\t.\t.\tOriginal name was IncFIB(K)_1_Kpn3_JN233704\n+IncFIB_Mar_.1_pNDM_Mar_JN420336\t0\t0\t.\t.\tOriginal name was IncFIB(Mar)_1_pNDM-Mar_JN420336\n+IncFIB_S_.1__FN432031\t0\t0\t.\t.\tOriginal name was IncFIB(S)_1__FN432031\n+IncFIB_pB171_.1_pB171_AB024946\t0\t0\t.\t.\tOriginal name was IncFIB(pB171)_1_pB171_AB024946\n+IncFIB_pCTU1_.1_pCTU1_FN543094\t0\t0\t.\t.\tOriginal name was IncFIB(pCTU1)_1_pCTU1_FN543094\n+IncFIB_pCTU3_.1_pCTU3_FN543096\t0\t0\t.\t.\tOriginal name was IncFIB(pCTU3)_1_pCTU3_FN543096\n+IncFIB_pECLA_.1_pECLA_CP001919\t0\t0\t.\t.\tOriginal name was IncFIB(pECLA)_1_pECLA_CP001919\n+IncFIB_pENTAS01_.1_pENTAS01_CP003027\t0\t0\t.\t.\tOriginal name was IncFIB(pENTAS01)_1_pENTAS01_CP003027\n+IncFIB_pENTE01_.1_pENTE01_CP000654\t0\t0\t.\t.\tOriginal name was IncFIB(pENTE01)_1_pENTE01_CP000654\n+IncFIB_pHCM2_.1_pHCM2_AL513384\t0\t0\t.\t.\tOriginal name was IncFIB(pHCM2)_1_pHCM2_AL513384\n+IncFIB_pKPHS1_.1_pKPHS1_CP003223\t0\t0\t.\t.\tOriginal name was IncFIB(pKPHS1)_1_pKPHS1_CP003223\n+IncFIB_pLF82_.1_pLF82_CU638872\t0\t0\t.\t.\tOriginal name was IncFIB(pLF82)_1_pLF82_CU638872\n+IncFIB_pQil_.1_pQil_JN233705\t0\t0\t.\t.\tOriginal name was IncFIB(pQil)_1_pQil_JN233705\n+IncFIC_FII_.1__AP001918\t0\t0\t.\t.\tOriginal name was IncFIC(FII)_1__AP001918\n+IncFII.1__AY458016\t0\t0\t.\t.\tOriginal name was IncFII_1__AY458016\n+IncFII.1_pKP91_CP000966\t0\t0\t.\t.\tOriginal name was IncFII_1_pKP91_CP000966\n+IncFII.1_pSFO_AF401292\t0\t0\t.\t.\tOriginal name was IncFII_1_pSFO_AF401292\n+IncFII_29_.1_pUTI89_CP003035\t0\t0\t.\t.\tOriginal name was IncFII(29)_1_pUTI89_CP003035\n+IncFII_K_.1__CP000648\t0\t0\t.\t.\tOriginal name was IncFII(K)_1__CP000648\n+IncFII_SARC14_'..b'13_rep(pSBK203)_U35036.1\n+rep7.14_rep_MSSA476__BX571857.1\t0\t0\t.\t.\tOriginal name was rep7_14_rep(MSSA476)_BX571857.1\n+rep7.15_rep_pS0385_2__AM990994.1\t0\t0\t.\t.\tOriginal name was rep7_15_rep(pS0385-2)_AM990994.1\n+rep7.16_repD_AY939911\t0\t0\t.\t.\tOriginal name was rep7_16_repD_AY939911\n+rep7.17_repC_pS0385_1__AM990993.1\t0\t0\t.\t.\tOriginal name was rep7_17_repC(pS0385-1)_AM990993.1\n+rep7.1_repC_Cassette__AB037671\t0\t0\t.\t.\tOriginal name was rep7_1_repC(Cassette)_AB037671\n+rep7.3_CDS1_pCW7__J03323\t0\t0\t.\t.\tOriginal name was rep7_3_CDS1(pCW7)_J03323\n+rep7.4_repD_pK214__NC009751\t0\t0\t.\t.\tOriginal name was rep7_4_repD(pK214)_NC009751\n+rep7.5_CDS1_pKC5b__AF378372\t0\t0\t.\t.\tOriginal name was rep7_5_CDS1(pKC5b)_AF378372\n+rep7.6_ORF_pKH1__SAU38656\t0\t0\t.\t.\tOriginal name was rep7_6_ORF(pKH1)_SAU38656\n+rep7.7_rep_pKH7__NC002096\t0\t0\t.\t.\tOriginal name was rep7_7_rep(pKH7)_NC002096\n+rep7.8_CDS4_pS194__NC005564\t0\t0\t.\t.\tOriginal name was rep7_8_CDS4(pS194)_NC005564\n+rep7.9_CDS3_pUSA02__NC007791\t0\t0\t.\t.\tOriginal name was rep7_9_CDS3(pUSA02)_NC007791\n+rep7b.1_repJ_pC223__NC_005243.1\t0\t0\t.\t.\tOriginal name was rep7b_1_repJ(pC223)_NC_005243.1\n+rep7b.2_pVGA_NC_011605.1\t0\t0\t.\t.\tOriginal name was rep7b_2_pVGA_NC_011605.1\n+rep7b.3_SAP089A_GQ900440.1\t0\t0\t.\t.\tOriginal name was rep7b_3_SAP089A_GQ900440.1\n+rep8.1_EP002__pAM373__NC002630\t0\t0\t.\t.\tOriginal name was rep8_1_EP002*(pAM373)_NC002630\n+rep8.2_repA_pEJ97_1__AJ49170\t0\t0\t.\t.\tOriginal name was rep8_2_repA(pEJ97-1)_AJ49170\n+rep9.1_repA_pAD1__L01794\t0\t0\t.\t.\tOriginal name was rep9_1_repA(pAD1)_L01794\n+rep9.2_prgW_pCF10__AY855841\t0\t0\t.\t.\tOriginal name was rep9_2_prgW(pCF10)_AY855841\n+rep9.3_repA_pPD1__D78016\t0\t0\t.\t.\tOriginal name was rep9_3_repA(pPD1)_D78016\n+rep9.4_repA2_pTEF2__AE016831\t0\t0\t.\t.\tOriginal name was rep9_4_repA2(pTEF2)_AE016831\n+repA.1_pKPC_2_CP013325\t0\t0\t.\t.\tOriginal name was repA_1_pKPC-2_CP013325\n+repA.2_pKPC_2_JX397875\t0\t0\t.\t.\tOriginal name was repA_2_pKPC-2_JX397875\n+repUS1._ORF_E.faeciumContig1258__JDOE\t0\t0\t.\t.\tOriginal name was repUS1__ORF(E.faeciumContig1258)_JDOE\n+repUS10._CDS25_pSSP1__AP008935\t0\t0\t.\t.\tOriginal name was repUS10__CDS25(pSSP1)_AP008935\n+repUS11._CDS16_pTEF3__AE016832\t0\t0\t.\t.\tOriginal name was repUS11__CDS16(pTEF3)_AE016832\n+repUS12._rep_pUB110__AF181950\t0\t0\t.\t.\tOriginal name was repUS12__rep(pUB110)_AF181950\n+repUS13._CDS1_pUSA01__NC007790\t0\t0\t.\t.\tOriginal name was repUS13__CDS1(pUSA01)_NC007790\n+repUS14._repA_VRSAp__AP003367\t0\t0\t.\t.\tOriginal name was repUS14__repA(VRSAp)_AP003367\n+repUS15._ORF_E.faecium287__NZAAAK010000287\t0\t0\t.\t.\tOriginal name was repUS15__ORF(E.faecium287)_NZAAAK010000287\n+repUS16._repF_pE194__M17811.1\t0\t0\t.\t.\tOriginal name was repUS16__repF(pE194)_M17811.1\n+repUS17._rep_pKKS825__FN377602.2\t0\t0\t.\t.\tOriginal name was repUS17__rep(pKKS825)_FN377602.2\n+repUS18._rep_pKKS825__FN377602.2\t0\t0\t.\t.\tOriginal name was repUS18__rep(pKKS825)_FN377602.2\n+repUS19._rep_pDLK3__GU562626.1\t0\t0\t.\t.\tOriginal name was repUS19__rep(pDLK3)_GU562626.1\n+repUS2._repA_pBI143__BFU30316\t0\t0\t.\t.\tOriginal name was repUS2__repA(pBI143)_BFU30316\n+repUS20._rep_pAVX__CP001784.1\t0\t0\t.\t.\tOriginal name was repUS20__rep(pAVX)_CP001784.1\n+repUS21._rep_pWBG764__GQ900468.1\t0\t0\t.\t.\tOriginal name was repUS21__rep(pWBG764)_GQ900468.1\n+repUS22._rep_SAP015B__GQ900502.1\t0\t0\t.\t.\tOriginal name was repUS22__rep(SAP015B)_GQ900502.1\n+repUS23._repA_SAP099B__GQ900449.1\t0\t0\t.\t.\tOriginal name was repUS23__repA(SAP099B)_GQ900449.1\n+repUS3._repM200_pBM200__DQ437521\t0\t0\t.\t.\tOriginal name was repUS3__repM200(pBM200)_DQ437521\n+repUS4._repA_pCI2000__AF178424\t0\t0\t.\t.\tOriginal name was repUS4__repA(pCI2000)_AF178424\n+repUS5._CDS20_pETB__NC003265\t0\t0\t.\t.\tOriginal name was repUS5__CDS20(pETB)_NC003265\n+repUS6._rep_pFL1__NC002132\t0\t0\t.\t.\tOriginal name was repUS6__rep(pFL1)_NC002132\n+repUS7._rep_pHTbeta__AB183714\t0\t0\t.\t.\tOriginal name was repUS7__rep(pHTbeta)_AB183714\n+repUS8._ORF1_pOg32__LOPPOG32\t0\t0\t.\t.\tOriginal name was repUS8__ORF1(pOg32)_LOPPOG32\n+repUS9._rep_pSK1__AF203376\t0\t0\t.\t.\tOriginal name was repUS9__rep(pSK1)_AF203376\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/plasmidfinder.db/02.cdhit.all.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder.db/02.cdhit.all.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,3682 @@\n+>Col156.1__NC_009781\n+TACGGGATGGGGCGAAACTGCCACCTGTTCGAAATGACGCGCAAATGGGCTTACAGGGCG\n+ATTCGTCAGGGCTGGCCTGAATTCTCACAGTGGCTTGATGCCGTGATTCAGCGTGTCGAA\n+ATGTACAACGCATCGCTTCCTGTTCCGCTTTCAC\n+>Col3M.1__JX514065\n+GATGTTAAAAACGCACTCAGAAGCTCGCAAAACCGTTCTAAACTTTCAGCGTAGATTTGG\n+GTGTTTTATAGGGTGATCGTGTCTTAAAATCGTTTTGAGGGGCTTTAATGGGGATGAACG\n+GGCGGTTTTTGCTAACTAACTCGCCCGTTTAACATAA\n+>Col440I.1__CP023920.1\n+ATGCACGAACCCCCCGTTCAGTCCGACTGCTGCGTCTTATCCGGTAACTATCATCTTGAG\n+TCCAACCCGGTAAGACATGCAAAAGCACCACTGGCAGCAGCCACCGGTAACTGA\n+>Col440II.1__CP023921.1\n+GTCGATTGCCATCAGTGCGGCCACAATCTGCACCCGGTCATGACCGGCACCACCGGCATT\n+CACTTTCCGGGCGATCTGGTTCAGGTTGTTCCCCATACCGGCAAGCTGGCGCAGCAGCGC\n+CGGCGATATCGACGGCAGTCTGCCGGCACGCGCCGGCTTCTCATCGAGGCAGGTCTGACG\n+CATCCACGCCGCCAGCTGCTTGCCGTCGCACCGCTCGAGCAGCCGCCGGTGTTCGTCTTC\n+CGTCACCCACATCGTGAGCATCTTGTTGCGTTTGTCTGCCAG\n+>Col8282.1__DQ995352\n+CTGAATTGCAAAAGACCATGACTGTTACCGCCGAAGAGTATTTCGACTCATTCCCTGATA\n+TGGGGCGGAAAAATGCCGAGGTTCAGCTACAGGAAGCAATTGATCGTTTGTGGGACAGGT\n+CGATCATCCTTAAGGACGATGAGAAGCGCGAGGAGTTCCGCTGGATCCAGTATCGGGCAC\n+AGTACGCTAAAGGTGAGGGCAAAGCCC\n+>ColE10.1__X01654\n+GGACTAAGAAAAACACTACACGATGCTTTAACTGCAAAAATTCAGCTCACCAGTTTTGAG\n+GCAAAATTTTTGAGTGACATGCAAAGTAAGTATGATCTCAATGGTTCGTTCTCATGGCTC\n+ACGCAAAAACAACGAACCACACTAGAGAACATACTGGCTAAATACGGAAGGATCTGA\n+>ColKP3.1__JN205800\n+CGCAAACGAAGTCCGGCACACGGCCAAGTCCATTGCCAAATGGACGCACCAGCACCTAAG\n+CCCCGCAGGGTTCAGAGAGGAGCAGGCCCGGAGAGGTGCGAAGGGCGGCAAGGTATCCAA\n+GGGAGGGGGAAGGCCGAGCAATAGCGGTAAGGACAAGTCCGATCTATTGCCGGAGGTTCT\n+GCGGCTTAAGGCTCAGGGGTACACCAACCGCGATATAGCGGACGATCTTCAAATCTCCCC\n+CAGTACGGTGAGCGTTTACCTAAAGCGTGATCGTCCGTGA\n+>ColRNAI.1__DQ298019\n+CTCGGCTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTAAGCAAGAACCCCCCGTTCAG\n+CCCGACTGCTGCGCCTTATCCGGTAACTGTTCACTTGAGTCCAACCCGGAAAAGCACGCA\n+AAACGCCACT\n+>Col_BS512_.1__NC_010656\n+ATGAATGCGGCGTTTAAGCGAATGGAAAAGCGAAAGGAGCTATCACCTGTTCAGGGGTGG\n+ATCAGGGCTACGGAGGTGACGCGAGGTAAGGATGGCAGCGCACATCCGCATTTTCACTGT\n+CTGCTGATGGTGCAACCTTCTTGGTTTAAAGGGAAGAACTACGTTAAGCACGAACGTTGG\n+GTAGAACTCTGGCGCGATTGCTTGCGGGTGAACTATGAGCCGAATATCGATAT\n+>Col_IMGS31_.1__NC_011406\n+TTATAATTTTAAAGCCTTTGGCTTATTCTGGGGTGTGTAGTTATTATTTTGCTGTTTCTG\n+TGAATATTCGGCATCTGCTGCTGCAATAGCAGCATTGAAGAGTTGTTTAAATTCTGCCGG\n+TTTATGCTCTTGTATTAGATCTAAAACATCACTGTTAATTTTATATTTTTCATATCTCTG\n+AGAAATTGAAGCATTTTC\n+>Col_IRGK_.1__AY543071\n+CGGTTTTACAGCAAAATCCTCCATAGCGAAGCAGAAGCCCGGAACGGGTAACTGGATGGT\n+TTTCCCCCGTGGGGGATTGATCTGTTACTTGAAAACCAATGATCTTAAAAGCCATCTCAA\n+AAGTTGAAAATTTCACCCCCTTAGTGTTCTTAAAATTCTTAGATGTTCTTAGGAGTTAAA\n+AAAC\n+>Col_KPHS6_.1__NC_016841\n+ATGCAAACTCAAAATGTTGTGACGGACAAAGAACGGGAAATCAGAAAAAGAGATCTTGAA\n+GATAAAGACCGTAAAAACGCCTCAGAGCGTCGACAGGAGCAAAAAAACCAAAACTTCACC\n+CAAGTATACCCTTTAGGCTGGAAGCGTCTCAGAGAGCTTTTCAGGAAGAATCCGGGGG\n+>Col_MG828_.1__NC_008486\n+ACCTCTCGCATGTTGTCGGTGATCCCGTTGTTGTTCTTTCAGGGATGAGTCGTCAGATAG\n+CCCTTCAAACGCGCTCAGAAGCTCTCAGACGCACTAAACGGGTCTTAAATGCCCGTCAGG\n+GCATGGGAGGCGCGAAAAACGCTTACAGAGCGTTTCAGGAGGTCAGGCGCGCCGATACCC\n+CTAACCAGGGGCTTTCAGGTCGCCAGGAACAGCGTCAGCCCCCTGCAAAGCCTATTTGCA\n+CGGCACAGGCAGCTATTCGGTT\n+>Col_MGD2_.1__NC_003789\n+TATGGCTTAGGCCGCAACTGCACTCTGTTCGATAAAACACGGAAGTGGGCTTATCGCGCT\n+ATCCGTCAGGGCTGGCCTGAATATGACCAGTGGCTGCAAGCTTTGCAATTTTCATCGGCT\n+CTGGATGATAATGAGG\n+>Col_MP18_.1__NC_013652\n+CCGTCATCTGTACCCTCTGCCATGCCATCCGCCATGATTAAATCCTCGTTCGTTTCCCGC\n+TCCAGTTGCAGAACGTTCTTAAGCGCTCCCCCCGTAGCAACAAAACGACGCTTGTGTACC\n+TGCCGTGTTAATTCGAGGAACCATTCAGGATCAGCCAGCATATCAGCAGGCTTTGTGGAA\n+TATTTCAGAGTTT\n+>Col_SD853_.1__NC_015392\n+TTGATTTATTCATCTGAAAACGATTATAGCATCCTCGAAGACAAAACCGCAACAGGTAAA\n+AAGCGGGATTGGAAGGGGAAAAAGAGACGTACGAACCTCATGGCGGAGCATTACGAAGCG\n+TTAGAGAGTAAGATTGGGGCACCTTACTATGGCAAAAAGGCTGAAAAGCTAATTGGTTGT\n+GCAGAGTATCTTTC\n+>Col_VCM04_.1__HM231165\n+CGTGTGGGTACTCCTGTTCGACGTTGACCAGCCCCTAGCGGCGCTGGCGTGGGAAGCAGC\n+CGGACTTCCGCCGCCAACGTGGACGGCACAAAACCCTGAGAACGGGCACGCCCACATTGC\n+CTACGCGCTGAGCGCTCCGGTAGCGAAGTCGGACGCGGCGAAGCTCAAGCCCCTGCG\n+>Col_YC_.1__NC_002144\n+CTAAACTTTCAATTTTATTTGCTTATCTTCTTTAAACGTAAAGCGAAGGGCAACAACTTT\n+TCTTCCATTCTTTATGGATTCAACAAAGACAGTGAGATCACTTTTTTCATTTAGTTCTTT\n+TAAAGCTGGTTTTATGACAGCCCTGTTCAAAAT\n+>Col_YF27601'..b'attcacgaaaatttatttggct\n+caattttcttctttttggaatttaaaaacacaagcaataagggtttttggttatattatg\n+acgaaattaataccaaggcaagatacttttatgttttttctagatgaatgtatggaatac\n+acaggctataaaggcaaaaacagtatttatattggtcttactagtttagtagaaaacaat\n+ataattgcgaggggtagaaatgatagccattattttataaatccaatggtagcgtttaat\n+ggggatagagtaacgtttgcaaaacttatataa\n+>repUS7._rep_pHTbeta__AB183714\n+atgttgaatagttgcgagtatgcggacgttttagctaaaattcttaaaaatggaattaaa\n+cagtttaatagcaaaaatctagttgcttttaaaaagaatagcaataagattggtgctatt\n+gccggatttacttctaaaacaaacatgataaagactaaaggtcttatatatcgttctatt\n+gatcgtgtcttggaagattcagatgtattaacacactggactcctaacgtgtattcatgg\n+cttggtggcggtgaaaacaaaacaatttttggtcacaaagaagctaacttaattcagatt\n+aatacttttgtagcagatattgactatccagtaggagaaaagaaaacggatttgaattta\n+ctagttctttatctattggaagaagggttattgcctacactgattgtagatacgccaaaa\n+ggttatcattgctattttctgattcaaaactataaccaagaaactgattcatttgataag\n+gcaagctatatttctaattcaaatgattttaaatctttgagagttgctaaaagaatatca\n+gaaaatatcagaaaatctatccaaaatcgtttaccacaagtcgatatgggctgtaatcat\n+tttggtatttttagatttccaactaaaaaaaatattgtacattatgaacctaatttcgta\n+gatacgtttgaagggtatttgaaatggtcaaaagactttgaagaaaaagaatatgcttta\n+aagaggtctaacttgtcattattagctcctaattctactggcaagaaagggtctaaacga\n+caaattgatactaaatggtacgactttttaattcatacggatattgctgaaggagataga\n+aataaaactatttttaccttagccctggcatgtaaatcaagtggcttatctattggcgag\n+tgtatggatcaattggatcaacttcaattcaataatgatttgtcctattctgaagttgag\n+agaacaataagaagtgcttatcgtggcgattacaaaggtgctaaaagttcatatgtcaat\n+gaaattatcgaaaattatgctacacctaccgagtttgaaaaatactcaataaatgtaaat\n+agacaagctgttaaacgtaaagggaatcgtgtcgatccgtctaattgggtgaaatttgct\n+aaacctagagaagaacgaaaatatagtcattttgaagaaagtaaagctgatttattagct\n+tacttagaaagaaaacaaagatcattgaaaaaaaatgagttgtttttaagtgtctctatg\n+ggaactatatctgaagaaacacaaattcctgtatctacgttaaaggtgattttaaaagag\n+cttagaacggcgaatacagtgatattacaaacgtctcgtggtcggtatggatcgactaaa\n+atagcaacaagcaaatttgtggaagctaaaatattaagtacagttattcagaataaaaaa\n+gataaacaagtatttgtcttagaattgttaggaacagcaaatagtcacgtagaaacgatt\n+ttaagacgttatgaagacaaaacagtaccgttccatgcgaacatactgaaagaaagagaa\n+aagagcaaacatgcgccaattagaggagctaatacaggttag\n+>repUS8._ORF1_pOg32__LOPPOG32\n+atgaccaaaacatctattgaaaagccggccccttctaacagccggctaagtgtaaaaaat\n+gtttacacttcatctataaagtggagcattgaccgtctaacgattgttggagaacttgct\n+ccattcttacctgcggggtatacaactaacaaaatatctggcgaagttaaaagcagaatt\n+actattgaagatatgttcaaagtttttgaacattttggtcattgtcgtttgtccggaaat\n+ggttatcaaatgataaccgatgatggagagaacgttgcttattttgaacgattaaagttt\n+gacaaaaataaagggcgcttagattttaacccgaacaagttagatagtttttttgaaaat\n+ggcttgaagcaatttatatctgatttattcatcacgccccatttttcaagggctgacatt\n+gctgccgatatttttgatgtccccgatgaaaaagttgtgtcttaccgattaggtgaacca\n+gttggaaatacatttttttatggaaaaagtggagatttacagaccgcgtattttggtgcc\n+aggtcatcagagaaacaaataaggctctataacaaaagaattgaaagaatcaaaaaaggc\n+agaattgaagaccttaaagaccccgaacaatgctactggcggttagaactacaactaaga\n+cgcgggagggctgatgattttcaaaagcaggtcgacgagagtttgaaacatttttattct\n+ccgcaagattttcctgatgatgtgtctgtgaacagcagaatatttttgaaagggctactt\n+gcagaccctgataactgggctagaatatcaagaccaacgaagtcaaaatatagacagata\n+gaggaacgagttgcctcttctgacaaattaacaattgaattgaaaaaaactttttctcaa\n+caaaataaaaaaatagaaaaagaattgaagaattggctacagacttttcaagttttgtag\n+>repUS9._rep_pSK1__AF203376\n+Atgtctaaatttaaaaaaatatctgcaagtgaattcgaaacattacgtttttatcaatta\n+cccaaatttttatttgaagatgaatacttttctaaaatgcccacagatgcaaaagttatg\n+tatgctttattaaaagatcgctttgaactatcaagattaaataactgggtagattcagaa\n+aataatatttatcttttatataccaataaacagttatgctcaattttaaattatgcagaa\n+ccaaaaatcattaaattaaaaaaagaattagaaaaatacaatttgattataaacgaaaga\n+caaggtttaaataaacctaacaaaatttatttactcgaacccacatatgacaaggaacta\n+ataaattctaagttccagaacaaagaatttattagttccagaactaataaatcatcagtt\n+caagaactaataaattctaagtcaagtgatactgattttaataatactgaatatatagag\n+actaagaataatgatacgaattatacgaatgatacatctaacatgatttctaagaattct\n+cattcgaatcatacaaatcatcaacaaaccgaatttaataatgatgccttaaaattccag\n+gcgcttgaagaattaccttcgcaaatcaaatcttatgtaagtaattttgaaattaaagac\n+atccgtattattaaaagtatcttactcaaggggaaaaagtcatttaataatacacatgat\n+acatattaccgtttagaagacgtcgaatttgaacttgtaagtgttttaaaacgttttaaa\n+gccatgttgctacaaaaaaatgaaaccgttgaaactatgcaaggctatttaatgcaatca\n+attaaagctgaacttgaagaaatacatgcattaaatatgcgtcgtcaaaacatacctcaa\n+tacaatatctttaatcaataa\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/plasmidfinder.db/02.cdhit.clusters.pickle |
| b |
| Binary file tool-data/plasmidfinder.db/02.cdhit.clusters.pickle has changed |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/plasmidfinder.db/02.cdhit.clusters.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder.db/02.cdhit.clusters.tsv Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,187 @@\n+Col156\tCol156.1__NC_009781\n+Col3M\tCol3M.1__JX514065\n+Col440I\tCol440I.1__CP023920.1\n+Col440II\tCol440II.1__CP023921.1\n+Col8282\tCol8282.1__DQ995352\n+ColE10\tColE10.1__X01654\n+ColKP3\tColKP3.1__JN205800\n+ColRNAI\tColRNAI.1__DQ298019\n+Col_BS512_\tCol_BS512_.1__NC_010656\n+Col_IMGS31_\tCol_IMGS31_.1__NC_011406\n+Col_IRGK_\tCol_IRGK_.1__AY543071\n+Col_KPHS6_\tCol_KPHS6_.1__NC_016841\n+Col_MG828_\tCol_MG828_.1__NC_008486\n+Col_MGD2_\tCol_MGD2_.1__NC_003789\n+Col_MP18_\tCol_MP18_.1__NC_013652\n+Col_SD853_\tCol_SD853_.1__NC_015392\n+Col_VCM04_\tCol_VCM04_.1__HM231165\n+Col_YC_\tCol_YC_.1__NC_002144\n+Col_YF27601_\tCol_YF27601_.1__JF937655\n+Col_Ye4449_\tCol_Ye4449_.1__FJ696405\n+Col_pWES_\tCol_pWES_.1__DQ268764\n+ColpVC\tColpVC.1__JX133088\n+FIA_pBK30683_+\tFIA_pBK30683_.1__KF954760\tIncFIA_HI1_.1_HI1_AF250878\n+FII_pBK30683_\tFII_pBK30683_.1__KF954760\n+IncA_C-\tIncA_C.1__FJ705807\tIncA_C2.1__JN157804\n+IncB_O_K_Z\tIncB_O_K_Z.1__CU928147\tIncB_O_K_Z.2__GU256641\tIncB_O_K_Z.3__GQ259888\tIncB_O_K_Z.4__FN868832\n+IncFI-\tIncFIC_FII_.1__AP001918\tIncFII.1__AY458016\tIncFII.1_pSFO_AF401292\tIncFII_29_.1_pUTI89_CP003035\tIncFII_pCoo_.1_pCoo_CR942285\tIncFII_pSE11_.1_pSE11_AP009242\n+IncFIA\tIncFIA.1__AP001918\n+IncFIB_-\tIncFIB_S_.1__FN432031\tIncFIB_pB171_.1_pB171_AB024946\n+IncFIB_AP001918_\tIncFIB_AP001918_.1__AP001918\n+IncFIB_K_\tIncFIB_K_.1_Kpn3_JN233704\n+IncFIB_Mar_\tIncFIB_Mar_.1_pNDM_Mar_JN420336\n+IncFIB_pCTU1_\tIncFIB_pCTU1_.1_pCTU1_FN543094\n+IncFIB_pCTU3_\tIncFIB_pCTU3_.1_pCTU3_FN543096\n+IncFIB_pECLA_\tIncFIB_pECLA_.1_pECLA_CP001919\n+IncFIB_pENTAS01_\tIncFIB_pENTAS01_.1_pENTAS01_CP003027\n+IncFIB_pENTE01_\tIncFIB_pENTE01_.1_pENTE01_CP000654\n+IncFIB_pHCM2_\tIncFIB_pHCM2_.1_pHCM2_AL513384\n+IncFIB_pKPHS1_\tIncFIB_pKPHS1_.1_pKPHS1_CP003223\n+IncFIB_pLF82_\tIncFIB_pLF82_.1_pLF82_CU638872\n+IncFIB_pQil_\tIncFIB_pQil_.1_pQil_JN233705\n+IncFII\tIncFII.1_pKP91_CP000966\n+IncFII_-\tIncFII_Yp_.1_Yersenia_CP000670\tIncFII_p14_.1_p14_JQ418538\n+IncFII_K_\tIncFII_K_.1__CP000648\n+IncFII_SARC14_\tIncFII_SARC14_.1_SARC14_JQ418540\n+IncFII_S_\tIncFII_S_.1__CP000858\n+IncFII_Serratia_\tIncFII_Serratia_.1_Serratia_NC_009829\n+IncFII_Y_\tIncFII_Y_.1_ps_CP001049\n+IncFII_p-\tIncFII_pAMA1167_NDM_5_.1_pAMA1167_NDM_5_CP024805.1\tIncFII_pHN7A8_.1_pHN7A8_JN232517\tIncFII_pRSB107_.1_pRSB107_AJ851089\n+IncFII_p96A_\tIncFII_p96A_.1_p96A_JQ418521\n+IncFII_pCRY_\tIncFII_pCRY_.1_pCRY_NC_005814\n+IncFII_pCTU2_\tIncFII_pCTU2_.1_pCTU2_FN543095\n+IncFII_pECLA_\tIncFII_pECLA_.1_pECLA_CP001919\n+IncFII_pENTA_\tIncFII_pENTA_.1_pENTA_CP003027\n+IncFII_pKPX1_\tIncFII_pKPX1_._AP012055\n+IncFII_pMET_\tIncFII_pMET_.1_pMET1_EU383016\n+IncFII_pYVa12790_\tIncFII_pYVa12790_.1_pYVa12790_AY150843\n+IncFII_pseudo_\tIncFII_pseudo_.1_pseudo_NC_011759\n+IncHI1A\tIncHI1A.1__AF250878\n+IncHI1A_CIT_\tIncHI1A_CIT_.1_pNDM_CIT_JX182975\n+IncHI1B\tIncHI1B.1_pNDM_MAR_JN420336\n+IncHI1B_-\tIncHI1B_CIT_.1_pNDM_CIT_JX182975\tIncHI1B_R27_.1_R27_AF250878\n+IncHI2\tIncHI2.1__BX664015\n+IncHI2A\tIncHI2A.1__BX664015\n+IncI-\tIncI.Gamma_1_AP011954\tIncI1.1_Alpha_AP005147\n+IncI2\tIncI2.1_Delta_AP002527\tIncI2.1__KP347127\n+IncL_M-\tIncL_M.1__AF550415\tIncL_M_pOXA_48_.1_pOXA_48_JN626286\n+IncL_M_pMU407_\tIncL_M_pMU407_.1_pMU407_U27345\n+IncN\tIncN.1__AY046276\n+IncN-\tIncN2.1__JF785549\tIncN3.1__EF219134\n+IncP1\tIncP1.2__U67194\n+IncP1_1\tIncP1.1__BN000925\n+IncP1_2\tIncP1.3__KX377410\n+IncP6\tIncP6.1__JF785550\n+IncQ1\tIncQ1.1__M28829.1\n+IncQ2\tIncQ2.1__FJ696404\n+IncR\tIncR.1__DQ449578\n+IncT\tIncT.1__AP004237\n+IncU\tIncU.1__DQ401103\n+IncW\tIncW.1__EF633507\n+IncX1\tIncX1.1__EU370913\tIncX1.3__CP001123\tIncX1.4__JN935898\n+IncX1_1\tIncX1.2__CP003417\n+IncX2\tIncX2.1__JQ269335\n+IncX3\tIncX3.1__JN247852\n+IncX3_pEC14_\tIncX3_pEC14_.1_pEC14_JN935899\n+IncX4\tIncX4.1__CP002895\n+IncX4_1\tIncX4.2__FN543504\n+IncX5\tIncX5.2__MF062700.1\n+IncX5_1\tIncX5.1__JX193302\n+IncX6\tIncX6.1__KU302800\n+IncX7\tIncX7.1__NC_015054\n+IncX8\tIncX8.1__AM942760\n+IncX9\tIncX9.1__NC_010257\n+IncY\tIncY.1__K02380\n+Rep\tRep.1_pKPC_2_CP011573\n+RepA\tRepA.1_pKPC_CAV1321_CP011611\n+p0111\tp0111.1__AP010962\n+pADAP\tpADAP.1__AF135182\n+pEC4115\tpEC4115.1__NC_011351\n+pENTAS02\tpENTAS02.1__CP003028\n'..b'_NC001994\trep10b.2_rep_pSK6__SAU96610\n+rep11\trep11.2_repA_pEF1071__AF164559\n+rep11_1\trep11.3_rep_pEFR__AF511037\n+rep11_2\trep11.1_repA_pB82__AB178871\n+rep12\trep12.1_CDS32_pBMB67__DQ363750\trep12.2_CDS1_plasmid__AY278324\n+rep13\trep13.3_rep_pWBG1773__EF537646\n+rep13_1\trep13.4_rep_pKH13__NC010426.1\n+rep13_2\trep13.1_ORF_pC194__NC002013\trep13.2_CDS39_pSSP1__AP008935\trep13.5_rep_pMC524_MBM__AJ312056.2\n+rep14\trep14.2_ORF_pKQ10__EFU01917\n+rep14_1\trep14.3_ORF_pRI1__EU327398\n+rep14_2\trep14.1_CDS2_pEFNP1__AB038522\n+rep15\trep15.1_repA_pLW043__AE017171\n+rep16\trep16.1_CDS8_pSAS__BX571858\trep16.2_CDS6_pSJH101__CP000737\trep16.3_rep_Saa6159__CP002115.1\trep16.4_unknown_SAP056A__GQ900478.1\trep16.5_unknown_pWBG759__GQ900401.1\trep16.6_unknown_SAP071A__GQ900485.1\trep16.7_rep_pBORa53__AY917098.1\n+rep17\trep17.1_CDS29_pRUM__AF507977\n+rep18\trep18.2_repA_pEF418__AF408195\n+rep18_1\trep18.1_repA_p200B__AB158402\n+rep19\trep19.4_repA_pUB101__NC005127\n+rep19_1\trep19.1_CDS45_pLEW6932__NC009130\n+rep2\trep2.1_ORF_E.faeciumContig1183__JDOE\trep2.2_repR_pEF1__DQ198088\n+rep20\trep20.10_repA_SAP057A__NC_013334.1\trep20.3_rep_pTW20__FN433597.1\trep20.4_repA_SAP102A__GQ900496.1\trep20.5_repA_pSK23__GQ900491.1\trep20.6_repA_SAP059A__GQ900480.1\trep20.7_repA_SAP074A__GQ900426.1\trep20.8_repA_SAP063A__GQ900418.1\trep20.9_repA_SAP055A__GQ900414.1\n+rep20_1\trep20.1_ORF1_EDINA__AP003089\n+rep21\trep21.14_rep_pKH21__EU350088.1\trep21.2_rep_pNVH01__AJ512814.1\trep21.3_pS0385_3_AM990995.1\trep21.4_repRC_pSK41__AF051917.1\trep21.5_repRC_pGO1__FM207042.1\trep21.6_rep_pBMSa1__AY541446.1\n+rep21_1\trep21.1_rep_pWBG754__GQ900396.1\n+rep22\trep22.1_repB_pUB110__X03408.1\trep22.2_repU_pKKS825__FN377602.2\n+rep23\trep23.1_rep_pPR9__GU237136.1\trep23.2_rep_pV030_8__EU366902.1\n+rep24\trep24.1_rep_pWBG745__GQ900389.1\n+rep24_1\trep24.2_rep_pWBG749__GQ900391.1\n+rep3\trep3.2_rep165_pBMB165__DQ242517\trep3.3_rep_pBT9727__CP000047\n+rep3_1\trep3.1_rep63A_pAW63__BTH011655\trep3.4_CDS38_pOX2__NC002146\n+rep4\trep4.3_ORF_pMBB1__EFU26268\n+rep4_1\trep4.1_CDS2_pCRL291.1__NC002799\trep4.2_CDS3_pKC5b__AF378372\n+rep5\trep5.7_rep_pJE1__AF051916.1\n+rep5_1\trep5.5_rep_pRJ6__AF241888.2\n+rep5_2\trep5.1_rep_pMW2__NC005011\trep5.3_rep_pWBG752__GQ900394.1\trep5.4_rep_SAP047A__GQ900405.1\n+rep5_3\trep5.6_rep_pRJ9__AF447813.1\n+rep6\trep6.1_repA_p703_5__AF109375\n+rep7\trep7.10_repC_pKH17__NC_010284.1\trep7.12_rep_SAP060B__GQ900417.1\trep7.17_repC_pS0385_1__AM990993.1\trep7.1_repC_Cassette__AB037671\trep7.5_CDS1_pKC5b__AF378372\trep7.6_ORF_pKH1__SAU38656\trep7.9_CDS3_pUSA02__NC007791\n+rep7_1\trep7.13_rep_pSBK203__U35036.1\trep7.3_CDS1_pCW7__J03323\n+rep7_2\trep7.15_rep_pS0385_2__AM990994.1\trep7.8_CDS4_pS194__NC005564\n+rep7_3\trep7.11_repD_pTZ4__NC010111.1\n+rep7_4\trep7.7_rep_pKH7__NC002096\n+rep7_5\trep7.16_repD_AY939911\trep7.4_repD_pK214__NC009751\n+rep7_6\trep7.14_rep_MSSA476__BX571857.1\n+rep7b\trep7b.1_repJ_pC223__NC_005243.1\trep7b.3_SAP089A_GQ900440.1\n+rep7b_1\trep7b.2_pVGA_NC_011605.1\n+rep8\trep8.1_EP002__pAM373__NC002630\n+rep8_1\trep8.2_repA_pEJ97_1__AJ49170\n+rep9\trep9.1_repA_pAD1__L01794\n+rep9_1\trep9.4_repA2_pTEF2__AE016831\n+rep9_2\trep9.2_prgW_pCF10__AY855841\trep9.3_repA_pPD1__D78016\n+repA\trepA.1_pKPC_2_CP013325\n+repA_1\trepA.2_pKPC_2_JX397875\n+repUS1\trepUS1._ORF_E.faeciumContig1258__JDOE\n+repUS10\trepUS10._CDS25_pSSP1__AP008935\n+repUS11\trepUS11._CDS16_pTEF3__AE016832\n+repUS12\trepUS12._rep_pUB110__AF181950\n+repUS15\trepUS15._ORF_E.faecium287__NZAAAK010000287\n+repUS16\trepUS16._repF_pE194__M17811.1\n+repUS17\trepUS17._rep_pKKS825__FN377602.2\n+repUS18\trepUS18._rep_pKKS825__FN377602.2\n+repUS19\trepUS19._rep_pDLK3__GU562626.1\n+repUS2\trepUS2._repA_pBI143__BFU30316\n+repUS20\trepUS20._rep_pAVX__CP001784.1\n+repUS21\trepUS21._rep_pWBG764__GQ900468.1\n+repUS22\trepUS22._rep_SAP015B__GQ900502.1\n+repUS23\trepUS23._repA_SAP099B__GQ900449.1\n+repUS3\trepUS3._repM200_pBM200__DQ437521\n+repUS4\trepUS4._repA_pCI2000__AF178424\n+repUS5\trepUS5._CDS20_pETB__NC003265\n+repUS6\trepUS6._rep_pFL1__NC002132\n+repUS7\trepUS7._rep_pHTbeta__AB183714\n+repUS8\trepUS8._ORF1_pOg32__LOPPOG32\n+repUS9\trepUS9._rep_pSK1__AF203376\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/plasmidfinder.db/02.cdhit.noncoding.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder.db/02.cdhit.noncoding.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,3682 @@\n+>Col156.1__NC_009781\n+TACGGGATGGGGCGAAACTGCCACCTGTTCGAAATGACGCGCAAATGGGCTTACAGGGCG\n+ATTCGTCAGGGCTGGCCTGAATTCTCACAGTGGCTTGATGCCGTGATTCAGCGTGTCGAA\n+ATGTACAACGCATCGCTTCCTGTTCCGCTTTCAC\n+>Col3M.1__JX514065\n+GATGTTAAAAACGCACTCAGAAGCTCGCAAAACCGTTCTAAACTTTCAGCGTAGATTTGG\n+GTGTTTTATAGGGTGATCGTGTCTTAAAATCGTTTTGAGGGGCTTTAATGGGGATGAACG\n+GGCGGTTTTTGCTAACTAACTCGCCCGTTTAACATAA\n+>Col440I.1__CP023920.1\n+ATGCACGAACCCCCCGTTCAGTCCGACTGCTGCGTCTTATCCGGTAACTATCATCTTGAG\n+TCCAACCCGGTAAGACATGCAAAAGCACCACTGGCAGCAGCCACCGGTAACTGA\n+>Col440II.1__CP023921.1\n+GTCGATTGCCATCAGTGCGGCCACAATCTGCACCCGGTCATGACCGGCACCACCGGCATT\n+CACTTTCCGGGCGATCTGGTTCAGGTTGTTCCCCATACCGGCAAGCTGGCGCAGCAGCGC\n+CGGCGATATCGACGGCAGTCTGCCGGCACGCGCCGGCTTCTCATCGAGGCAGGTCTGACG\n+CATCCACGCCGCCAGCTGCTTGCCGTCGCACCGCTCGAGCAGCCGCCGGTGTTCGTCTTC\n+CGTCACCCACATCGTGAGCATCTTGTTGCGTTTGTCTGCCAG\n+>Col8282.1__DQ995352\n+CTGAATTGCAAAAGACCATGACTGTTACCGCCGAAGAGTATTTCGACTCATTCCCTGATA\n+TGGGGCGGAAAAATGCCGAGGTTCAGCTACAGGAAGCAATTGATCGTTTGTGGGACAGGT\n+CGATCATCCTTAAGGACGATGAGAAGCGCGAGGAGTTCCGCTGGATCCAGTATCGGGCAC\n+AGTACGCTAAAGGTGAGGGCAAAGCCC\n+>ColE10.1__X01654\n+GGACTAAGAAAAACACTACACGATGCTTTAACTGCAAAAATTCAGCTCACCAGTTTTGAG\n+GCAAAATTTTTGAGTGACATGCAAAGTAAGTATGATCTCAATGGTTCGTTCTCATGGCTC\n+ACGCAAAAACAACGAACCACACTAGAGAACATACTGGCTAAATACGGAAGGATCTGA\n+>ColKP3.1__JN205800\n+CGCAAACGAAGTCCGGCACACGGCCAAGTCCATTGCCAAATGGACGCACCAGCACCTAAG\n+CCCCGCAGGGTTCAGAGAGGAGCAGGCCCGGAGAGGTGCGAAGGGCGGCAAGGTATCCAA\n+GGGAGGGGGAAGGCCGAGCAATAGCGGTAAGGACAAGTCCGATCTATTGCCGGAGGTTCT\n+GCGGCTTAAGGCTCAGGGGTACACCAACCGCGATATAGCGGACGATCTTCAAATCTCCCC\n+CAGTACGGTGAGCGTTTACCTAAAGCGTGATCGTCCGTGA\n+>ColRNAI.1__DQ298019\n+CTCGGCTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTAAGCAAGAACCCCCCGTTCAG\n+CCCGACTGCTGCGCCTTATCCGGTAACTGTTCACTTGAGTCCAACCCGGAAAAGCACGCA\n+AAACGCCACT\n+>Col_BS512_.1__NC_010656\n+ATGAATGCGGCGTTTAAGCGAATGGAAAAGCGAAAGGAGCTATCACCTGTTCAGGGGTGG\n+ATCAGGGCTACGGAGGTGACGCGAGGTAAGGATGGCAGCGCACATCCGCATTTTCACTGT\n+CTGCTGATGGTGCAACCTTCTTGGTTTAAAGGGAAGAACTACGTTAAGCACGAACGTTGG\n+GTAGAACTCTGGCGCGATTGCTTGCGGGTGAACTATGAGCCGAATATCGATAT\n+>Col_IMGS31_.1__NC_011406\n+TTATAATTTTAAAGCCTTTGGCTTATTCTGGGGTGTGTAGTTATTATTTTGCTGTTTCTG\n+TGAATATTCGGCATCTGCTGCTGCAATAGCAGCATTGAAGAGTTGTTTAAATTCTGCCGG\n+TTTATGCTCTTGTATTAGATCTAAAACATCACTGTTAATTTTATATTTTTCATATCTCTG\n+AGAAATTGAAGCATTTTC\n+>Col_IRGK_.1__AY543071\n+CGGTTTTACAGCAAAATCCTCCATAGCGAAGCAGAAGCCCGGAACGGGTAACTGGATGGT\n+TTTCCCCCGTGGGGGATTGATCTGTTACTTGAAAACCAATGATCTTAAAAGCCATCTCAA\n+AAGTTGAAAATTTCACCCCCTTAGTGTTCTTAAAATTCTTAGATGTTCTTAGGAGTTAAA\n+AAAC\n+>Col_KPHS6_.1__NC_016841\n+ATGCAAACTCAAAATGTTGTGACGGACAAAGAACGGGAAATCAGAAAAAGAGATCTTGAA\n+GATAAAGACCGTAAAAACGCCTCAGAGCGTCGACAGGAGCAAAAAAACCAAAACTTCACC\n+CAAGTATACCCTTTAGGCTGGAAGCGTCTCAGAGAGCTTTTCAGGAAGAATCCGGGGG\n+>Col_MG828_.1__NC_008486\n+ACCTCTCGCATGTTGTCGGTGATCCCGTTGTTGTTCTTTCAGGGATGAGTCGTCAGATAG\n+CCCTTCAAACGCGCTCAGAAGCTCTCAGACGCACTAAACGGGTCTTAAATGCCCGTCAGG\n+GCATGGGAGGCGCGAAAAACGCTTACAGAGCGTTTCAGGAGGTCAGGCGCGCCGATACCC\n+CTAACCAGGGGCTTTCAGGTCGCCAGGAACAGCGTCAGCCCCCTGCAAAGCCTATTTGCA\n+CGGCACAGGCAGCTATTCGGTT\n+>Col_MGD2_.1__NC_003789\n+TATGGCTTAGGCCGCAACTGCACTCTGTTCGATAAAACACGGAAGTGGGCTTATCGCGCT\n+ATCCGTCAGGGCTGGCCTGAATATGACCAGTGGCTGCAAGCTTTGCAATTTTCATCGGCT\n+CTGGATGATAATGAGG\n+>Col_MP18_.1__NC_013652\n+CCGTCATCTGTACCCTCTGCCATGCCATCCGCCATGATTAAATCCTCGTTCGTTTCCCGC\n+TCCAGTTGCAGAACGTTCTTAAGCGCTCCCCCCGTAGCAACAAAACGACGCTTGTGTACC\n+TGCCGTGTTAATTCGAGGAACCATTCAGGATCAGCCAGCATATCAGCAGGCTTTGTGGAA\n+TATTTCAGAGTTT\n+>Col_SD853_.1__NC_015392\n+TTGATTTATTCATCTGAAAACGATTATAGCATCCTCGAAGACAAAACCGCAACAGGTAAA\n+AAGCGGGATTGGAAGGGGAAAAAGAGACGTACGAACCTCATGGCGGAGCATTACGAAGCG\n+TTAGAGAGTAAGATTGGGGCACCTTACTATGGCAAAAAGGCTGAAAAGCTAATTGGTTGT\n+GCAGAGTATCTTTC\n+>Col_VCM04_.1__HM231165\n+CGTGTGGGTACTCCTGTTCGACGTTGACCAGCCCCTAGCGGCGCTGGCGTGGGAAGCAGC\n+CGGACTTCCGCCGCCAACGTGGACGGCACAAAACCCTGAGAACGGGCACGCCCACATTGC\n+CTACGCGCTGAGCGCTCCGGTAGCGAAGTCGGACGCGGCGAAGCTCAAGCCCCTGCG\n+>Col_YC_.1__NC_002144\n+CTAAACTTTCAATTTTATTTGCTTATCTTCTTTAAACGTAAAGCGAAGGGCAACAACTTT\n+TCTTCCATTCTTTATGGATTCAACAAAGACAGTGAGATCACTTTTTTCATTTAGTTCTTT\n+TAAAGCTGGTTTTATGACAGCCCTGTTCAAAAT\n+>Col_YF27601'..b'attcacgaaaatttatttggct\n+caattttcttctttttggaatttaaaaacacaagcaataagggtttttggttatattatg\n+acgaaattaataccaaggcaagatacttttatgttttttctagatgaatgtatggaatac\n+acaggctataaaggcaaaaacagtatttatattggtcttactagtttagtagaaaacaat\n+ataattgcgaggggtagaaatgatagccattattttataaatccaatggtagcgtttaat\n+ggggatagagtaacgtttgcaaaacttatataa\n+>repUS7._rep_pHTbeta__AB183714\n+atgttgaatagttgcgagtatgcggacgttttagctaaaattcttaaaaatggaattaaa\n+cagtttaatagcaaaaatctagttgcttttaaaaagaatagcaataagattggtgctatt\n+gccggatttacttctaaaacaaacatgataaagactaaaggtcttatatatcgttctatt\n+gatcgtgtcttggaagattcagatgtattaacacactggactcctaacgtgtattcatgg\n+cttggtggcggtgaaaacaaaacaatttttggtcacaaagaagctaacttaattcagatt\n+aatacttttgtagcagatattgactatccagtaggagaaaagaaaacggatttgaattta\n+ctagttctttatctattggaagaagggttattgcctacactgattgtagatacgccaaaa\n+ggttatcattgctattttctgattcaaaactataaccaagaaactgattcatttgataag\n+gcaagctatatttctaattcaaatgattttaaatctttgagagttgctaaaagaatatca\n+gaaaatatcagaaaatctatccaaaatcgtttaccacaagtcgatatgggctgtaatcat\n+tttggtatttttagatttccaactaaaaaaaatattgtacattatgaacctaatttcgta\n+gatacgtttgaagggtatttgaaatggtcaaaagactttgaagaaaaagaatatgcttta\n+aagaggtctaacttgtcattattagctcctaattctactggcaagaaagggtctaaacga\n+caaattgatactaaatggtacgactttttaattcatacggatattgctgaaggagataga\n+aataaaactatttttaccttagccctggcatgtaaatcaagtggcttatctattggcgag\n+tgtatggatcaattggatcaacttcaattcaataatgatttgtcctattctgaagttgag\n+agaacaataagaagtgcttatcgtggcgattacaaaggtgctaaaagttcatatgtcaat\n+gaaattatcgaaaattatgctacacctaccgagtttgaaaaatactcaataaatgtaaat\n+agacaagctgttaaacgtaaagggaatcgtgtcgatccgtctaattgggtgaaatttgct\n+aaacctagagaagaacgaaaatatagtcattttgaagaaagtaaagctgatttattagct\n+tacttagaaagaaaacaaagatcattgaaaaaaaatgagttgtttttaagtgtctctatg\n+ggaactatatctgaagaaacacaaattcctgtatctacgttaaaggtgattttaaaagag\n+cttagaacggcgaatacagtgatattacaaacgtctcgtggtcggtatggatcgactaaa\n+atagcaacaagcaaatttgtggaagctaaaatattaagtacagttattcagaataaaaaa\n+gataaacaagtatttgtcttagaattgttaggaacagcaaatagtcacgtagaaacgatt\n+ttaagacgttatgaagacaaaacagtaccgttccatgcgaacatactgaaagaaagagaa\n+aagagcaaacatgcgccaattagaggagctaatacaggttag\n+>repUS8._ORF1_pOg32__LOPPOG32\n+atgaccaaaacatctattgaaaagccggccccttctaacagccggctaagtgtaaaaaat\n+gtttacacttcatctataaagtggagcattgaccgtctaacgattgttggagaacttgct\n+ccattcttacctgcggggtatacaactaacaaaatatctggcgaagttaaaagcagaatt\n+actattgaagatatgttcaaagtttttgaacattttggtcattgtcgtttgtccggaaat\n+ggttatcaaatgataaccgatgatggagagaacgttgcttattttgaacgattaaagttt\n+gacaaaaataaagggcgcttagattttaacccgaacaagttagatagtttttttgaaaat\n+ggcttgaagcaatttatatctgatttattcatcacgccccatttttcaagggctgacatt\n+gctgccgatatttttgatgtccccgatgaaaaagttgtgtcttaccgattaggtgaacca\n+gttggaaatacatttttttatggaaaaagtggagatttacagaccgcgtattttggtgcc\n+aggtcatcagagaaacaaataaggctctataacaaaagaattgaaagaatcaaaaaaggc\n+agaattgaagaccttaaagaccccgaacaatgctactggcggttagaactacaactaaga\n+cgcgggagggctgatgattttcaaaagcaggtcgacgagagtttgaaacatttttattct\n+ccgcaagattttcctgatgatgtgtctgtgaacagcagaatatttttgaaagggctactt\n+gcagaccctgataactgggctagaatatcaagaccaacgaagtcaaaatatagacagata\n+gaggaacgagttgcctcttctgacaaattaacaattgaattgaaaaaaactttttctcaa\n+caaaataaaaaaatagaaaaagaattgaagaattggctacagacttttcaagttttgtag\n+>repUS9._rep_pSK1__AF203376\n+Atgtctaaatttaaaaaaatatctgcaagtgaattcgaaacattacgtttttatcaatta\n+cccaaatttttatttgaagatgaatacttttctaaaatgcccacagatgcaaaagttatg\n+tatgctttattaaaagatcgctttgaactatcaagattaaataactgggtagattcagaa\n+aataatatttatcttttatataccaataaacagttatgctcaattttaaattatgcagaa\n+ccaaaaatcattaaattaaaaaaagaattagaaaaatacaatttgattataaacgaaaga\n+caaggtttaaataaacctaacaaaatttatttactcgaacccacatatgacaaggaacta\n+ataaattctaagttccagaacaaagaatttattagttccagaactaataaatcatcagtt\n+caagaactaataaattctaagtcaagtgatactgattttaataatactgaatatatagag\n+actaagaataatgatacgaattatacgaatgatacatctaacatgatttctaagaattct\n+cattcgaatcatacaaatcatcaacaaaccgaatttaataatgatgccttaaaattccag\n+gcgcttgaagaattaccttcgcaaatcaaatcttatgtaagtaattttgaaattaaagac\n+atccgtattattaaaagtatcttactcaaggggaaaaagtcatttaataatacacatgat\n+acatattaccgtttagaagacgtcgaatttgaacttgtaagtgttttaaaacgttttaaa\n+gccatgttgctacaaaaaaatgaaaccgttgaaactatgcaaggctatttaatgcaatca\n+attaaagctgaacttgaagaaatacatgcattaaatatgcgtcgtcaaaacatacctcaa\n+tacaatatctttaatcaataa\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/prepare_ref.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/prepare_ref.sh Tue Jan 08 10:26:30 2019 -0500 |
| [ |
| @@ -0,0 +1,9 @@ +#!/usr/bin/env bash +declare -a listdb=("card" "resfinder" "megares" "argannot" "virulencefinder" "plasmidfinder") + +for i in "${listdb[@]}" +do + ariba getref $i $i + ariba prepareref -f ${i}.fa -m ${i}.tsv ${i}.db + rm *.{fa,tsv,log} +done |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/resfinder.db/00.info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/resfinder.db/00.info.txt Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,3 @@ +input fasta file: resfinder.fa +input tsv file: resfinder.tsv +genetic_code 11 |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/resfinder.db/00.rename_info --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/resfinder.db/00.rename_info Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b"@@ -0,0 +1,2315 @@\n+ARR-2.1_HQ141279\tARR_2.1_HQ141279\n+ARR-3.1_JF806499\tARR_3.1_JF806499\n+ARR-3.4_FM207631\tARR_3.4_FM207631\n+ARR-4.1_EF660562\tARR_4.1_EF660562\n+ARR-5.1_EF660563\tARR_5.1_EF660563\n+ARR-6.1_FM955585\tARR_6.1_FM955585\n+ARR-6.2_FM897214\tARR_6.2_FM897214\n+ARR-6.3_JF922883\tARR_6.3_JF922883\n+ARR-7.1_FN397623\tARR_7.1_FN397623\n+POM-1.1_GU002295\tPOM_1.1_GU002295\n+aac(2')-IIa.1_AB669090\taac_2___IIa.1_AB669090\n+aac(2')-Ia.1_L06156\taac_2___Ia.1_L06156\n+aac(2')-Ib.1_U41471\taac_2___Ib.1_U41471\n+aac(2')-Ic.1_U72714\taac_2___Ic.1_U72714\n+aac(2')-Id.1_U72743\taac_2___Id.1_U72743\n+aac(2')-Ie.1_NC011896\taac_2___Ie.1_NC011896\n+aac(3)-I.1_AJ877225\taac_3__I.1_AJ877225\n+aac(3)-IIIa.1_X55652\taac_3__IIIa.1_X55652\n+aac(3)-IIIb.1_L06160\taac_3__IIIb.1_L06160\n+aac(3)-IIIb.2_LLLC01000048\taac_3__IIIb.2_LLLC01000048\n+aac(3)-IIIc.1_L06161\taac_3__IIIc.1_L06161\n+aac(3)-IIa.1_X51534\taac_3__IIa.1_X51534\n+aac(3)-IIa.2_AY138987\taac_3__IIa.2_AY138987\n+aac(3)-IIa.3_X13543\taac_3__IIa.3_X13543\n+aac(3)-IIa.4_L22613\taac_3__IIa.4_L22613\n+aac(3)-IIa.5_FJ012882\taac_3__IIa.5_FJ012882\n+aac(3)-IIb.1_M97172\taac_3__IIb.1_M97172\n+aac(3)-IIc.1_X54723\taac_3__IIc.1_X54723\n+aac(3)-IId.1_EU022314\taac_3__IId.1_EU022314\n+aac(3)-IIe.1_EU022315\taac_3__IIe.1_EU022315\n+aac(3)-IV.1_DQ241380\taac_3__IV.1_DQ241380\n+aac(3)-IVa.1_X01385\taac_3__IVa.1_X01385\n+aac(3)-IXa.1_M55427\taac_3__IXa.1_M55427\n+aac(3)-Ia.1_X15852\taac_3__Ia.1_X15852\n+aac(3)-Ib-aac(6')-Ib'.1_AF355189\taac_3__Ib_aac_6___Ib_.1_AF355189\n+aac(3)-Ib.1_L06157\taac_3__Ib.1_L06157\n+aac(3)-Ic.1_AJ511268\taac_3__Ic.1_AJ511268\n+aac(3)-Id.1_AB114632\taac_3__Id.1_AB114632\n+aac(3)-If.1_AY884051\taac_3__If.1_AY884051\n+aac(3)-Ig.1_CP000282\taac_3__Ig.1_CP000282\n+aac(3)-Ih.1_CP000490\taac_3__Ih.1_CP000490\n+aac(3)-Ii.1_CP000356\taac_3__Ii.1_CP000356\n+aac(3)-VIII.1_AB211959\taac_3__VIII.1_AB211959\n+aac(3)-VIII.2_AJ843080\taac_3__VIII.2_AJ843080\n+aac(3)-VIII.3_AJ748131\taac_3__VIII.3_AJ748131\n+aac(3)-VIIIa.1_M55426\taac_3__VIIIa.1_M55426\n+aac(3)-VIIa.1_M22999\taac_3__VIIa.1_M22999\n+aac(3)-VIa.1_M88012\taac_3__VIa.1_M88012\n+aac(3)-VIa.2_NC_009838\taac_3__VIa.2_NC_009838\n+aac(3)-XI.1_CTEG01000046\taac_3__XI.1_CTEG01000046\n+aac(3)-Xa.1_AB028210\taac_3__Xa.1_AB028210\n+aac(6')-29a.1_AF263519\taac_6___29a.1_AF263519\n+aac(6')-29b.1_AF263519\taac_6___29b.1_AF263519\n+aac(6')-30-aac(6')-Ib'.1_AJ584652\taac_6___30_aac_6___Ib_.1_AJ584652\n+aac(6')-31.1_AM283489\taac_6___31.1_AM283489\n+aac(6')-32.1_EF614235\taac_6___32.1_EF614235\n+aac(6')-33.1_GQ337064\taac_6___33.1_GQ337064\n+aac(6')-I30.1_AY289608\taac_6___I30.1_AY289608\n+aac(6')-IIa.1_M29695\taac_6___IIa.1_M29695\n+aac(6')-IIb.1_L06163\taac_6___IIb.1_L06163\n+aac(6')-IIc.1_NC_012555\taac_6___IIc.1_NC_012555\n+aac(6')-Ia.1_M18967\taac_6___Ia.1_M18967\n+aac(6')-Ia.2_M86913\taac_6___Ia.2_M86913\n+aac(6')-Iaa.1_NC_003197\taac_6___Iaa.1_NC_003197\n+aac(6')-Iad.1_AB119105\taac_6___Iad.1_AB119105\n+aac(6')-Iae.1_AB104852\taac_6___Iae.1_AB104852\n+aac(6')-Iaf.1_AB462903\taac_6___Iaf.1_AB462903\n+aac(6')-Iag.1_AB472901\taac_6___Iag.1_AB472901\n+aac(6')-Iai.1_EU886977\taac_6___Iai.1_EU886977\n+aac(6')-Iaj.1_AB709942\taac_6___Iaj.1_AB709942\n+aac(6')-Iak.1_AB894482\taac_6___Iak.1_AB894482\n+aac(6')-Ian.1_AP014611\taac_6___Ian.1_AP014611\n+aac(6')-Ib-Hangzhou.1_FJ503047\taac_6___Ib_Hangzhou.1_FJ503047\n+aac(6')-Ib-Suzhou.1_EU085533\taac_6___Ib_Suzhou.1_EU085533\n+aac(6')-Ib-cr.1_DQ303918\taac_6___Ib_cr.1_DQ303918\n+aac(6')-Ib-cr.1_DQ303918_2\taac_6___Ib_cr.1_DQ303918_2\n+aac(6')-Ib-cr.2_EF636461\taac_6___Ib_cr.2_EF636461\n+aac(6')-Ib-cr.2_EF636461_2\taac_6___Ib_cr.2_EF636461_2\n+aac(6')-Ib.1_M21682\taac_6___Ib.1_M21682\n+aac(6')-Ib.2_M23634\taac_6___Ib.2_M23634\n+aac(6')-Ib11.1_AY136758\taac_6___Ib11.1_AY136758\n+aac(6')-Ib3.1_X60321\taac_6___Ib3.1_X60321\n+aac(6')-Ic.1_M94066\taac_6___Ic.1_M94066\n+aac(6')-If.1_X55353\taac_6___If.1_X55353\n+aac(6')-Ig.1_L09246\taac_6___Ig.1_L09246\n+aac(6')-Ih.1_L29044\taac_6___Ih.1_L29044\n+aac(6')-Ih.2_KT778788\taac_6___Ih.2_KT778788\n+aac(6')-Ii.1_L12710\taac_6___Ii.1_L12710\n+aac(6')-Iid.1_AJ584700\taac_6___Iid.1_AJ584700\n+aac(6')-Iih.1_AJ584701\taac_6___I"..b'L).7_X60828\ttet_L_.7_X60828\n+tet(L).8_AY081910\ttet_L_.8_AY081910\n+tet(M).10_EU182585\ttet_M_.10_EU182585\n+tet(M).11_JN846696\ttet_M_.11_JN846696\n+tet(M).12_FR671418\ttet_M_.12_FR671418\n+tet(M).13_AM990992\ttet_M_.13_AM990992\n+tet(M).1_X92947\ttet_M_.1_X92947\n+tet(M).2_X90939\ttet_M_.2_X90939\n+tet(M).3_U08812\ttet_M_.3_U08812\n+tet(M).4_X75073\ttet_M_.4_X75073\n+tet(M).5_U58985\ttet_M_.5_U58985\n+tet(M).6_M21136\ttet_M_.6_M21136\n+tet(M).7_FN433596\ttet_M_.7_FN433596\n+tet(M).8_X04388\ttet_M_.8_X04388\n+tet(M).9_X56353\ttet_M_.9_X56353\n+tet(O).1_M18896\ttet_O_.1_M18896\n+tet(O).2_M20925\ttet_O_.2_M20925\n+tet(O).3_Y07780\ttet_O_.3_Y07780\n+tet(O/32/O).1_JQ740052\ttet_O_32_O_.1_JQ740052\n+tet(O/32/O).2_AJ295238\ttet_O_32_O_.2_AJ295238\n+tet(O/32/O).3_NZ_AUJS01000017\ttet_O_32_O_.3_NZ_AUJS01000017\n+tet(O/32/O).4_AIOQ01000025\ttet_O_32_O_.4_AIOQ01000025\n+tet(O/32/O).5_FP929050\ttet_O_32_O_.5_FP929050\n+tet(O/W)-1.1_AY485126\ttet_O_W__1.1_AY485126\n+tet(O/W)-2.1_AY485122\ttet_O_W__2.1_AY485122\n+tet(O/W).1_AM889118\ttet_O_W_.1_AM889118\n+tet(O/W).2_AM889119\ttet_O_W_.2_AM889119\n+tet(O/W).3_AM889120\ttet_O_W_.3_AM889120\n+tet(O/W).4_AM889121\ttet_O_W_.4_AM889121\n+tet(O/W).5_AM889122\ttet_O_W_.5_AM889122\n+tet(O/W/32/O).1_EF065523\ttet_O_W_32_O_.1_EF065523\n+tet(O/W/32/O).2_FM164392\ttet_O_W_32_O_.2_FM164392\n+tet(O/W/32/O).5_JQ740053\ttet_O_W_32_O_.5_JQ740053\n+tet(O/W/32/O/W/O).1_DQ525023\ttet_O_W_32_O_W_O_.1_DQ525023\n+tet(O/W/32/O/W/O).2_DQ679926\ttet_O_W_32_O_W_O_.2_DQ679926\n+tet(O/W/O)-1.1_AY196921\ttet_O_W_O__1.1_AY196921\n+tet(O/W/O)-2.1_AY196920\ttet_O_W_O__2.1_AY196920\n+tet(O/W/O)-3.1_EF065524\ttet_O_W_O__3.1_EF065524\n+tet(Q).1_L33696\ttet_Q_.1_L33696\n+tet(Q).2_X58717\ttet_Q_.2_X58717\n+tet(Q).3_U73497\ttet_Q_.3_U73497\n+tet(Q).4_Z21523\ttet_Q_.4_Z21523\n+tet(S).1_DQ377340\ttet_S_.1_DQ377340\n+tet(S).2_L09756\ttet_S_.2_L09756\n+tet(S).3_X92946\ttet_S_.3_X92946\n+tet(S/M).1_HM367711\ttet_S_M_.1_HM367711\n+tet(S/M).2_AY534326\ttet_S_M_.2_AY534326\n+tet(T).1_L42544\ttet_T_.1_L42544\n+tet(T).2_AY660530\ttet_T_.2_AY660530\n+tet(V).1_AF030344\ttet_V_.1_AF030344\n+tet(W).1_DQ060146\ttet_W_.1_DQ060146\n+tet(W).2_AY049983\ttet_W_.2_AY049983\n+tet(W).3_AJ427421\ttet_W_.3_AJ427421\n+tet(W).4_FN396364\ttet_W_.4_FN396364\n+tet(W).5_AJ427422\ttet_W_.5_AJ427422\n+tet(W/32/O).1_AM710601\ttet_W_32_O_.1_AM710601\n+tet(W/32/O).2_AM710602\ttet_W_32_O_.2_AM710602\n+tet(W/32/O).3_AM710603\ttet_W_32_O_.3_AM710603\n+tet(W/32/O).4_AM710605\ttet_W_32_O_.4_AM710605\n+tet(X).1_GU014535\ttet_X_.1_GU014535\n+tet(X).2_M37699\ttet_X_.2_M37699\n+tet(X).3_AB097942\ttet_X_.3_AB097942\n+tet(Y).1_EF495198\ttet_Y_.1_EF495198\n+tet(Y).2_AB089606\ttet_Y_.2_AB089606\n+tet(Z).1_AF121000\ttet_Z_.1_AF121000\n+tetA(46).1_HQ652506\ttetA_46_.1_HQ652506\n+tetA(60).1_KX000272\ttetA_60_.1_KX000272\n+tetA(P).1_AB054980\ttetA_P_.1_AB054980\n+tetA(P).2_L20800\ttetA_P_.2_L20800\n+tetA(P).3_AB001076\ttetA_P_.3_AB001076\n+tetB(46).1_HQ652506\ttetB_46_.1_HQ652506\n+tetB(60).1_KX000273\ttetB_60_.1_KX000273\n+tetB(P).1_NC_010937\ttetB_P_.1_NC_010937\n+tlr(C).1_M57437\ttlr_C_.1_M57437\n+tva(A).1_ENA_SOX29786\ttva_A_.1_ENA_SOX29786\n+vat(A).1_L07778\tvat_A_.1_L07778\n+vat(B).1_U19459\tvat_B_.1_U19459\n+vat(C).1_AF015628\tvat_C_.1_AF015628\n+vat(D).1_L12033\tvat_D_.1_L12033\n+vat(E).10_AY043212\tvat_E_.10_AY043212\n+vat(E).11_AY043213\tvat_E_.11_AY043213\n+vat(E).3_AF153312\tvat_E_.3_AF153312\n+vat(E).5_AJ488494\tvat_E_.5_AJ488494\n+vat(E).7_AY043211\tvat_E_.7_AY043211\n+vat(E).8_AY043209\tvat_E_.8_AY043209\n+vat(E).9_AY043210\tvat_E_.9_AY043210\n+vat(F).1_AF170730\tvat_F_.1_AF170730\n+vat(H).1_GQ205627\tvat_H_.1_GQ205627\n+vga(A).1_M90056\tvga_A_.1_M90056\n+vga(A).2_FN546261\tvga_A_.2_FN546261\n+vga(A).3_JQ312422\tvga_A_.3_JQ312422\n+vga(A)LC.1_GQ891882\tvga_A_LC.1_GQ891882\n+vga(A)LC.2_DQ823382\tvga_A_LC.2_DQ823382\n+vga(A)LC.3_FN806791\tvga_A_LC.3_FN806791\n+vga(A)LC.4_JQ312423\tvga_A_LC.4_JQ312423\n+vga(A)V.1_AF186237\tvga_A_V.1_AF186237\n+vga(B).1_U82085\tvga_B_.1_U82085\n+vga(C).1_FN806792\tvga_C_.1_FN806792\n+vga(D).1_GQ205627\tvga_D_.1_GQ205627\n+vga(E).1_FR772051\tvga_E_.1_FR772051\n+vgb(A).1_M20129\tvgb_A_.1_M20129\n+vgb(B).1_AF015628\tvgb_B_.1_AF015628\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/resfinder.db/00.version_info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/resfinder.db/00.version_info.txt Tue Jan 08 10:26:30 2019 -0500 |
| [ |
| @@ -0,0 +1,28 @@ +ARIBA run with this command: +/Users/leviet/miniconda3/bin/ariba prepareref prepareref -f resfinder.fa -m resfinder.tsv resfinder.db +from this directory: /Users/leviet/Documents/bioinformatics/quadram/galaxy-tools/ariba/database + +ARIBA version: 2.13.2 + +External dependencies: +bowtie2 2.3.4.3 /Users/leviet/miniconda3/bin/bowtie2 +cdhit 4.7 /Users/leviet/miniconda3/bin/cd-hit-est +nucmer 3.1 /Users/leviet/miniconda3/bin/nucmer + +External dependencies OK: True + +Python version: +3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:55:02) +[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] + +Python packages: +ariba 2.13.2 /Users/leviet/miniconda3/lib/python3.6/site-packages/ariba/__init__.py +bs4 4.6.3 /Users/leviet/miniconda3/lib/python3.6/site-packages/bs4/__init__.py +dendropy 4.4.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/dendropy/__init__.py +pyfastaq 3.17.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/pyfastaq/__init__.py +pymummer 0.10.3 /Users/leviet/miniconda3/lib/python3.6/site-packages/pymummer/__init__.py +pysam 0.15.0 /Users/leviet/miniconda3/lib/python3.6/site-packages/pysam/__init__.py + +Python packages OK: True + +Everything looks OK: True |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/resfinder.db/01.filter.check_genes.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/resfinder.db/01.filter.check_genes.log Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,3057 @@\n+ARR_2.1_HQ141279\tKEEP\tMade into gene. strand=+, frame=0\n+ARR_3.1_JF806499\tKEEP\tMade into gene. strand=+, frame=0\n+ARR_3.4_FM207631\tKEEP\tMade into gene. strand=+, frame=0\n+ARR_4.1_EF660562\tKEEP\tMade into gene. strand=+, frame=0\n+ARR_5.1_EF660563\tKEEP\tMade into gene. strand=+, frame=0\n+ARR_6.1_FM955585\tKEEP\tMade into gene. strand=+, frame=0\n+ARR_6.2_FM897214\tKEEP\tMade into gene. strand=+, frame=0\n+ARR_6.3_JF922883\tKEEP\tMade into gene. strand=+, frame=0\n+ARR_7.1_FN397623\tKEEP\tMade into gene. strand=+, frame=0\n+EstDL136.1_JN242251\tKEEP\tMade into gene. strand=+, frame=0\n+POM_1.1_GU002295\tREMOVE\tDoes not look like a gene (tried both strands and all reading frames) GTGCGTACCCTGACCACCTTCGGCCTTGCCCTGCTGCTGGCCCAACCCGCCATGGCCGCCCAGGCCGTCCTGCCGCAACTGCAGCCCTACACCGCCCCGGCCGCCTGGCTGACCCCGGTGGCACCGCTGCGTATCGCCGACAACACCTGGCACATCGGCACCGCCAGCATCACCGCGCTGCTGGTGAAGACGCCGGAAGGCGCCGTGCTGCTGGACGGCGGCATGCCCCAGGTGGCCGACCACCTGCTGGCCAACATGCGCGAGCTGGGTGTGGCGCCGGGCGACCTCAAGCTGATCCTGCACAGCCACGCCCACATCGATCACGTCGGCCCGCTGGCCGCCATCAAGAAGGCCACCGGCGCGCAACTGGTGAGCAACGCCGAATCGGCCGTGCTGCTGCAGCGCGGCGACAGCCAGGACATCCACTTCGGCGACGACATGGTCTTCGCCCCGGTGCAGGTGGACCGCCTGGTGCAGGACGGCGAAACCGTGGAGCTGGGCGGCATGACCTTCACCGCCCACTTCACCCCCGGGCACACCCCCGGCAGCCTGAGCTGGACCTGGACCGACCGTCGCGACGGCAAGCCCCTGCGCATCGCCTACAGCGACAGCTTGAGCGCCCCCGGATACAGCCTGTGGATGAACCCGCGCTTCTCGAAGATCGCCGAGGCCTTCCGCAGCGGCTTCGCCGCCGTCCGCGCCCTGCCCTGCGACCTGCTGATCACCCCCCACGCCGAGGCCAGCGGCTGGGACTACACCAACGCCGAACACCCCAACCCGTCGCCCATGAGCTGCAAGGCCTACGCCGACAAGGCCGAGGC\n+VanA.bc_1_Y15704\tKEEP\tMade into gene. strand=+, frame=0\n+VanC1XY.1_AF162694\tREMOVE\tDoes not look like a gene (tried both strands and all reading frames) ATGAAAAAAATTGCCGTTTTATTTGGAGGGAATTCTCCAGAATACTCAGTGTCACTAACCTCAGCAGCAAGTGTGATCCAAGCTATTGACCCGCTGAAATATGAAGTAATGACCATTGGCATCGCACCAACAATGGATTGGTATTGGTATCAAGGAAACCTCGCGAATGTTCGCAATGATACTTGGCTAGAAGATCACAAAAACTGTCACCAGCTGACTTTTTCTAGCCAAGGATTTATATTAGGAGAAAAACGAATCGTCCCTGATGTCCTCTTTCCAGTCTTGCATGGGAAGTATGGCGAGGATGGCTGTATCCAAGGACTGCTTGAACTAATGAACCTGCCTTATGTTGGTTGCCATGTCGCTGCCTCCGCATTATGTATGAACAAATGGCTCTTGCATCAACTTGCTGATACCATGGGAATCGCTAGTGCTCCCACTTTGCTTTTATCCCGCTATGAAAACGATCCTGCCACAATCGATCGTTTTATTCAAGACCATGGATTCCCGATCTTTATCAAGCCGAATGAAGCCGGTTCTTCAAAAGGGATCACAAAAGTAACTGACAAAACAGCGCTCCAATCTGCATTAACGACTGCTTTTGCTTACGGTTCTACTGTGTTGATCCAAAAGGCGATAGCGGGTATTGAAATTGGCTGCGGCATCTTAGGAAATGAGCAATTGACGATTGGTGCTTGTGATGCGATTTCTCTTGTCGACGGTTTTTTTGATTTTGAAGAGAAATACCAATTAATCAGCGCCACGATCACTGTCCCAGCACCATTGCCTCTCGCGCTTGAATCACAGATCAAGGAGCAGGCACAGCTGCTTTATCGAAACTTGGGATTGACGGGTCTGGCTCGAATCGATTTTTTCGTCACCAATCAAGGAGCGATTTATTTAAACGAAATCAACACCATGCCGGGATTTACTGGGCACTCCCGCTACCCAGCTATGATGGCGGAAGTCGGGTTATCCTACGAAATATTAGTAGAGCAATTGATTGCACTGGCAGAGGAGGACAAACGATGAACACATTACAATTGATCAATAAAAACCATCCATTGAAAAAAAATCAAGAGCCCCCGCACTTAGTGCTAGCTCCTTTTAGCGATCACGATGTTTACCTGCAGCCAGAAGTGGCAAAACAATGGGAACGACTCGTACGAGCAACCGGACTAGAAAAGGACATTCGTCTGGTAGATGGGTATCGTACGGAAAAAGAACAGCGACGCTTGTGGGAGTATTCTCTAAAAGAAAACGGGTTAGCTTATACCAAACAATTCGTTGCTTTGCCAGGTTGCAGTGAACATCAAATCGGTCTGGCCATTGATGTAGGACTAAAGAAACAAGAAGATGATGATCTTATCTGCCCTCATTTTCGAGATAGTGCTGCTGCTGATTTATTTATGCAGCAGATGATGAATTATGGCTTTATTCTACGCTATCCGGAAGATAAACAAGAGATCACCGGTATCAGTTATGAACCTTGGCATTTTCGTTATGTCGGGCTTCCCCATAGCCAAGTCATCACTGCCCAAAAATGGACTCTGGAAGAATACCATGATTACTTGGCTCAGACAGTGAGGCAGTTCGCATGA\n+VanC1XY.2_DQ022190\tREMOVE\tDoes not look like a gene (tried both strands and all reading frames) ATGAAAAAAATTGCCGTTTTATTTGGAGGGAATTCTCCAGAATACTCAGTGTCACTAGCCTCAGCAGCAAGTGTGATCCAAGCTATTGACCCGCTGAAATATGAAGTAATGACCATTGGCATCGCGCCAACAATGGATTGGTATTTGTATCAAGGAAACCTCGCGAATGTTCGCAATGATACTTGGCTAGAAGATCACAAAAACTGTCACCAGCTGACTTTTTCTAGCCAAGGATTTATATTAGGAGAAAAACGAATCGTCCCTGATGTCCTCTTTCCAGTCTTGCATGGGAAGTATGGCGAGGATGGCTGTATTCAAGGACTGCTTGAACTAATGAACCTGCCTTATGTTGGTTGCCATGTCGCTGCCTCCGCATTATGTATGAACAAATGGCTCTTGCATCAACTTGCTGATACCATGGGAATCGCTAGTGCTCCCACTTTGCTTTTATCCCGCTATGAAAACGATCCTGCCACAATCGATCGTTTTATTCAAGACCATGGATTCCCGATCTTTATCAAGCCGAATGAAGCCGGTTCTTCAAAAGGGATCACAAAAGTAACTGACAAAACAGCGCTCCAATCTGCATTAACGACTGCTTTTGCTTACGGTTCTACTGTGTTGATCCAAAAGGCGA'..b'GTGGCGGAGCGGCTGGGCGTGCCTCTGAAACGGGCCGCCGCCGCACTCAGGGATTACCGCCCCCTGGCCATGCGCCAGCAGATTTACCATGTCAATGAGGTTGCCGTCATTGATGATTCCTACAACTCCAGTCCCGGCGCGGCCAAAAGCAGCCTGAGTGTTCTTGCGGGGTTCCGGGCCGGCCGCAGAGTAGCCGTGCTGGCGGATATGCTGGAACTGGGGGAGTATTCCCGGCAGGCGCATTTTGAAGTCGGCGTCTGCGCTGCGGAAAACGGAGTGGATATTTTACTCACCGTCGGTCAGGAGGCGAAAGCCGTGGCCGAGGGTGCCCGCTCCGTCCGGGCCGGGATCGACTGCCGCGTTTTGGACAATAACTATCAGGCCGCTGAGGAGTTGAAATCCTTTCTGTCTCCCGGTGACGCAGTTCTGGTCAAAGGCTCCCGCGGCATGCATACGGAGGAGATCGTCCGCGCCCTGCTTTAGCTTCCCGTTAACCGGGCTTTCCAGCTGTACTTAAAACGGCGGTAGGGTGGTGAAACCATATTCCTGAAAGGGGTCTCGACATGAAAAGAAAAAGATTGACTCAGTTATTCCCATTCCTGCTGCCGGTCCGCAGGATACAACGGAAATTATGCTTCTATACCAAGATGTACCTTGACCGGAACCACTATGCCAAAGCAAAGGCTCCAGAGTTTTTGCCTTTTTGCATTTATGAAACCAAGTCGAAGCTTCTCAATGAAAATACCGGCATGGATATAAAATACCAGGAGAACAAGGTGTTTAATCTGCGCCTTGCTGCGGAGCCCGTCAATGGCCTATTGATCCGCCCTGGCGAAACATTTTCATTTTGGCAGCGGGTGAGATATGCCGAGAAAAATGAGCGGTATAAGGACGGTCTATGCGTGGTCAATGACGAATTGGTTACGGTTCCGGGAGGCGGTTTGTGTCATCTCAGCAATTTGCTGTTTTGGCTCTTTCTGCATACTCCCCTCACGATTGTCGAACGGCATGCTCATGAGATTAAAGATTTTCCTTCTCCCGATGAGGATGAACCGGATGGTGTGGACGCGACAATCCACGAAGGGTGGTTGGATTTAAAGGTCAAAAACGATACCAATCTTACCTTCCAAATTGAACTATCCATTGATGGGCCTTACATCTATGGCCGTATTTTTATGGATCAGGCTAAAGGGTATAGTTACGAGGTTGTTAATCGTGATAAGCGCTTTCTCCAAAAAGAGGGAAAAATATTTGAGCGGGTTTCCGTTTGCCGGCAGGTGATCGACAACAAATCCAAGCAAGTTATTTCCGAAAATATGCTTTATACGGATGTATTTGAAATCGGGTATCCGCTTCCGGAAGGAACTGCTATCGCAGAGGAAAAGGAAATTTGAAAGGAGAAAGCTTATGAGTAAGTTGAAAATCGCAATTATCTTCGGAGGCTGTTCCGAAGAACATCCCGTCTCCGTTAAATCTGCTGGGGAGGTGGCCAAAAACCTGGATCTCGAAAAGTATGAACCCTTCTATATCGGGATTACGAAAGATGGGGTTTGGCAGCTTTGTCACTACCCTGAGGCCAATTGGGAAAAGGGCAGTTGCCGTCCGGCTATCCTGTCACCGGACAGAAGCGTCCAGGGATTGCTTGTTCTGGAGCAGGGGCAATACCAAAGGATCCCCTTGGATCTGGTGTTTCCCGTTCTGCATGGCAAATTTGGCGAGGATGGCGCGATACAGGGTTTGTTGGAGCTTTCCGGCATCCCCTATGTGGGCTGCGATATCCCGAGTTCGGCTCTGTGCATGGACAAATCCCTGGCTTATATCGTCGCTGGAAAGGCAGGAATTGCCACGCCAAAGTTCCGGACGGTCACTGCGAAGGAGACTATTGACGCCGAACGGCTTGCTTATCCCGTTTATGTCAAGCCGGCCCGTTCGGGTTCATCCTTCGGCGTCACTAAGGTATGCCGCCAAGAAGAATTGCTGAGTGCGGTGGAAATCGCCAGACAGTATGACTCGAAGGTGCTGATTGAAGAGGCTGTCGTCGGCAGCGAGGTAGGCTGTGCGATATTTGGAAACGATCTGGATTTGATGGCCGGTGAGGTCGATCAGATCTGTCTGTCTCATGGCTTTTTCAGAATCCATCAGGAGAATGAGCCGGAAAAGGGTTCCGAAAACTCAACACTAATCGTTCCCGCCGACATTTCCCCAGAGGCGCGCTCGCGGGTTCAGGAGACGGCAAAAGCCATCTATCGCGCTTTGGGCTGCAGGGGACTGGCGCGGGTGGATATGTTTCTGAAAGAAGATGGAACAGTAATCCTCAACGAGGTGAATACTTTGCCCGGCATGACCTCATACAGCCGTTTTCCGAGAATGATGGCGGCCGCAGGCTTGCCCTTTGCCGAAGTGATCGACCGGCTTGTCTCGTTGGCCTTTTAA\n+vat_A_.1_L07778\tKEEP\tMade into gene. strand=+, frame=0\n+vat_B_.1_U19459\tKEEP\tMade into gene. strand=+, frame=0\n+vat_C_.1_AF015628\tKEEP\tMade into gene. strand=+, frame=0\n+vat_D_.1_L12033\tKEEP\tMade into gene. strand=+, frame=0\n+vat_E_.10_AY043212\tKEEP\tMade into gene. strand=+, frame=0\n+vat_E_.11_AY043213\tKEEP\tMade into gene. strand=+, frame=0\n+vat_E_.3_AF153312\tKEEP\tMade into gene. strand=+, frame=0\n+vat_E_.5_AJ488494\tKEEP\tMade into gene. strand=+, frame=0\n+vat_E_.7_AY043211\tKEEP\tMade into gene. strand=+, frame=0\n+vat_E_.8_AY043209\tKEEP\tMade into gene. strand=+, frame=0\n+vat_E_.9_AY043210\tKEEP\tMade into gene. strand=+, frame=0\n+vat_F_.1_AF170730\tKEEP\tMade into gene. strand=+, frame=0\n+vat_H_.1_GQ205627\tKEEP\tMade into gene. strand=+, frame=0\n+vga_A_.1_M90056\tKEEP\tMade into gene. strand=+, frame=0\n+vga_A_.2_FN546261\tKEEP\tMade into gene. strand=+, frame=0\n+vga_A_.3_JQ312422\tKEEP\tMade into gene. strand=+, frame=0\n+vga_A_LC.1_GQ891882\tKEEP\tMade into gene. strand=+, frame=0\n+vga_A_LC.2_DQ823382\tKEEP\tMade into gene. strand=+, frame=0\n+vga_A_LC.3_FN806791\tKEEP\tMade into gene. strand=+, frame=0\n+vga_A_LC.4_JQ312423\tKEEP\tMade into gene. strand=+, frame=0\n+vga_A_V.1_AF186237\tKEEP\tMade into gene. strand=+, frame=0\n+vga_B_.1_U82085\tKEEP\tMade into gene. strand=+, frame=0\n+vga_C_.1_FN806792\tKEEP\tMade into gene. strand=+, frame=0\n+vga_D_.1_GQ205627\tKEEP\tMade into gene. strand=+, frame=0\n+vga_E_.1_FR772051\tKEEP\tMade into gene. strand=+, frame=0\n+vgb_A_.1_M20129\tKEEP\tMade into gene. strand=+, frame=0\n+vgb_B_.1_AF015628\tKEEP\tMade into gene. strand=+, frame=0\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/resfinder.db/01.filter.check_metadata.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/resfinder.db/01.filter.check_metadata.log Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,140 @@\n+POM_1.1_GU002295 was removed because does not look like a gene, so removing its metadata\n+VanC1XY.1_AF162694 was removed because does not look like a gene, so removing its metadata\n+VanC1XY.2_DQ022190 was removed because does not look like a gene, so removing its metadata\n+VanC2XY.1_EU151754 was removed because does not look like a gene, so removing its metadata\n+VanC2XY.2_EU151755 was removed because does not look like a gene, so removing its metadata\n+VanC2XY.3_EU151757 was removed because does not look like a gene, so removing its metadata\n+VanC2XY.4_EU151758 was removed because does not look like a gene, so removing its metadata\n+VanC2XY.5_EU151760 was removed because does not look like a gene, so removing its metadata\n+VanC3XY.1_AY033764 was removed because does not look like a gene, so removing its metadata\n+VanC3XY.2_EU151759 was removed because does not look like a gene, so removing its metadata\n+VanC4XY.1_EU151752 was removed because does not look like a gene, so removing its metadata\n+VanC4XY.2_EU151753 was removed because does not look like a gene, so removing its metadata\n+VanC4XY.3_EU151756 was removed because does not look like a gene, so removing its metadata\n+VanE.1_AF136925 was removed because does not look like a gene, so removing its metadata\n+VanEXY.1_FJ872411 was removed because does not look like a gene, so removing its metadata\n+VanG2XY.1_FJ872410 was removed because does not look like a gene, so removing its metadata\n+VanGXY.1_AY271782 was removed because does not look like a gene, so removing its metadata\n+VanHAX.1_FJ866609 was removed because does not look like a gene, so removing its metadata\n+VanHAX.2_M97297 was removed because does not look like a gene, so removing its metadata\n+VanHAX.PA_1_DQ018711 was removed because does not look like a gene, so removing its metadata\n+VanHAX.PT_1_DQ018710 was removed because does not look like a gene, so removing its metadata\n+VanHAX.PT_2_AY926880 was removed because does not look like a gene, so removing its metadata\n+VanHBX.1_AF192329 was removed because does not look like a gene, so removing its metadata\n+VanHBX.2_U35369 was removed because does not look like a gene, so removing its metadata\n+VanHDX.1_AF130997 was removed because does not look like a gene, so removing its metadata\n+VanHDX.2_EU999036 was removed because does not look like a gene, so removing its metadata\n+VanHDX.3_AF175293 was removed because does not look like a gene, so removing its metadata\n+VanHDX.4_AY082011 was removed because does not look like a gene, so removing its metadata\n+VanHDX.5_AY489045 was removed because does not look like a gene, so removing its metadata\n+VanHDX.6_DQ172830 was removed because does not look like a gene, so removing its metadata\n+VanHDX.7_AB242319 was removed because does not look like a gene, so removing its metadata\n+VanHFX.1_AF155139 was removed because does not look like a gene, so removing its metadata\n+VanHMX.1_FJ349556 was removed because does not look like a gene, so removing its metadata\n+VanHOX.1_KF478993 was removed because does not look like a gene, so removing its metadata\n+VanLXY.1_EU250284 was removed because does not look like a gene, so removing its metadata\n+VanNXY.1_JF802084 was removed because does not look like a gene, so removing its metadata\n+VanX.bc_1_Y15708 was removed because does not look like a gene, so removing its metadata\n+aac_6___29a.1_AF263519 was removed because does not look like a gene, so removing its metadata\n+aac_6___29b.1_AF263519 was removed because does not look like a gene, so removing its metadata\n+blaA.1_DQ424965 was removed because does not look like a gene, so removing its metadata\n+blaACC_3.1_AF180958 was removed because does not look like a gene, so removing its metadata\n+blaACT_16.1_AB737978 was removed because does not look like a gene, so removing its metadata\n+blaCMG.1_AY265892 was removed because does not look like a gene, so removing its metadata\n+blaCMY_12.1_Y16785 was removed because d'..b'0516 was removed because does not look like a gene, so removing its metadata\n+blaTEM_21.1_Y17582 was removed because does not look like a gene, so removing its metadata\n+blaTEM_22.1_Y17583 was removed because does not look like a gene, so removing its metadata\n+blaZ.52_NZ_JVWM01000127 was removed because does not look like a gene, so removing its metadata\n+blaZEG_1.1_AY265891 was removed because does not look like a gene, so removing its metadata\n+catS.1_X74948 was removed because does not look like a gene, so removing its metadata\n+dfrA29.1_AM237806 was removed because does not look like a gene, so removing its metadata\n+dldHA2X.1_AL939117 was removed because does not look like a gene, so removing its metadata\n+erm_A_.3_EU348758 was removed because does not look like a gene, so removing its metadata\n+erm_B_.22_X52632 was removed because does not look like a gene, so removing its metadata\n+erm_B_.7_AF368302 was removed because does not look like a gene, so removing its metadata\n+erm_V_.1_U59450 was removed because does not look like a gene, so removing its metadata\n+fmrO.1_Q08325 was removed because does not look like a gene, so removing its metadata\n+fomB.1_AB016934 was removed because does not look like a gene, so removing its metadata\n+fosA4.1_AB908992 was removed because does not look like a gene, so removing its metadata\n+fosA6.1_KU254579 was removed because does not look like a gene, so removing its metadata\n+mph_D_.1_AB048591 was removed because does not look like a gene, so removing its metadata\n+nimE.1_AJ244018 was removed because does not look like a gene, so removing its metadata\n+nimE.1_AM042593 was removed because does not look like a gene, so removing its metadata\n+nimF.1_AJ515145 was removed because does not look like a gene, so removing its metadata\n+nimH.1_KX576455 was removed because does not look like a gene, so removing its metadata\n+nimI.1_FJ940883 was removed because does not look like a gene, so removing its metadata\n+nimI.1_FJ940884 was removed because does not look like a gene, so removing its metadata\n+nimI.1_FJ940886 was removed because does not look like a gene, so removing its metadata\n+nimI.1_FJ940887 was removed because does not look like a gene, so removing its metadata\n+nimI.1_FJ940889 was removed because does not look like a gene, so removing its metadata\n+qnrB41.1_JN166690 was removed because does not look like a gene, so removing its metadata\n+qnrB43.1_JQ349151 was removed because does not look like a gene, so removing its metadata\n+qnrB44.1_JQ349153 was removed because does not look like a gene, so removing its metadata\n+qnrB45.1_JQ349152 was removed because does not look like a gene, so removing its metadata\n+qnrB46.1_JQ349154 was removed because does not look like a gene, so removing its metadata\n+qnrB47.1_JQ349155 was removed because does not look like a gene, so removing its metadata\n+qnrS3.1_EU077611 was removed because does not look like a gene, so removing its metadata\n+str.3_AM932524 was removed because does not look like a gene, so removing its metadata\n+sul4.1_MG649393 was removed because does not look like a gene, so removing its metadata\n+tet_E_.1_Y19116 was removed because does not look like a gene, so removing its metadata\n+tet_O_W_.1_AM889118 was removed because does not look like a gene, so removing its metadata\n+tet_O_W_.2_AM889119 was removed because does not look like a gene, so removing its metadata\n+tet_O_W_.3_AM889120 was removed because does not look like a gene, so removing its metadata\n+tet_O_W_.4_AM889121 was removed because does not look like a gene, so removing its metadata\n+tet_O_W_.5_AM889122 was removed because does not look like a gene, so removing its metadata\n+vanXmurFvanKWI.1_NZAGAF01000127 was removed because does not look like a gene, so removing its metadata\n+vanXmurFvanKWI.2_AP008230 was removed because does not look like a gene, so removing its metadata\n+vanXmurFvanWI.1_CP001336 was removed because does not look like a gene, so removing its metadata\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/resfinder.db/01.filter.check_metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/resfinder.db/01.filter.check_metadata.tsv Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b"@@ -0,0 +1,2917 @@\n+ARR_2.1_HQ141279\t1\t0\t.\t.\tOriginal name: ARR-2_1_HQ141279\n+ARR_3.1_JF806499\t1\t0\t.\t.\tOriginal name: ARR-3_1_JF806499\n+ARR_3.4_FM207631\t1\t0\t.\t.\tOriginal name: ARR-3_4_FM207631\n+ARR_4.1_EF660562\t1\t0\t.\t.\tOriginal name: ARR-4_1_EF660562\n+ARR_5.1_EF660563\t1\t0\t.\t.\tOriginal name: ARR-5_1_EF660563\n+ARR_6.1_FM955585\t1\t0\t.\t.\tOriginal name: ARR-6_1_FM955585\n+ARR_6.2_FM897214\t1\t0\t.\t.\tOriginal name: ARR-6_2_FM897214\n+ARR_6.3_JF922883\t1\t0\t.\t.\tOriginal name: ARR-6_3_JF922883\n+ARR_7.1_FN397623\t1\t0\t.\t.\tOriginal name: ARR-7_1_FN397623\n+EstDL136.1_JN242251\t1\t0\t.\t.\tOriginal name: EstDL136_1_JN242251\n+VanA.bc_1_Y15704\t1\t0\t.\t.\tOriginal name: VanA_bc_1_Y15704\n+VanC2.1_L29638\t1\t0\t.\t.\tOriginal name: VanC2_1_L29638\n+VanH.bc_1_Y15705\t1\t0\t.\t.\tOriginal name: VanH_bc_1_Y15705\n+VanXY.C2_1_AY033089\t1\t0\t.\t.\tOriginal name: VanXY_C2_1_AY033089\n+aacA43.1_HQ247816\t1\t0\t.\t.\tOriginal name: aacA43_1_HQ247816\n+aac_2___IIa.1_AB669090\t1\t0\t.\t.\tOriginal name: aac(2')-IIa_1_AB669090\n+aac_2___Ia.1_L06156\t1\t0\t.\t.\tOriginal name: aac(2')-Ia_1_L06156\n+aac_2___Ib.1_U41471\t1\t0\t.\t.\tOriginal name: aac(2')-Ib_1_U41471\n+aac_2___Ic.1_U72714\t1\t0\t.\t.\tOriginal name: aac(2')-Ic_1_U72714\n+aac_2___Id.1_U72743\t1\t0\t.\t.\tOriginal name: aac(2')-Id_1_U72743\n+aac_2___Ie.1_NC011896\t1\t0\t.\t.\tOriginal name: aac(2')-Ie_1_NC011896\n+aac_3__I.1_AJ877225\t1\t0\t.\t.\tOriginal name: aac(3)-I_1_AJ877225\n+aac_3__IIIa.1_X55652\t1\t0\t.\t.\tOriginal name: aac(3)-IIIa_1_X55652\n+aac_3__IIIb.1_L06160\t1\t0\t.\t.\tOriginal name: aac(3)-IIIb_1_L06160\n+aac_3__IIIb.2_LLLC01000048\t1\t0\t.\t.\tOriginal name: aac(3)-IIIb_2_LLLC01000048\n+aac_3__IIIc.1_L06161\t1\t0\t.\t.\tOriginal name: aac(3)-IIIc_1_L06161\n+aac_3__IIa.1_X51534\t1\t0\t.\t.\tOriginal name: aac(3)-IIa_1_X51534\n+aac_3__IIa.2_AY138987\t1\t0\t.\t.\tOriginal name: aac(3)-IIa_2_AY138987\n+aac_3__IIa.3_X13543\t1\t0\t.\t.\tOriginal name: aac(3)-IIa_3_X13543\n+aac_3__IIa.4_L22613\t1\t0\t.\t.\tOriginal name: aac(3)-IIa_4_L22613\n+aac_3__IIa.5_FJ012882\t1\t0\t.\t.\tOriginal name: aac(3)-IIa_5_FJ012882\n+aac_3__IIb.1_M97172\t1\t0\t.\t.\tOriginal name: aac(3)-IIb_1_M97172\n+aac_3__IIc.1_X54723\t1\t0\t.\t.\tOriginal name: aac(3)-IIc_1_X54723\n+aac_3__IId.1_EU022314\t1\t0\t.\t.\tOriginal name: aac(3)-IId_1_EU022314\n+aac_3__IIe.1_EU022315\t1\t0\t.\t.\tOriginal name: aac(3)-IIe_1_EU022315\n+aac_3__IV.1_DQ241380\t1\t0\t.\t.\tOriginal name: aac(3)-IV_1_DQ241380\n+aac_3__IVa.1_X01385\t1\t0\t.\t.\tOriginal name: aac(3)-IVa_1_X01385\n+aac_3__IXa.1_M55427\t1\t0\t.\t.\tOriginal name: aac(3)-IXa_1_M55427\n+aac_3__Ia.1_X15852\t1\t0\t.\t.\tOriginal name: aac(3)-Ia_1_X15852\n+aac_3__Ib.1_L06157\t1\t0\t.\t.\tOriginal name: aac(3)-Ib_1_L06157\n+aac_3__Ib_aac_6___Ib_.1_AF355189\t1\t0\t.\t.\tOriginal name: aac(3)-Ib-aac(6')-Ib'_1_AF355189\n+aac_3__Ic.1_AJ511268\t1\t0\t.\t.\tOriginal name: aac(3)-Ic_1_AJ511268\n+aac_3__Id.1_AB114632\t1\t0\t.\t.\tOriginal name: aac(3)-Id_1_AB114632\n+aac_3__If.1_AY884051\t1\t0\t.\t.\tOriginal name: aac(3)-If_1_AY884051\n+aac_3__Ig.1_CP000282\t1\t0\t.\t.\tOriginal name: aac(3)-Ig_1_CP000282\n+aac_3__Ih.1_CP000490\t1\t0\t.\t.\tOriginal name: aac(3)-Ih_1_CP000490\n+aac_3__Ii.1_CP000356\t1\t0\t.\t.\tOriginal name: aac(3)-Ii_1_CP000356\n+aac_3__VIII.1_AB211959\t1\t0\t.\t.\tOriginal name: aac(3)-VIII_1_AB211959\n+aac_3__VIII.2_AJ843080\t1\t0\t.\t.\tOriginal name: aac(3)-VIII_2_AJ843080\n+aac_3__VIII.3_AJ748131\t1\t0\t.\t.\tOriginal name: aac(3)-VIII_3_AJ748131\n+aac_3__VIIIa.1_M55426\t1\t0\t.\t.\tOriginal name: aac(3)-VIIIa_1_M55426\n+aac_3__VIIa.1_M22999\t1\t0\t.\t.\tOriginal name: aac(3)-VIIa_1_M22999\n+aac_3__VIa.1_M88012\t1\t0\t.\t.\tOriginal name: aac(3)-VIa_1_M88012\n+aac_3__VIa.2_NC_009838\t1\t0\t.\t.\tOriginal name: aac(3)-VIa_2_NC_009838\n+aac_3__XI.1_CTEG01000046\t1\t0\t.\t.\tOriginal name: aac(3)-XI_1_CTEG01000046\n+aac_3__Xa.1_AB028210\t1\t0\t.\t.\tOriginal name: aac(3)-Xa_1_AB028210\n+aac_6___30_aac_6___Ib_.1_AJ584652\t1\t0\t.\t.\tOriginal name: aac(6')-30-aac(6')-Ib'_1_AJ584652\n+aac_6___31.1_AM283489\t1\t0\t.\t.\tOriginal name: aac(6')-31_1_AM283489\n+aac_6___32.1_EF614235\t1\t0\t.\t.\tOriginal name: aac(6')-32_1_EF614235\n+aac_6___33.1_GQ337064\t1\t0\t.\t.\tOriginal name: aac(6')-33_1_GQ337064\n+aac_6___I30.1_AY289608\t1\t0\t.\t.\tOriginal name: aac(6')-I"..b'name: tet(O/W/32/O)_2_FM164392\n+tet_O_W_32_O_.5_JQ740053\t1\t0\t.\t.\tOriginal name: tet(O/W/32/O)_5_JQ740053\n+tet_O_W_32_O_W_O_.1_DQ525023\t1\t0\t.\t.\tOriginal name: tet(O/W/32/O/W/O)_1_DQ525023\n+tet_O_W_32_O_W_O_.2_DQ679926\t1\t0\t.\t.\tOriginal name: tet(O/W/32/O/W/O)_2_DQ679926\n+tet_O_W_O__1.1_AY196921\t1\t0\t.\t.\tOriginal name: tet(O/W/O)-1_1_AY196921\n+tet_O_W_O__2.1_AY196920\t1\t0\t.\t.\tOriginal name: tet(O/W/O)-2_1_AY196920\n+tet_O_W_O__3.1_EF065524\t1\t0\t.\t.\tOriginal name: tet(O/W/O)-3_1_EF065524\n+tet_O_W__1.1_AY485126\t1\t0\t.\t.\tOriginal name: tet(O/W)-1_1_AY485126\n+tet_O_W__2.1_AY485122\t1\t0\t.\t.\tOriginal name: tet(O/W)-2_1_AY485122\n+tet_Q_.1_L33696\t1\t0\t.\t.\tOriginal name: tet(Q)_1_L33696\n+tet_Q_.2_X58717\t1\t0\t.\t.\tOriginal name: tet(Q)_2_X58717\n+tet_Q_.3_U73497\t1\t0\t.\t.\tOriginal name: tet(Q)_3_U73497\n+tet_Q_.4_Z21523\t1\t0\t.\t.\tOriginal name: tet(Q)_4_Z21523\n+tet_S_.1_DQ377340\t1\t0\t.\t.\tOriginal name: tet(S)_1_DQ377340\n+tet_S_.2_L09756\t1\t0\t.\t.\tOriginal name: tet(S)_2_L09756\n+tet_S_.3_X92946\t1\t0\t.\t.\tOriginal name: tet(S)_3_X92946\n+tet_S_M_.1_HM367711\t1\t0\t.\t.\tOriginal name: tet(S/M)_1_HM367711\n+tet_S_M_.2_AY534326\t1\t0\t.\t.\tOriginal name: tet(S/M)_2_AY534326\n+tet_T_.1_L42544\t1\t0\t.\t.\tOriginal name: tet(T)_1_L42544\n+tet_T_.2_AY660530\t1\t0\t.\t.\tOriginal name: tet(T)_2_AY660530\n+tet_V_.1_AF030344\t1\t0\t.\t.\tOriginal name: tet(V)_1_AF030344\n+tet_W_.1_DQ060146\t1\t0\t.\t.\tOriginal name: tet(W)_1_DQ060146\n+tet_W_.2_AY049983\t1\t0\t.\t.\tOriginal name: tet(W)_2_AY049983\n+tet_W_.3_AJ427421\t1\t0\t.\t.\tOriginal name: tet(W)_3_AJ427421\n+tet_W_.4_FN396364\t1\t0\t.\t.\tOriginal name: tet(W)_4_FN396364\n+tet_W_.5_AJ427422\t1\t0\t.\t.\tOriginal name: tet(W)_5_AJ427422\n+tet_W_32_O_.1_AM710601\t1\t0\t.\t.\tOriginal name: tet(W/32/O)_1_AM710601\n+tet_W_32_O_.2_AM710602\t1\t0\t.\t.\tOriginal name: tet(W/32/O)_2_AM710602\n+tet_W_32_O_.3_AM710603\t1\t0\t.\t.\tOriginal name: tet(W/32/O)_3_AM710603\n+tet_W_32_O_.4_AM710605\t1\t0\t.\t.\tOriginal name: tet(W/32/O)_4_AM710605\n+tet_X_.1_GU014535\t1\t0\t.\t.\tOriginal name: tet(X)_1_GU014535\n+tet_X_.2_M37699\t1\t0\t.\t.\tOriginal name: tet(X)_2_M37699\n+tet_X_.3_AB097942\t1\t0\t.\t.\tOriginal name: tet(X)_3_AB097942\n+tet_Y_.1_EF495198\t1\t0\t.\t.\tOriginal name: tet(Y)_1_EF495198\n+tet_Y_.2_AB089606\t1\t0\t.\t.\tOriginal name: tet(Y)_2_AB089606\n+tet_Z_.1_AF121000\t1\t0\t.\t.\tOriginal name: tet(Z)_1_AF121000\n+tlr_C_.1_M57437\t1\t0\t.\t.\tOriginal name: tlr(C)_1_M57437\n+tva_A_.1_ENA_SOX29786\t1\t0\t.\t.\tOriginal name: tva(A)_1_ENA_SOX29786\n+vat_A_.1_L07778\t1\t0\t.\t.\tOriginal name: vat(A)_1_L07778\n+vat_B_.1_U19459\t1\t0\t.\t.\tOriginal name: vat(B)_1_U19459\n+vat_C_.1_AF015628\t1\t0\t.\t.\tOriginal name: vat(C)_1_AF015628\n+vat_D_.1_L12033\t1\t0\t.\t.\tOriginal name: vat(D)_1_L12033\n+vat_E_.10_AY043212\t1\t0\t.\t.\tOriginal name: vat(E)_10_AY043212\n+vat_E_.11_AY043213\t1\t0\t.\t.\tOriginal name: vat(E)_11_AY043213\n+vat_E_.3_AF153312\t1\t0\t.\t.\tOriginal name: vat(E)_3_AF153312\n+vat_E_.5_AJ488494\t1\t0\t.\t.\tOriginal name: vat(E)_5_AJ488494\n+vat_E_.7_AY043211\t1\t0\t.\t.\tOriginal name: vat(E)_7_AY043211\n+vat_E_.8_AY043209\t1\t0\t.\t.\tOriginal name: vat(E)_8_AY043209\n+vat_E_.9_AY043210\t1\t0\t.\t.\tOriginal name: vat(E)_9_AY043210\n+vat_F_.1_AF170730\t1\t0\t.\t.\tOriginal name: vat(F)_1_AF170730\n+vat_H_.1_GQ205627\t1\t0\t.\t.\tOriginal name: vat(H)_1_GQ205627\n+vga_A_.1_M90056\t1\t0\t.\t.\tOriginal name: vga(A)_1_M90056\n+vga_A_.2_FN546261\t1\t0\t.\t.\tOriginal name: vga(A)_2_FN546261\n+vga_A_.3_JQ312422\t1\t0\t.\t.\tOriginal name: vga(A)_3_JQ312422\n+vga_A_LC.1_GQ891882\t1\t0\t.\t.\tOriginal name: vga(A)LC_1_GQ891882\n+vga_A_LC.2_DQ823382\t1\t0\t.\t.\tOriginal name: vga(A)LC_2_DQ823382\n+vga_A_LC.3_FN806791\t1\t0\t.\t.\tOriginal name: vga(A)LC_3_FN806791\n+vga_A_LC.4_JQ312423\t1\t0\t.\t.\tOriginal name: vga(A)LC_4_JQ312423\n+vga_A_V.1_AF186237\t1\t0\t.\t.\tOriginal name: vga(A)V_1_AF186237\n+vga_B_.1_U82085\t1\t0\t.\t.\tOriginal name: vga(B)_1_U82085\n+vga_C_.1_FN806792\t1\t0\t.\t.\tOriginal name: vga(C)_1_FN806792\n+vga_D_.1_GQ205627\t1\t0\t.\t.\tOriginal name: vga(D)_1_GQ205627\n+vga_E_.1_FR772051\t1\t0\t.\t.\tOriginal name: vga(E)_1_FR772051\n+vgb_A_.1_M20129\t1\t0\t.\t.\tOriginal name: vgb(A)_1_M20129\n+vgb_B_.1_AF015628\t1\t0\t.\t.\tOriginal name: vgb(B)_1_AF015628\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/resfinder.db/02.cdhit.all.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/resfinder.db/02.cdhit.all.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,48245 @@\n+>ARR_2.1_HQ141279\n+ATGGTAAAAGATTGGATTCCCATCTCTCATGATAATTACAAGCAGGTGCAAGGACCGTTC\n+TATCATGGAACCAAAGCCAATTTGGCGATTGGTGACTTGCTAACCACAGGGTTCATCTCT\n+CATTTCGAGGACGGTCGTATTCTTAAGCACATCTACTTTTCAGCCTTGATGGAGCCAGCA\n+GTTTGGGGAGCTGAACTTGCTATGTCACTGTCTGGCCTCGAGGGTCGCGGCTACATATAC\n+ATAGTTGAGCCAACAGGACCGTTCGAAGACGATCCGAATCTTACGAACAAAAAATTTCCC\n+GGTAATCCAACACAGTCCTATAGAACCTGCGAACCCTTGAGAATTGTTGGCGTTGTTGAA\n+GACTGGGAGGGGCATCCTGTTGAATTAATAAGGGGAATGTTGGATTCGTTAGAGGACTTA\n+AAGCGCCGTGGTTTACACGTCATTGAAGACTAG\n+>ARR_3.1_JF806499\n+ATGGTAAAAGATTGGATTCCCATCTCTCATGATAATTACAAGCAGGTGCAAGGACCGTTC\n+TATCATGGAACCAAAGCCAATTTGGCGATTGGTGACTTGCTAACCACAGGGTTCATCTCT\n+CATTTCGAGGACGGTCGTATTCTTAAGCACATCTACTTTTCAGCCTTGATGGAGCCAGCA\n+GTTTGGGGAGCTGAACTTGCTATGTCACTGTCTGGCCTCGAGGGTCGCGGCTACATATAC\n+ATAGTTGAGCCAACAGGACCGTTCGAAGACGATCCGAATCTTACGAACAAAAGATTTCCC\n+GGTAATCCAACACAGTCCTATAGAACCTGCGAACCCTTGAGAATTGTTGGCGTTGTTGAA\n+GACTGGGAGGGGCATCCTGTTGAATTAATAAGGGGAATGTTGGATTCGTTGGAGGACTTA\n+AAGCGCCGTGGTTTACACGTCATTGAAGACTAG\n+>ARR_3.4_FM207631\n+ATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTATGC\n+AGCCAAATCCCAACAATTAAGGGTCTTAAAATGGTAAAAGATTGGATTCCCATCTCTCAT\n+GATAATTACAAGCAGGTGCAAGGACCGTTCTATCATGGAACCAAAGCCAATTTGGCGATT\n+GGTGACTTGCTAACCACAGGGTTCATCTTTCATTTCGAGGACGGTCGTATTCTTAAGCAC\n+ATCTACTTTTCAGCCTTGATGGAGCCAGCAGTTTGGGGAGCTGAACTTGCTATGTCACTG\n+TCTGGCCTCGAGGGTCGCGGCTACATATACATAGTTGAGCCAACAGGACCGTTCGAAGAC\n+GATCCGAATCTTACGAACAAAAAATTTCCCGGTAATCCAACACAGTCCTATAGAACCTGC\n+GAACCCTTGAGAATTGTTGGCGTTGTTGAAGACTGGGAGGGGCATCCTGTTGAATTAATA\n+AGGGGAATGTTGGATTCGTTAGAGGACTTAAAGCGCCGTGGTTTACACGTCATTGAAGAC\n+TAG\n+>ARR_4.1_EF660562\n+ATGACGAATGACTGGATTCCCACTTCGCATGACAACTGCTCGCAAGTAGCGGGGCCGTTC\n+TATCACGGCACCAAAGCCAAACTCACGGTTGGTGACTTGCTTTCCCCAGGACACCCGTCT\n+CACTTTGAGCAAGGTCGCAAGCTCAAACACATCTACTTTGCCGCCCTGATGGAACCAGCC\n+ATCTGGGGAGCGGAGCTTGCGATGTCGCTGTCAAGCCTAGAGGGGCGCGGCCACATCTAC\n+ATCGTTGAACCGCTCGGCCCATTTGAGGACGACCCGAACCTTACAAACAAGAAATTCCCG\n+GGAAATCCAACCAAGTCCTATCGCACCACTGAGCCGCTGCGGATTGTTGGGATCGTAGAA\n+GACTGGCAAGGCCACTCACCGGAGGTGTTACAGGGCATGTTGGCGTCTCTGGAGGATCTT\n+CAGCGTCGTGGCCTCGCCATCATTGAGGACTAA\n+>ARR_5.1_EF660563\n+ATGACGGTAGACTGGATCCCCATTTCGCACGACAACTACCATCAAGTGCGTGGCCCGTTT\n+TATCACGGAACAAAAGCCGAACTCGCCATTGGCGACTTAATTTCAACCGGATTTATTTCT\n+CACTTTGAGCGGGACAGAGCACTAAAGCATGTGTACTTTTCCGCGCTGATGGAGCCAGCA\n+ATCTGGGGGGCCGAGCTCGCTGTAGCACTCTCTGGCTCTGACGGGCCAGGCCATATTTAC\n+ATCATTGAGCCAACCGGCCCGTTTGAAGACGACCCCAATCTCACAAACAAACGATTCCCT\n+GGCAATCCAACACAGTCCTATCGCACATGCCACCCACTTAAAATTGTTGGCATACTGCGG\n+GAGTGGGAGCGCCATTCTCCTGAAGCATTGAAGACCATGCTAGATTCTCTGGCAGACCTC\n+AAGCGACGCGGCTTGGCCATCATTGAAGAATGA\n+>ARR_6.1_FM955585\n+ATGTCGAGTGACTGGACTCCCATCTCACATGAGAATTGCCAGCAGGTGCGTGGGCCGTTC\n+TATCACGGCACCAAAGCCCATCTATCGATTGGCGACTTGATAACAACTGGGCATCTCTCC\n+CACTTTGAAGATGGACGCGCTCTTAAACACGTCTACTTTTCAGCTTTGATGGAGCCTGCC\n+ATTTGGGGGGCGGAACTTGCAATGTCGTTGTCACGCCTAGATGGCCGTGGCTACATATAC\n+ATCGTCGAACCAACTGGACCGTTTGAGGACGACCCGAATCTTACGAACAAAAGATTTCCT\n+GGAAATCCAACAAAGTCCTATCGCACGTGCGATCCGCTACGAATTGTCGGGTCAGTCGAA\n+GACTGGCAAGGGCATCCCGCTGATGTGCTGCAACAGATGTTGGAGTCTTTAGAGGACCTA\n+GAGCGCCGTGGTCTTGCCATCATCGAGGATTAG\n+>ARR_6.2_FM897214\n+ATGTCGAGTGACTGGACTCCCATCTCACATGAGAATTGCCAGCAGGTGCGTGGGCCGTTC\n+TATCACGGCACCAAAGCCCATCTATCGATTGGCGACTTGATAACAACTGGGCATCTCTCC\n+CACTTTGAAGATGGACGCGCTCTTAAACACGTCTACTTTTCAGCTTTGATGGAGCCTGCC\n+ATTTGGGGGGCGGAACTTGCAATGTCGTTGTCACGCCTAGATGGCCGTGGCTACATATAC\n+ATCGTCGAACCAACTGGACCGTTTGAGGACGACCCGAATCTTACGAACAAAAGATTTCCT\n+GGAAATCCAACAAAGTCCTATCGCACGTGCGATCCGCTACGAATTGTCGGGTCAGTCGAA\n+GACTGGCAAGGGCATCCCGCTGATGTGCTGCAACAGATGTTGGAGTCTTTAGAGGACCTA\n+AAGCGCCGTGGTCTTGCCATCATCGAGGATTAG\n+>ARR_6.3_JF922883\n+ATGGTAAAAGATTGGATTCCCATCTCTCATGATAATTACAAGCAGGTGCAAGGACCGTTC\n+TATCATGGAACCAAAGCCAATTTGGCGATTGGTGACTTGCTAACCACAGGGTTCATCTCT\n+CATTTCGAGGACGGTCGTATTCTTAAGCACATCTACTTTTCAGCCTTGATGGAGCCAGCA\n+GTTTGGGGAGCTGAACTTGCTATGTCACTGTCTGGCCTCGAGGGTCGCGGCTACATATAC\n+ATAGTTGAGCCAACAGGACCGTTCGAAGACGATCCGAATCTTACGAACAAAAGATTTCCC\n+GGTAATCCAACACAGTCCTATAGAACCTGCGAACCCTTGAGAATTGTTGGCGTTGTTGAA\n+GACTGGGAGGGGCATCCTGTTGAATTAATAAGGGGAATGTTGGATTCGTTAGAGGACTTA\n+AAGCGCCGTGGTTTA'..b'AAGGAAGTT\n+CAAGTCCTAAGTGGTGGGGAACGTGTGAAGGTTGCTTTTGCAAAACTATTTGTTAGCGAC\n+TATAATACGTTGATTCTGGATGAACCAACAAATTATTTAGACATTGATGCCATAGAAGCG\n+TTAGAGGAGCTCCTAATTAACTATGAGGGGGCAGTACTATTTGTATCTCATGATTGTCGT\n+TTCGTTCAAAATATTGCATCCAAAATTATTGAACTATCCGACCAGAAGGTTATAGAGTTT\n+CTTGGAAGCTATAAAGCGTTTAGAGAAAGATCTCAAGAGACAGAGCGTGACTATATGAAG\n+GAAGAACTTCTTAAAATTGAGATCAAACTCACTCAAATGATTAGTGAAATGAATGACGAG\n+GCATCAAATGAATTAGAAAAAGAATTCCAAATGTTGATTCATGAACGTAATCAGTTAAGA\n+AATCAAGTAAACAATTAG\n+>vga_E_.1_FR772051\n+ATGTTATTATTTGAAGGTACATCATTGAAAAAACACATACAAGACAGATTATTATTTGAT\n+ATAGATTTAATACAAGTACATGAACATCAGCGAATAGGATTAGTAGGTAGGAATGGAACG\n+GGGAAAACAAGTCTATTAAAAATTATTACAGGTGAAGAACTAGTTGATGGAGGGAATGTT\n+AATCATTTTACCTCTGTAAAATTAGTACCACAATTTAAAGAAACAAGATCGGAGAAAAGT\n+GGTGGAGAAATAACGCAACAATATTTGCAATTAGCATTTAATGAAAAGCCAGGATTATTA\n+ATTTTAGATGAACCAACGACTCATTTAGATACACAAAGAATTGATTGGTTAGAAAAGAAA\n+TTAGCAAACTATCAAGGAGCATTTGTTGTCGTATCACATGATCGGACATTTCTAAATAAT\n+GTGTGTACTGAAATATGGGAAATAGAAGATGGTAGTCTAAACGCGTTTAAAGGGGATTAT\n+AATGCTTATGCGGAACAAAAGGAATTAATAAAAACACAGCAGCAGATTGCATTTGAAAAG\n+TACGAACGAGAGAAAAAGCAATTAGAAAAAGCAATACGACAAAAAGAGGAAAGAGCACAG\n+CGAGCAACAAAGAAACCTAAAAATCTGAGTTCTTCAGAGGCAAGAATAACAGGAGCTAAA\n+ACCCATTATGCCAATATACAGAAAAAGTTGAGGGGTTCTGCAAAAGCATTAGAAACAAGG\n+TTGGAACAACTGGATAGGATTGACAAGGTGAAAGAACTACCTGAAATTAAGATGGATATA\n+TTAAATAAAGAAAGTCTAACAAACCAGTCTGTGTTACGCGCTGAAAACATTAAGGGAGAG\n+GTTGACGGACGTAAGCTTTGGAATCCCTTTAGTTTATATTTATATGGCGGCGATAAAGTT\n+GCTATCATTGGGAAAAATGGCACGGGTAAAACAACCTTACTTAAAAAAATAGTTGAGCGA\n+GATGAAAGAATAGCAATCCCAGAAAAGGTGAGGATAGGTTATTTTTCCCAACACCTCACA\n+ATTCTCGATGATGATAAAACAATCATAGAAAATATACAATTGACCTCTAGTCAGGATGAA\n+ACATTAATTAGAACAGTTTTAGCAAGAATGCATTTTTGGGATGAAGATGTCTATAAAAAG\n+GTCGGCATATTAAGTGGTGGTGAAAAAGTAAAAGTAGCACTAGCTAAACTATTCTTAAGT\n+GACGTGAATATGCTGGTGTTAGATGAACCTACAAATTTTTTAGATATTGAATCTTTAGAA\n+GCGCTAGAAACATTAATGAAAAGTTATCATGGAACGATTCTATTTGTTACTCACGACCGA\n+ACGTTAGTAACAAATATAGCTACAAAAATAATTGATATAAAAGATGGTAAGATAACAGTA\n+TTCGATGGATCATACGAAGCATATGAAGAGTGGTTAGAGAATCAAACAAAGTCCAACAAT\n+GATGATCAACTTTTACTAATCGAAACTAAAATATCTGACGTTCTGGGTAGGTTGAGTTTG\n+GAGCCTTCACGAGAGTTAGAAGATGAATTTCAAAGATTATTGAAAGAAAAGAAAGAACTG\n+ACTAAAAAACTATAA\n+>vgb_A_.1_M20129\n+ATGGAATTTAAATTACAAGAATTAAATCTTACTAACCAAGATACAGGACCATATGGTATA\n+ACCGTTTCAGATAAGGGGAAAGTTTGGATTACACAACATAAAGCAAATATGATAAGTTGC\n+ATCAATTTAGATGGAAAAATTACAGAGTACCCACTACCGACACCAGATGCAAAAGTCATG\n+TGTTTAACTATATCCTCAGATGGGGAAGTTTGGTTTACTGAGAATGCAGCAAACAAAATA\n+GGGAGGATTACAAAAAAAGGGATTATTAAGGAATATACATTGCCTAACCCAGATTCAGCA\n+CCCTACGGTATTACAGAAGGACCAAATGGAGATATATGGTTTACAGAAATGAATGGCAAC\n+CGTATTGGACGTATTACGGACGACGGTAAAATTCGTGAATACGAGCTGCCTAATAAAGGA\n+TCTTACCCTTCTTTTATCACTTTGGGTTCTGATAATGCCCTGTGGTTCACAGAAAATCAA\n+AATAATGCTATTGGTAGAATTACAGAAAGTGGGGATATTACAGAGTTTAAAATTCCTACA\n+CCTGCATCAGGACCAGTTGGTATTACAAAGGGGAACGACGATGCTTTATGGTTTGTGGAA\n+ATTATCGGTAATAAGATAGGGCGAATAACTCCTCTGGGGGAAATTACCGAATTCAAAATT\n+CCAACGCCAAACGCTCGACCTCATGCAATTACTGCTGGAGCAGGAATTGATTTATGGTTT\n+ACTGAATGGGGGGCTAATAAAATAGGAAGGCTGACAAGCAATAATATAATTGAGGAATAC\n+CCAATTCAAATCAAAAGTGCTGAACCACATGGCATTTGTTTCGATGGTGAAACAATTTGG\n+TTTGCAATGGAGTGTGACAAGATAGGCAAATTAACTCTCATTAAGGATAATATGGAGTGA\n+>vgb_B_.1_AF015628\n+ATGAATTTTTATTTAGAGGAGTTTAACTTGTCTATTCCCGATTCAGGTCCATACGGTATA\n+ACTTCATCAGAAGACGGAAAGGTATGGTTCACACAACATAAGGCAAACAAAATCAGCAGT\n+CTAGATCAGAGTGGTAGGATAAAAGAATTCGAAGTTCCTACCCCTGATGCTAAAGTGATG\n+TGTTTAATTGTATCTTCACTTGGAGACATATGGTTTACAGAGAATGGTGCAAATAAAATC\n+GGAAAGCTCTCAAAAAAAGGTGGCTTTACAGAATATCCATTGCCACAGCCGGATTCTGGT\n+CCTTACGGAATAACGGAAGGTCTAAATGGCGATATATGGTTTACCCAATTGAATGGAGAT\n+CGTATAGGAAAGTTGACAGCTGATGGGACTATTTATGAATATGATTTGCCAAATAAGGGA\n+TCTTATCCTGCTTTTATTACTTTAGGTTCGGATAACGCACTTTGGTTCACGGAGAACCAA\n+AATAATTCTATTGGAAGGATTACAAATACAGGGAAATTAGAAGAATATCCTCTACCAACA\n+AATGCAGCGGCTCCAGTGGGTATCACTAGTGGTAACGATGGTGCACTCTGGTTTGTCGAA\n+ATTATGGGCAACAAAATAGGTCGAATCACTACAACTGGTGAGATTAGCGAATATGATATT\n+CCAACTCCAAACGCACGTCCACACGCTATAACCGCGGGGAAAAATAGCGAAATATGGTTT\n+ACTGAATGGGGGGCAAATCAAATCGGCAGAATTACAAACGACAAAACAATTCAAGAATAT\n+CAACTTCAAACAGAAAATGCGGAACCTCATGGTATTACCTTTGGAAAAGATGGATCCGTA\n+TGGTTTGCATTAAAATGTAAAATTGGGAAGCTGAATTTGAACGAATGA\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/resfinder.db/02.cdhit.clusters.pickle |
| b |
| Binary file tool-data/resfinder.db/02.cdhit.clusters.pickle has changed |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/resfinder.db/02.cdhit.clusters.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/resfinder.db/02.cdhit.clusters.tsv Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,652 @@\n+ARR_-\tARR_2.1_HQ141279\tARR_3.1_JF806499\tARR_3.4_FM207631\tARR_6.3_JF922883\n+ARR_4\tARR_4.1_EF660562\n+ARR_5\tARR_5.1_EF660563\n+ARR_6\tARR_6.1_FM955585\tARR_6.2_FM897214\n+ARR_7\tARR_7.1_FN397623\n+EstDL136\tEstDL136.1_JN242251\n+VanA\tVanA.bc_1_Y15704\n+VanC2\tVanC2.1_L29638\n+VanH\tVanH.bc_1_Y15705\n+VanXY\tVanXY.C2_1_AY033089\n+aacA43\taacA43.1_HQ247816\n+aac_2___IIa\taac_2___IIa.1_AB669090\n+aac_2___Ia\taac_2___Ia.1_L06156\n+aac_2___Ib\taac_2___Ib.1_U41471\n+aac_2___Ic\taac_2___Ic.1_U72714\n+aac_2___Id\taac_2___Id.1_U72743\n+aac_2___Ie\taac_2___Ie.1_NC011896\n+aac_3__I-\taac_3__I.1_AJ877225\taac_3__Ia.1_X15852\n+aac_3__II-\taac_3__IIa.1_X51534\taac_3__IIa.2_AY138987\taac_3__IIa.3_X13543\taac_3__IIa.4_L22613\taac_3__IIa.5_FJ012882\taac_3__IIc.1_X54723\taac_3__IId.1_EU022314\taac_3__IIe.1_EU022315\n+aac_3__IIIa\taac_3__IIIa.1_X55652\n+aac_3__IIIb\taac_3__IIIb.1_L06160\taac_3__IIIb.2_LLLC01000048\n+aac_3__IIIc\taac_3__IIIc.1_L06161\n+aac_3__IIb\taac_3__IIb.1_M97172\n+aac_3__IV-\taac_3__IV.1_DQ241380\taac_3__IVa.1_X01385\n+aac_3__IXa\taac_3__IXa.1_M55427\n+aac_3__Ib\taac_3__Ib.1_L06157\n+aac_3__Ib_aac_6___Ib_\taac_3__Ib_aac_6___Ib_.1_AF355189\n+aac_3__Ic\taac_3__Ic.1_AJ511268\n+aac_3__Id\taac_3__Id.1_AB114632\n+aac_3__If\taac_3__If.1_AY884051\n+aac_3__Ig\taac_3__Ig.1_CP000282\n+aac_3__Ih\taac_3__Ih.1_CP000490\n+aac_3__Ii\taac_3__Ii.1_CP000356\n+aac_3__VIII\taac_3__VIII.3_AJ748131\n+aac_3__VIII-\taac_3__VIII.1_AB211959\taac_3__VIII.2_AJ843080\taac_3__VIIIa.1_M55426\n+aac_3__VIIa\taac_3__VIIa.1_M22999\n+aac_3__VIa\taac_3__VIa.1_M88012\taac_3__VIa.2_NC_009838\n+aac_3__XI\taac_3__XI.1_CTEG01000046\n+aac_3__Xa\taac_3__Xa.1_AB028210\n+aac_6___-\taac_6___33.1_GQ337064\taac_6___I30.1_AY289608\n+aac_6___30_aac_6___Ib_\taac_6___30_aac_6___Ib_.1_AJ584652\n+aac_6___31\taac_6___31.1_AM283489\n+aac_6___32\taac_6___32.1_EF614235\n+aac_6___I-\taac_6___Iaf.1_AB462903\taac_6___Ip.1_Z54241\taac_6___Iq.1_AF047556\n+aac_6___I-_1\taac_6___Ih.1_L29044\taac_6___Ih.2_KT778788\taac_6___It.1_AF031328\taac_6___Iv.1_AF031330\n+aac_6___I-_2\taac_6___Is.1_AF031327\taac_6___Iu.1_AF031329\taac_6___Ix.1_AF031332\n+aac_6___IIa\taac_6___IIa.1_M29695\n+aac_6___IIb\taac_6___IIb.1_L06163\n+aac_6___IIc\taac_6___IIc.1_NC_012555\n+aac_6___Ia\taac_6___Ia.1_M18967\taac_6___Ia.2_M86913\n+aac_6___Iaa\taac_6___Iaa.1_NC_003197\n+aac_6___Iad\taac_6___Iad.1_AB119105\n+aac_6___Iae\taac_6___Iae.1_AB104852\n+aac_6___Iag\taac_6___Iag.1_AB472901\n+aac_6___Iai\taac_6___Iai.1_EU886977\n+aac_6___Iaj\taac_6___Iaj.1_AB709942\n+aac_6___Iak\taac_6___Iak.1_AB894482\n+aac_6___Ian\taac_6___Ian.1_AP014611\n+aac_6___Ib_cr+\taac_6___Ib.1_M21682\taac_6___Ib.2_M23634\taac_6___Ib11.1_AY136758\taac_6___Ib3.1_X60321\taac_6___Ib_Hangzhou.1_FJ503047\taac_6___Ib_Suzhou.1_EU085533\taac_6___Ib_cr.1_DQ303918\taac_6___Ib_cr.1_DQ303918_2\taac_6___Ib_cr.2_EF636461\taac_6___Ib_cr.2_EF636461_2\taadA10.2_AM087405\taadA11.1_AY144590\taadA6.1_AF140629\tant_3____Ii_aac_6___IId.1_AF453998\n+aac_6___Ic\taac_6___Ic.1_M94066\n+aac_6___If\taac_6___If.1_X55353\n+aac_6___Ig\taac_6___Ig.1_L09246\n+aac_6___Ii\taac_6___Ii.1_L12710\n+aac_6___Iid\taac_6___Iid.1_AJ584700\n+aac_6___Iih\taac_6___Iih.1_AJ584701\n+aac_6___Ij\taac_6___Ij.1_L29045\n+aac_6___Ik\taac_6___Ik.1_L29510\n+aac_6___Il\taac_6___Il.1_U13880\n+aac_6___Im\taac_6___Im.1_AF337947\n+aac_6___Ir\taac_6___Ir.1_AF031326\n+aac_6___Isa\taac_6___Isa.1_AB116646\n+aac_6___Iw\taac_6___Iw.1_AF031331\n+aac_6___Iz\taac_6___Iz.1_AF140221\taac_6___Iz.2_AB971834\n+aadA-\taadA11.2_AJ567827\taadA12.1_AY665771\taadA15.1_DQ393783\taadA17.1_FJ460181\taadA2.1_NC_010870\taadA2.2_JQ364967\taadA2b.1_D43625\taadA3.1_AF047479\n+aadA-_1\taadA4.1_Z50802\taadA5.1_AF137361\n+aadA1+\taadA1.2_FJ591054\taadA1.3_JQ414041\taadA1.4_JQ480156\taadA1.5_JX185132\taadA1b.1_M95287\taadA21.1_AY171244\taadA22.1_AM261837\taadA23.1_AJ809407\taadA24.1_AM711129\taadA24.1_DQ677333\taadA8.1_AF326210\taadA8b.1_AY139603\taadA8b.2_AM040708\tant_3____Ia.1_X02340\n+aadA10\taadA10.1_U37105\n+aadA13\taadA13.1_AY713504\taadA13.2_NC010643\n+aadA14\taadA14.1_AJ884726\n+aadA16\taadA16.1_EU675686\n+aadA7\taadA7.1_AF224733\taadA7.2_AB114632\n+aadA9\taadA9.1_AJ420072\n+aadD\taadD.1_AF181950\taadD.2_M19465\taadD.2_M19465_2\n+aadE_'..b'497970\tsul2.13_AJ289135\tsul2.14_AJ514834\tsul2.15_FJ968160\tsul2.17_U57647\tsul2.18_AJ830714\tsul2.19_AJ319822\tsul2.1_AF542061\tsul2.20_AJ830710\tsul2.21_AB366440\tsul2.2_AY034138\tsul2.3_HQ840942\tsul2.5_AY524415\tsul2.6_FN995456\tsul2.7_HM486907\tsul2.8_AJ877041\tsul2.9_FJ197818\n+sul3\tsul3.2_AJ459418\n+tcr3\ttcr3.1_D38215\n+tet\ttet.1_M74049\n+tetA_46_\ttetA_46_.1_HQ652506\n+tetA_60_\ttetA_60_.1_KX000272\n+tetA_P_\ttetA_P_.1_AB054980\ttetA_P_.2_L20800\ttetA_P_.3_AB001076\n+tetB_46_\ttetB_46_.1_HQ652506\n+tetB_60_\ttetB_60_.1_KX000273\n+tetB_P_\ttetB_P_.1_NC_010937\n+tet_-\ttet_M_.10_EU182585\ttet_M_.11_JN846696\ttet_M_.12_FR671418\ttet_M_.13_AM990992\ttet_M_.1_X92947\ttet_M_.2_X90939\ttet_M_.3_U08812\ttet_M_.4_X75073\ttet_M_.5_U58985\ttet_M_.6_M21136\ttet_M_.7_FN433596\ttet_M_.8_X04388\ttet_M_.9_X56353\ttet_S_M_.1_HM367711\n+tet_-_1\ttet_O_W_32_O_.1_EF065523\ttet_O_W_32_O_.2_FM164392\ttet_O_W_32_O_.5_JQ740053\ttet_O_W_32_O_W_O_.1_DQ525023\ttet_O_W_32_O_W_O_.2_DQ679926\ttet_O_W_O__1.1_AY196921\ttet_W_32_O_.1_AM710601\ttet_W_32_O_.2_AM710602\ttet_W_32_O_.3_AM710603\ttet_W_32_O_.4_AM710605\n+tet_-_2\ttet_O_W_O__2.1_AY196920\ttet_O_W_O__3.1_EF065524\ttet_O_W__1.1_AY485126\ttet_O_W__2.1_AY485122\ttet_W_.1_DQ060146\n+tet_30_\ttet_30_.1_AF090987\n+tet_31_\ttet_31_.1_GQ283908\ttet_31_.2_AJ250203\n+tet_32_\ttet_32_.1_EU722333\ttet_32_.2_EF626943\n+tet_33_\ttet_33_.1_AY255627\ttet_33_.2_DQ390458\n+tet_34_\ttet_34_.1_AB061440\n+tet_35_\ttet_35_.1_AF353562\n+tet_36_\ttet_36_.1_AJ514254\n+tet_37_\ttet_37_.1_AF540889\n+tet_39_\ttet_39_.1_KT346360\n+tet_40_\ttet_40_.1_FJ158002\ttet_40_.2_AM419751\n+tet_41_\ttet_41_.1_AY264780\n+tet_42_\ttet_42_.1_EU523697\n+tet_43_\ttet_43_.1_GQ244501\n+tet_44_\ttet_44_.1_NZ_ABDU01000081\ttet_44_.2_FN594949\n+tet_45_\ttet_45_.1_JF837331\n+tet_47_\ttet_47_.1_KR857681\n+tet_48_\ttet_48_.1_KR857682\n+tet_49_\ttet_49_.1_KR857683\n+tet_50_\ttet_50_.1_KR857684\n+tet_51_\ttet_51_.1_KR857685\n+tet_52_\ttet_52_.1_KR857686\n+tet_53_\ttet_53_.1_KR857687\n+tet_54_\ttet_54_.1_KR857688\n+tet_55_\ttet_55_.1_KR857689\n+tet_57_\ttet_57_.1_KP137702\n+tet_59_\ttet_59_.1_KU736878\n+tet_A_\ttet_A_.1_AJ313332\ttet_A_.2_X00006\ttet_A_.3_AY196695\ttet_A_.4_AJ517790\ttet_A_.5_AJ419171\ttet_A_.6_AF534183\n+tet_B_\ttet_B_.1_AP000342\ttet_B_.2_AF326777\ttet_B_.3_AJ277653\n+tet_C_\ttet_C_.1_NC_003123\ttet_C_.2_AY046276\ttet_C_.3_AF055345\n+tet_D_\ttet_D_.1_AF467077\ttet_D_.2_X65876\n+tet_E_\ttet_E_.2_L06940\ttet_E_.3_CP000645\n+tet_G_\ttet_G_.1_AF133139\ttet_G_.2_AF133140\ttet_G_.3_S52437\n+tet_H_\ttet_H_.1_Y16103\ttet_H_.2_AJ245947\ttet_H_.3_Y15510\ttet_H_.4_U00792\n+tet_J_\ttet_J_.1_ACLE01000065\ttet_J_.2_AF038993\n+tet_K_\ttet_K_.1_U38656\ttet_K_.2_J01764\n+tet_L_\ttet_L_.1_HM235948\n+tet_L__1\ttet_L_.2_M29725\ttet_L_.3_M11036\ttet_L_.4_D00006\ttet_L_.7_X60828\ttet_L_.8_AY081910\n+tet_L__2\ttet_L_.5_X08034\ttet_L_.6_D12567\n+tet_O_-\ttet_O_.1_M18896\ttet_O_.2_M20925\ttet_O_.3_Y07780\ttet_O_32_O_.3_NZ_AUJS01000017\ttet_O_32_O_.4_AIOQ01000025\ttet_O_32_O_.5_FP929050\n+tet_O_32_O_\ttet_O_32_O_.1_JQ740052\ttet_O_32_O_.2_AJ295238\n+tet_Q_\ttet_Q_.1_L33696\ttet_Q_.2_X58717\ttet_Q_.3_U73497\ttet_Q_.4_Z21523\n+tet_S_-\ttet_S_.1_DQ377340\ttet_S_.2_L09756\ttet_S_.3_X92946\ttet_S_M_.2_AY534326\n+tet_T_\ttet_T_.1_L42544\ttet_T_.2_AY660530\n+tet_V_\ttet_V_.1_AF030344\n+tet_W_\ttet_W_.2_AY049983\ttet_W_.3_AJ427421\ttet_W_.4_FN396364\ttet_W_.5_AJ427422\n+tet_X_\ttet_X_.1_GU014535\ttet_X_.2_M37699\n+tet_X__1\ttet_X_.3_AB097942\n+tet_Y_\ttet_Y_.1_EF495198\ttet_Y_.2_AB089606\n+tet_Z_\ttet_Z_.1_AF121000\n+tlr_C_\ttlr_C_.1_M57437\n+tva_A_\ttva_A_.1_ENA_SOX29786\n+vat_A_\tvat_A_.1_L07778\n+vat_B_\tvat_B_.1_U19459\n+vat_C_\tvat_C_.1_AF015628\n+vat_D_\tvat_D_.1_L12033\n+vat_E_\tvat_E_.10_AY043212\tvat_E_.11_AY043213\tvat_E_.3_AF153312\tvat_E_.5_AJ488494\tvat_E_.7_AY043211\tvat_E_.8_AY043209\tvat_E_.9_AY043210\n+vat_F_\tvat_F_.1_AF170730\n+vat_H_\tvat_H_.1_GQ205627\n+vga_A_-\tvga_A_.1_M90056\tvga_A_.2_FN546261\tvga_A_.3_JQ312422\tvga_A_LC.1_GQ891882\tvga_A_LC.2_DQ823382\tvga_A_LC.3_FN806791\tvga_A_LC.4_JQ312423\n+vga_A_V\tvga_A_V.1_AF186237\n+vga_B_\tvga_B_.1_U82085\n+vga_C_\tvga_C_.1_FN806792\n+vga_D_\tvga_D_.1_GQ205627\n+vga_E_\tvga_E_.1_FR772051\n+vgb_A_\tvgb_A_.1_M20129\n+vgb_B_\tvgb_B_.1_AF015628\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool-data/resfinder.db/02.cdhit.gene.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/resfinder.db/02.cdhit.gene.fa Tue Jan 08 10:26:30 2019 -0500 |
| b |
| b'@@ -0,0 +1,48245 @@\n+>ARR_2.1_HQ141279\n+ATGGTAAAAGATTGGATTCCCATCTCTCATGATAATTACAAGCAGGTGCAAGGACCGTTC\n+TATCATGGAACCAAAGCCAATTTGGCGATTGGTGACTTGCTAACCACAGGGTTCATCTCT\n+CATTTCGAGGACGGTCGTATTCTTAAGCACATCTACTTTTCAGCCTTGATGGAGCCAGCA\n+GTTTGGGGAGCTGAACTTGCTATGTCACTGTCTGGCCTCGAGGGTCGCGGCTACATATAC\n+ATAGTTGAGCCAACAGGACCGTTCGAAGACGATCCGAATCTTACGAACAAAAAATTTCCC\n+GGTAATCCAACACAGTCCTATAGAACCTGCGAACCCTTGAGAATTGTTGGCGTTGTTGAA\n+GACTGGGAGGGGCATCCTGTTGAATTAATAAGGGGAATGTTGGATTCGTTAGAGGACTTA\n+AAGCGCCGTGGTTTACACGTCATTGAAGACTAG\n+>ARR_3.1_JF806499\n+ATGGTAAAAGATTGGATTCCCATCTCTCATGATAATTACAAGCAGGTGCAAGGACCGTTC\n+TATCATGGAACCAAAGCCAATTTGGCGATTGGTGACTTGCTAACCACAGGGTTCATCTCT\n+CATTTCGAGGACGGTCGTATTCTTAAGCACATCTACTTTTCAGCCTTGATGGAGCCAGCA\n+GTTTGGGGAGCTGAACTTGCTATGTCACTGTCTGGCCTCGAGGGTCGCGGCTACATATAC\n+ATAGTTGAGCCAACAGGACCGTTCGAAGACGATCCGAATCTTACGAACAAAAGATTTCCC\n+GGTAATCCAACACAGTCCTATAGAACCTGCGAACCCTTGAGAATTGTTGGCGTTGTTGAA\n+GACTGGGAGGGGCATCCTGTTGAATTAATAAGGGGAATGTTGGATTCGTTGGAGGACTTA\n+AAGCGCCGTGGTTTACACGTCATTGAAGACTAG\n+>ARR_3.4_FM207631\n+ATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTATGC\n+AGCCAAATCCCAACAATTAAGGGTCTTAAAATGGTAAAAGATTGGATTCCCATCTCTCAT\n+GATAATTACAAGCAGGTGCAAGGACCGTTCTATCATGGAACCAAAGCCAATTTGGCGATT\n+GGTGACTTGCTAACCACAGGGTTCATCTTTCATTTCGAGGACGGTCGTATTCTTAAGCAC\n+ATCTACTTTTCAGCCTTGATGGAGCCAGCAGTTTGGGGAGCTGAACTTGCTATGTCACTG\n+TCTGGCCTCGAGGGTCGCGGCTACATATACATAGTTGAGCCAACAGGACCGTTCGAAGAC\n+GATCCGAATCTTACGAACAAAAAATTTCCCGGTAATCCAACACAGTCCTATAGAACCTGC\n+GAACCCTTGAGAATTGTTGGCGTTGTTGAAGACTGGGAGGGGCATCCTGTTGAATTAATA\n+AGGGGAATGTTGGATTCGTTAGAGGACTTAAAGCGCCGTGGTTTACACGTCATTGAAGAC\n+TAG\n+>ARR_4.1_EF660562\n+ATGACGAATGACTGGATTCCCACTTCGCATGACAACTGCTCGCAAGTAGCGGGGCCGTTC\n+TATCACGGCACCAAAGCCAAACTCACGGTTGGTGACTTGCTTTCCCCAGGACACCCGTCT\n+CACTTTGAGCAAGGTCGCAAGCTCAAACACATCTACTTTGCCGCCCTGATGGAACCAGCC\n+ATCTGGGGAGCGGAGCTTGCGATGTCGCTGTCAAGCCTAGAGGGGCGCGGCCACATCTAC\n+ATCGTTGAACCGCTCGGCCCATTTGAGGACGACCCGAACCTTACAAACAAGAAATTCCCG\n+GGAAATCCAACCAAGTCCTATCGCACCACTGAGCCGCTGCGGATTGTTGGGATCGTAGAA\n+GACTGGCAAGGCCACTCACCGGAGGTGTTACAGGGCATGTTGGCGTCTCTGGAGGATCTT\n+CAGCGTCGTGGCCTCGCCATCATTGAGGACTAA\n+>ARR_5.1_EF660563\n+ATGACGGTAGACTGGATCCCCATTTCGCACGACAACTACCATCAAGTGCGTGGCCCGTTT\n+TATCACGGAACAAAAGCCGAACTCGCCATTGGCGACTTAATTTCAACCGGATTTATTTCT\n+CACTTTGAGCGGGACAGAGCACTAAAGCATGTGTACTTTTCCGCGCTGATGGAGCCAGCA\n+ATCTGGGGGGCCGAGCTCGCTGTAGCACTCTCTGGCTCTGACGGGCCAGGCCATATTTAC\n+ATCATTGAGCCAACCGGCCCGTTTGAAGACGACCCCAATCTCACAAACAAACGATTCCCT\n+GGCAATCCAACACAGTCCTATCGCACATGCCACCCACTTAAAATTGTTGGCATACTGCGG\n+GAGTGGGAGCGCCATTCTCCTGAAGCATTGAAGACCATGCTAGATTCTCTGGCAGACCTC\n+AAGCGACGCGGCTTGGCCATCATTGAAGAATGA\n+>ARR_6.1_FM955585\n+ATGTCGAGTGACTGGACTCCCATCTCACATGAGAATTGCCAGCAGGTGCGTGGGCCGTTC\n+TATCACGGCACCAAAGCCCATCTATCGATTGGCGACTTGATAACAACTGGGCATCTCTCC\n+CACTTTGAAGATGGACGCGCTCTTAAACACGTCTACTTTTCAGCTTTGATGGAGCCTGCC\n+ATTTGGGGGGCGGAACTTGCAATGTCGTTGTCACGCCTAGATGGCCGTGGCTACATATAC\n+ATCGTCGAACCAACTGGACCGTTTGAGGACGACCCGAATCTTACGAACAAAAGATTTCCT\n+GGAAATCCAACAAAGTCCTATCGCACGTGCGATCCGCTACGAATTGTCGGGTCAGTCGAA\n+GACTGGCAAGGGCATCCCGCTGATGTGCTGCAACAGATGTTGGAGTCTTTAGAGGACCTA\n+GAGCGCCGTGGTCTTGCCATCATCGAGGATTAG\n+>ARR_6.2_FM897214\n+ATGTCGAGTGACTGGACTCCCATCTCACATGAGAATTGCCAGCAGGTGCGTGGGCCGTTC\n+TATCACGGCACCAAAGCCCATCTATCGATTGGCGACTTGATAACAACTGGGCATCTCTCC\n+CACTTTGAAGATGGACGCGCTCTTAAACACGTCTACTTTTCAGCTTTGATGGAGCCTGCC\n+ATTTGGGGGGCGGAACTTGCAATGTCGTTGTCACGCCTAGATGGCCGTGGCTACATATAC\n+ATCGTCGAACCAACTGGACCGTTTGAGGACGACCCGAATCTTACGAACAAAAGATTTCCT\n+GGAAATCCAACAAAGTCCTATCGCACGTGCGATCCGCTACGAATTGTCGGGTCAGTCGAA\n+GACTGGCAAGGGCATCCCGCTGATGTGCTGCAACAGATGTTGGAGTCTTTAGAGGACCTA\n+AAGCGCCGTGGTCTTGCCATCATCGAGGATTAG\n+>ARR_6.3_JF922883\n+ATGGTAAAAGATTGGATTCCCATCTCTCATGATAATTACAAGCAGGTGCAAGGACCGTTC\n+TATCATGGAACCAAAGCCAATTTGGCGATTGGTGACTTGCTAACCACAGGGTTCATCTCT\n+CATTTCGAGGACGGTCGTATTCTTAAGCACATCTACTTTTCAGCCTTGATGGAGCCAGCA\n+GTTTGGGGAGCTGAACTTGCTATGTCACTGTCTGGCCTCGAGGGTCGCGGCTACATATAC\n+ATAGTTGAGCCAACAGGACCGTTCGAAGACGATCCGAATCTTACGAACAAAAGATTTCCC\n+GGTAATCCAACACAGTCCTATAGAACCTGCGAACCCTTGAGAATTGTTGGCGTTGTTGAA\n+GACTGGGAGGGGCATCCTGTTGAATTAATAAGGGGAATGTTGGATTCGTTAGAGGACTTA\n+AAGCGCCGTGGTTTA'..b'AAGGAAGTT\n+CAAGTCCTAAGTGGTGGGGAACGTGTGAAGGTTGCTTTTGCAAAACTATTTGTTAGCGAC\n+TATAATACGTTGATTCTGGATGAACCAACAAATTATTTAGACATTGATGCCATAGAAGCG\n+TTAGAGGAGCTCCTAATTAACTATGAGGGGGCAGTACTATTTGTATCTCATGATTGTCGT\n+TTCGTTCAAAATATTGCATCCAAAATTATTGAACTATCCGACCAGAAGGTTATAGAGTTT\n+CTTGGAAGCTATAAAGCGTTTAGAGAAAGATCTCAAGAGACAGAGCGTGACTATATGAAG\n+GAAGAACTTCTTAAAATTGAGATCAAACTCACTCAAATGATTAGTGAAATGAATGACGAG\n+GCATCAAATGAATTAGAAAAAGAATTCCAAATGTTGATTCATGAACGTAATCAGTTAAGA\n+AATCAAGTAAACAATTAG\n+>vga_E_.1_FR772051\n+ATGTTATTATTTGAAGGTACATCATTGAAAAAACACATACAAGACAGATTATTATTTGAT\n+ATAGATTTAATACAAGTACATGAACATCAGCGAATAGGATTAGTAGGTAGGAATGGAACG\n+GGGAAAACAAGTCTATTAAAAATTATTACAGGTGAAGAACTAGTTGATGGAGGGAATGTT\n+AATCATTTTACCTCTGTAAAATTAGTACCACAATTTAAAGAAACAAGATCGGAGAAAAGT\n+GGTGGAGAAATAACGCAACAATATTTGCAATTAGCATTTAATGAAAAGCCAGGATTATTA\n+ATTTTAGATGAACCAACGACTCATTTAGATACACAAAGAATTGATTGGTTAGAAAAGAAA\n+TTAGCAAACTATCAAGGAGCATTTGTTGTCGTATCACATGATCGGACATTTCTAAATAAT\n+GTGTGTACTGAAATATGGGAAATAGAAGATGGTAGTCTAAACGCGTTTAAAGGGGATTAT\n+AATGCTTATGCGGAACAAAAGGAATTAATAAAAACACAGCAGCAGATTGCATTTGAAAAG\n+TACGAACGAGAGAAAAAGCAATTAGAAAAAGCAATACGACAAAAAGAGGAAAGAGCACAG\n+CGAGCAACAAAGAAACCTAAAAATCTGAGTTCTTCAGAGGCAAGAATAACAGGAGCTAAA\n+ACCCATTATGCCAATATACAGAAAAAGTTGAGGGGTTCTGCAAAAGCATTAGAAACAAGG\n+TTGGAACAACTGGATAGGATTGACAAGGTGAAAGAACTACCTGAAATTAAGATGGATATA\n+TTAAATAAAGAAAGTCTAACAAACCAGTCTGTGTTACGCGCTGAAAACATTAAGGGAGAG\n+GTTGACGGACGTAAGCTTTGGAATCCCTTTAGTTTATATTTATATGGCGGCGATAAAGTT\n+GCTATCATTGGGAAAAATGGCACGGGTAAAACAACCTTACTTAAAAAAATAGTTGAGCGA\n+GATGAAAGAATAGCAATCCCAGAAAAGGTGAGGATAGGTTATTTTTCCCAACACCTCACA\n+ATTCTCGATGATGATAAAACAATCATAGAAAATATACAATTGACCTCTAGTCAGGATGAA\n+ACATTAATTAGAACAGTTTTAGCAAGAATGCATTTTTGGGATGAAGATGTCTATAAAAAG\n+GTCGGCATATTAAGTGGTGGTGAAAAAGTAAAAGTAGCACTAGCTAAACTATTCTTAAGT\n+GACGTGAATATGCTGGTGTTAGATGAACCTACAAATTTTTTAGATATTGAATCTTTAGAA\n+GCGCTAGAAACATTAATGAAAAGTTATCATGGAACGATTCTATTTGTTACTCACGACCGA\n+ACGTTAGTAACAAATATAGCTACAAAAATAATTGATATAAAAGATGGTAAGATAACAGTA\n+TTCGATGGATCATACGAAGCATATGAAGAGTGGTTAGAGAATCAAACAAAGTCCAACAAT\n+GATGATCAACTTTTACTAATCGAAACTAAAATATCTGACGTTCTGGGTAGGTTGAGTTTG\n+GAGCCTTCACGAGAGTTAGAAGATGAATTTCAAAGATTATTGAAAGAAAAGAAAGAACTG\n+ACTAAAAAACTATAA\n+>vgb_A_.1_M20129\n+ATGGAATTTAAATTACAAGAATTAAATCTTACTAACCAAGATACAGGACCATATGGTATA\n+ACCGTTTCAGATAAGGGGAAAGTTTGGATTACACAACATAAAGCAAATATGATAAGTTGC\n+ATCAATTTAGATGGAAAAATTACAGAGTACCCACTACCGACACCAGATGCAAAAGTCATG\n+TGTTTAACTATATCCTCAGATGGGGAAGTTTGGTTTACTGAGAATGCAGCAAACAAAATA\n+GGGAGGATTACAAAAAAAGGGATTATTAAGGAATATACATTGCCTAACCCAGATTCAGCA\n+CCCTACGGTATTACAGAAGGACCAAATGGAGATATATGGTTTACAGAAATGAATGGCAAC\n+CGTATTGGACGTATTACGGACGACGGTAAAATTCGTGAATACGAGCTGCCTAATAAAGGA\n+TCTTACCCTTCTTTTATCACTTTGGGTTCTGATAATGCCCTGTGGTTCACAGAAAATCAA\n+AATAATGCTATTGGTAGAATTACAGAAAGTGGGGATATTACAGAGTTTAAAATTCCTACA\n+CCTGCATCAGGACCAGTTGGTATTACAAAGGGGAACGACGATGCTTTATGGTTTGTGGAA\n+ATTATCGGTAATAAGATAGGGCGAATAACTCCTCTGGGGGAAATTACCGAATTCAAAATT\n+CCAACGCCAAACGCTCGACCTCATGCAATTACTGCTGGAGCAGGAATTGATTTATGGTTT\n+ACTGAATGGGGGGCTAATAAAATAGGAAGGCTGACAAGCAATAATATAATTGAGGAATAC\n+CCAATTCAAATCAAAAGTGCTGAACCACATGGCATTTGTTTCGATGGTGAAACAATTTGG\n+TTTGCAATGGAGTGTGACAAGATAGGCAAATTAACTCTCATTAAGGATAATATGGAGTGA\n+>vgb_B_.1_AF015628\n+ATGAATTTTTATTTAGAGGAGTTTAACTTGTCTATTCCCGATTCAGGTCCATACGGTATA\n+ACTTCATCAGAAGACGGAAAGGTATGGTTCACACAACATAAGGCAAACAAAATCAGCAGT\n+CTAGATCAGAGTGGTAGGATAAAAGAATTCGAAGTTCCTACCCCTGATGCTAAAGTGATG\n+TGTTTAATTGTATCTTCACTTGGAGACATATGGTTTACAGAGAATGGTGCAAATAAAATC\n+GGAAAGCTCTCAAAAAAAGGTGGCTTTACAGAATATCCATTGCCACAGCCGGATTCTGGT\n+CCTTACGGAATAACGGAAGGTCTAAATGGCGATATATGGTTTACCCAATTGAATGGAGAT\n+CGTATAGGAAAGTTGACAGCTGATGGGACTATTTATGAATATGATTTGCCAAATAAGGGA\n+TCTTATCCTGCTTTTATTACTTTAGGTTCGGATAACGCACTTTGGTTCACGGAGAACCAA\n+AATAATTCTATTGGAAGGATTACAAATACAGGGAAATTAGAAGAATATCCTCTACCAACA\n+AATGCAGCGGCTCCAGTGGGTATCACTAGTGGTAACGATGGTGCACTCTGGTTTGTCGAA\n+ATTATGGGCAACAAAATAGGTCGAATCACTACAACTGGTGAGATTAGCGAATATGATATT\n+CCAACTCCAAACGCACGTCCACACGCTATAACCGCGGGGAAAAATAGCGAAATATGGTTT\n+ACTGAATGGGGGGCAAATCAAATCGGCAGAATTACAAACGACAAAACAATTCAAGAATAT\n+CAACTTCAAACAGAAAATGCGGAACCTCATGGTATTACCTTTGGAAAAGATGGATCCGTA\n+TGGTTTGCATTAAAATGTAAAATTGGGAAGCTGAATTTGAACGAATGA\n' |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of ariba database in the required format --> + <table name="ariba_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/ariba_databases.loc" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r 000000000000 -r 79b55c74fb80 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Jan 08 10:26:30 2019 -0500 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of ariba database in the required format --> + <table name="ariba_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/test_ariba_databases.loc" /> + </table> +</tables> \ No newline at end of file |