| Previous changeset 29:aecdffbc08fc (2013-09-23) Next changeset 31:f2478dc77ccb (2013-10-10) |
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Commit message:
Uploaded v0.0.21, includes support for masking, uses macros internally, and now targets BLAST+ 2.2.27 rather than BLAST+ 2.2.26 |
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modified:
test-data/blastn_rhodopsin_vs_three_human.tabular test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastx_rhodopsin_vs_four_human.tabular test-data/blastx_rhodopsin_vs_four_human.xml test-data/blastx_rhodopsin_vs_four_human_converted.tabular test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular test-data/blastx_rhodopsin_vs_four_human_ext.tabular test-data/tblastn_four_human_vs_rhodopsin.html test-data/tblastn_four_human_vs_rhodopsin.xml tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml tools/ncbi_blast_plus/repository_dependencies.xml tools/ncbi_blast_plus/tool_dependencies.xml |
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added:
test-data/dustmasker_three_human.fasta test-data/dustmasker_three_human.maskinfo-asn1 test-data/dustmasker_three_human.maskinfo-asn1-binary tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastn_rhodopsin_vs_three_human.tabular --- a/test-data/blastn_rhodopsin_vs_three_human.tabular Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastn_rhodopsin_vs_three_human.tabular Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,7 +1,7 @@ -gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.10 1050 77 6 1 1047 88 1134 0.0 1474 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.07 1047 83 0 1 1047 88 1134 0.0 1474 gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.59 333 28 0 1 333 118 450 9e-133 460 gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.36 243 19 2 3127 3368 782 1023 7e-94 331 gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 94.22 173 10 0 1410 1582 448 620 8e-74 265 -gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.98 171 10 2 2854 3023 615 784 8e-69 248 -gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.58 962 75 6 1 959 118 1076 0.0 1323 -gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.55 1052 121 10 1 1047 88 1134 0.0 1208 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.94 170 12 0 2854 3023 615 784 8e-69 248 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.55 959 81 0 1 959 118 1076 0.0 1323 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.50 1048 129 2 1 1047 88 1134 0.0 1208 |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastp</BlastOutput_program> - <BlastOutput_version>BLASTP 2.2.26+</BlastOutput_version> + <BlastOutput_version>BLASTP 2.2.27+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID> |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastx_rhodopsin_vs_four_human.tabular --- a/test-data/blastx_rhodopsin_vs_four_human.tabular Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human.tabular Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,10 +1,10 @@ -gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 662 -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 575 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-68 224 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-36 129 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 3e-33 120 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 2e-32 118 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 2e-12 56.2 -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 613 -gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 641 -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 0.0 559 +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastx_rhodopsin_vs_four_human.xml --- a/test-data/blastx_rhodopsin_vs_four_human.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| b'@@ -2,7 +2,7 @@\n <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n <BlastOutput>\n <BlastOutput_program>blastx</BlastOutput_program>\n- <BlastOutput_version>BLASTX 2.2.26+</BlastOutput_version>\n+ <BlastOutput_version>BLASTX 2.2.27+</BlastOutput_version>\n <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>\n <BlastOutput_db></BlastOutput_db>\n <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>\n@@ -28,8 +28,8 @@\n <Statistics>\n <Statistics_db-num>0</Statistics_db-num>\n <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>29</Statistics_hsp-len>\n- <Statistics_eff-space>102080</Statistics_eff-space>\n+ <Statistics_hsp-len>30</Statistics_hsp-len>\n+ <Statistics_eff-space>119944</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n@@ -47,8 +47,8 @@\n <Statistics>\n <Statistics_db-num>0</Statistics_db-num>\n <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>29</Statistics_hsp-len>\n- <Statistics_eff-space>102080</Statistics_eff-space>\n+ <Statistics_hsp-len>30</Statistics_hsp-len>\n+ <Statistics_eff-space>119944</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n@@ -66,8 +66,8 @@\n <Statistics>\n <Statistics_db-num>0</Statistics_db-num>\n <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>29</Statistics_hsp-len>\n- <Statistics_eff-space>102080</Statistics_eff-space>\n+ <Statistics_hsp-len>30</Statistics_hsp-len>\n+ <Statistics_eff-space>119944</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n@@ -90,8 +90,8 @@\n <Hit_hsps>\n <Hsp>\n <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>662.144</Hsp_bit-score>\n- <Hsp_score>1707</Hsp_score>\n+ <Hsp_bit-score>639.032</Hsp_bit-score>\n+ <Hsp_score>1647</Hsp_score>\n <Hsp_evalue>0</Hsp_evalue>\n <Hsp_query-from>1</Hsp_query-from>\n <Hsp_query-to>1044</Hsp_query-to>\n@@ -114,8 +114,8 @@\n <Statistics>\n <Statistics_db-num>0</Statistics_db-num>\n <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>29</Statistics_hsp-len>\n- <Statistics_eff-space>102080</Statistics_eff-space>\n+ <Statistics_hsp-len>30</Statistics_hsp-len>\n+ <Statistics_eff-space>119944</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n@@ -132,8 +132,8 @@\n <Statistics>\n <Statistics_db-num>0</Statistics_db-num>\n <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>32</Statistics_hsp-len>\n- <Statistics_eff-space>155472</Statistics_eff-space>\n+ <Statistics_hsp-len>33</Statistics_hsp-len>\n+ <Statistics_eff-space>183143</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n@@ -151,8 +151,8 @@\n <Statistics>\n <Statistics_db-num>0</Statistics_db-num>\n '..b'cs_eff-space>155584</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n@@ -686,22 +686,22 @@\n <Hit_hsps>\n <Hsp>\n <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>559.296</Hsp_bit-score>\n- <Hsp_score>1440</Hsp_score>\n+ <Hsp_bit-score>532.717</Hsp_bit-score>\n+ <Hsp_score>1371</Hsp_score>\n <Hsp_evalue>0</Hsp_evalue>\n <Hsp_query-from>23</Hsp_query-from>\n- <Hsp_query-to>1018</Hsp_query-to>\n+ <Hsp_query-to>1021</Hsp_query-to>\n <Hsp_hit-from>1</Hsp_hit-from>\n- <Hsp_hit-to>332</Hsp_hit-to>\n+ <Hsp_hit-to>333</Hsp_hit-to>\n <Hsp_query-frame>2</Hsp_query-frame>\n <Hsp_hit-frame>0</Hsp_hit-frame>\n <Hsp_identity>272</Hsp_identity>\n <Hsp_positive>307</Hsp_positive>\n <Hsp_gaps>0</Hsp_gaps>\n- <Hsp_align-len>332</Hsp_align-len>\n- <Hsp_qseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED</Hsp_qseq>\n- <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE</Hsp_hseq>\n- <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +++</Hsp_midline>\n+ <Hsp_align-len>333</Hsp_align-len>\n+ <Hsp_qseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG</Hsp_qseq>\n+ <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA</Hsp_hseq>\n+ <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +++ </Hsp_midline>\n </Hsp>\n </Hit_hsps>\n </Hit>\n@@ -710,8 +710,8 @@\n <Statistics>\n <Statistics_db-num>0</Statistics_db-num>\n <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>31</Statistics_hsp-len>\n- <Statistics_eff-space>132189</Statistics_eff-space>\n+ <Statistics_hsp-len>32</Statistics_hsp-len>\n+ <Statistics_eff-space>155584</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n' |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastx_rhodopsin_vs_four_human_converted.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,10 +1,10 @@ -gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 662 -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 575 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-68 224 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-36 129 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 3e-33 120 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 2e-32 118 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 2e-12 56.2 -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 613 -gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 641 -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 0.0 559 +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Tue Oct 08 05:08:26 2013 -0400 |
| b |
| b'@@ -1,10 +1,10 @@\n-gi|57163782|ref|NM_001009242.1|\tsp|P08100|OPSD_HUMAN\t96.55\t348\t12\t0\t1\t1044\t1\t348\t0.0\t662\tsp|P08100|OPSD_HUMAN\t1707\t336\t343\t0\t98.56\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\n-gi|2734705|gb|U59921.1|BBU59921\tsp|P08100|OPSD_HUMAN\t85.24\t332\t49\t0\t42\t1037\t1\t332\t0.0\t575\tsp|P08100|OPSD_HUMAN\t1481\t283\t315\t0\t94.88\t3\t0\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1574\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.40\t111\t4\t0\t1\t333\t11\t121\t2e-68\t224\tsp|P08100|OPSD_HUMAN\t570\t107\t109\t0\t98.20\t1\t0\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.31\t65\t5\t0\t3174\t3368\t248\t312\t5e-36\t129\tsp|P08100|OPSD_HUMAN\t324\t60\t64\t0\t98.46\t3\t0\tKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\tKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.43\t56\t2\t0\t2855\t3022\t177\t232\t3e-33\t120\tsp|P08100|OPSD_HUMAN\t302\t54\t56\t0\t100.00\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t2e-32\t118\tsp|P08100|OPSD_HUMAN\t295\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.00\t25\t2\t0\t4222\t4296\t312\t336\t2e-12\t56.2\tsp|P08100|OPSD_HUMAN\t134\t23\t24\t0\t96.00\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTT\tQFRNCMLTTICCGKNPLGDDEASAT\t4301\t348\n-gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t0.0\t613\tsp|P08100|OPSD_HUMAN\t1582\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\n-gi|18148870|dbj|AB062417.1|\tsp|P08100|OPSD_HUMAN\t93.39\t348\t23\t0\t1\t1044\t1\t348\t0.0\t641\tsp|P08100|OPSD_HUMAN\t1654\t325\t337\t0\t96.84\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAY'..b'HAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1574\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.40\t111\t4\t0\t1\t333\t11\t121\t4e-67\t220\tsp|P08100|OPSD_HUMAN\t560\t107\t109\t0\t98.20\t1\t0\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.31\t65\t5\t0\t3174\t3368\t248\t312\t2e-35\t127\tsp|P08100|OPSD_HUMAN\t319\t60\t64\t0\t98.46\t3\t0\tKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\tKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t91.53\t59\t5\t0\t2855\t3031\t177\t235\t2e-33\t121\tsp|P08100|OPSD_HUMAN\t303\t54\t57\t0\t96.61\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t1e-25\t97.1\tsp|P08100|OPSD_HUMAN\t240\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t88.46\t26\t3\t0\t4222\t4299\t312\t337\t1e-12\t57.0\tsp|P08100|OPSD_HUMAN\t136\t23\t24\t0\t92.31\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTTA\tQFRNCMLTTICCGKNPLGDDEASATV\t4301\t348\n+gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t0.0\t589\tsp|P08100|OPSD_HUMAN\t1518\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\n+gi|18148870|dbj|AB062417.1|\tsp|P08100|OPSD_HUMAN\t93.39\t348\t23\t0\t1\t1044\t1\t348\t0.0\t619\tsp|P08100|OPSD_HUMAN\t1596\t325\t337\t0\t96.84\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\n+gi|12583664|dbj|AB043817.1|\tsp|P08100|OPSD_HUMAN\t81.68\t333\t61\t0\t23\t1021\t1\t333\t0.0\t532\tsp|P08100|OPSD_HUMAN\t1371\t272\t307\t0\t92.19\t2\t0\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA\t1344\t348\n' |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastx_rhodopsin_vs_four_human_ext.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Tue Oct 08 05:08:26 2013 -0400 |
| b |
| b'@@ -1,10 +1,10 @@\n-gi|57163782|ref|NM_001009242.1|\tsp|P08100|OPSD_HUMAN\t96.55\t348\t12\t0\t1\t1044\t1\t348\t0.0\t 662\tsp|P08100|OPSD_HUMAN\t1707\t336\t343\t0\t98.56\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\n-gi|2734705|gb|U59921.1|BBU59921\tsp|P08100|OPSD_HUMAN\t85.24\t332\t49\t0\t42\t1037\t1\t332\t0.0\t 575\tsp|P08100|OPSD_HUMAN\t1481\t283\t315\t0\t94.88\t3\t0\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1574\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.40\t111\t4\t0\t1\t333\t11\t121\t2e-68\t 224\tsp|P08100|OPSD_HUMAN\t570\t107\t109\t0\t98.20\t1\t0\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.31\t65\t5\t0\t3174\t3368\t248\t312\t5e-36\t 129\tsp|P08100|OPSD_HUMAN\t324\t60\t64\t0\t98.46\t3\t0\tKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\tKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.43\t56\t2\t0\t2855\t3022\t177\t232\t3e-33\t 120\tsp|P08100|OPSD_HUMAN\t302\t54\t56\t0\t100.00\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t2e-32\t 118\tsp|P08100|OPSD_HUMAN\t295\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.00\t25\t2\t0\t4222\t4296\t312\t336\t2e-12\t56.2\tsp|P08100|OPSD_HUMAN\t134\t23\t24\t0\t96.00\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTT\tQFRNCMLTTICCGKNPLGDDEASAT\t4301\t348\n-gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t0.0\t 613\tsp|P08100|OPSD_HUMAN\t1582\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\n-gi|18148870|dbj|AB062417.1|\tsp|P08100|OPSD_HUMAN\t93.39\t348\t23\t0\t1\t1044\t1\t348\t0.0\t 641\tsp|P08100|OPSD_HUMAN\t1654\t325\t337\t0\t96.84\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPW'..b'AFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1574\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.40\t111\t4\t0\t1\t333\t11\t121\t4e-67\t 220\tsp|P08100|OPSD_HUMAN\t560\t107\t109\t0\t98.20\t1\t0\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.31\t65\t5\t0\t3174\t3368\t248\t312\t2e-35\t 127\tsp|P08100|OPSD_HUMAN\t319\t60\t64\t0\t98.46\t3\t0\tKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\tKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t91.53\t59\t5\t0\t2855\t3031\t177\t235\t2e-33\t 121\tsp|P08100|OPSD_HUMAN\t303\t54\t57\t0\t96.61\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t1e-25\t97.1\tsp|P08100|OPSD_HUMAN\t240\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t88.46\t26\t3\t0\t4222\t4299\t312\t337\t1e-12\t57.0\tsp|P08100|OPSD_HUMAN\t136\t23\t24\t0\t92.31\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTTA\tQFRNCMLTTICCGKNPLGDDEASATV\t4301\t348\n+gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t0.0\t 589\tsp|P08100|OPSD_HUMAN\t1518\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\n+gi|18148870|dbj|AB062417.1|\tsp|P08100|OPSD_HUMAN\t93.39\t348\t23\t0\t1\t1044\t1\t348\t0.0\t 619\tsp|P08100|OPSD_HUMAN\t1596\t325\t337\t0\t96.84\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\n+gi|12583664|dbj|AB043817.1|\tsp|P08100|OPSD_HUMAN\t81.68\t333\t61\t0\t23\t1021\t1\t333\t0.0\t 532\tsp|P08100|OPSD_HUMAN\t1371\t272\t307\t0\t92.19\t2\t0\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA\t1344\t348\n' |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c test-data/dustmasker_three_human.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dustmasker_three_human.fasta Tue Oct 08 05:08:26 2013 -0400 |
| b |
| b'@@ -0,0 +1,183 @@\n+>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds\n+GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAG\n+CCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCAC\n+GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC\n+CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA\n+TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC\n+TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT\n+TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA\n+CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA\n+TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA\n+CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC\n+TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA\n+TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT\n+TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG\n+GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA\n+TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA\n+ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG\n+TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA\n+CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC\n+AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT\n+CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA\n+ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC\n+CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA\n+TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG\n+CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC\n+TATGTGTatttttattttgaataaacagaaagaaattttgggtttttaatttttttCTCC\n+CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTaaaaaaaaaaaaaCCTGCTA\n+GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT\n+ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA\n+GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT\n+CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT\n+GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA\n+TTGCTTATGAAAATTCCATAGTGGTAtttttttGGATTCTTAATGTGTAACTTAAACATA\n+CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA\n+AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG\n+GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG\n+AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT\n+TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT\n+TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACtt\n+tttttCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG\n+CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA\n+CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT\n+TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC\n+TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT\n+GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT\n+AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT\n+TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT\n+GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT\n+TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA\n+GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA\n+TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA\n+TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT\n+AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT\n+TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT\n+ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT\n+GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA\n+GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT\n+GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT\n+TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT\n+TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT\n+AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG\n+AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC\n+TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT\n+CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTA'..b'GAAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCT\n+CAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAG\n+ACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGAT\n+TACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGAC\n+CCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTG\n+CCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAG\n+CACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACAC\n+TTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGC\n+AGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTT\n+GGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCG\n+AAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAG\n+GAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGT\n+GGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGC\n+TCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATT\n+GCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGT\n+ATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCT\n+TCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGAC\n+GAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTC\n+GGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTG\n+GCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAG\n+GCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCC\n+AAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTAC\n+CTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAA\n+GAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAG\n+TTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAA\n+ATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGC\n+AAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACC\n+ACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAA\n+CAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTAT\n+CTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAA\n+TTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTG\n+CACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGT\n+GAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCAC\n+TGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGC\n+TACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTG\n+ACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTT\n+CCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCT\n+ACCATGTCCAGTGGAGTTCAGAGATCGTTCCTATACATTTCTGTTCATCTTAAGGTGGAC\n+TCGTTTGGTTACCAATTTAACTAGTCCTGCAGAGGATTTAACTGTGAACCTGGAGGGCAA\n+GGGGTTTCCACAGTTGCTGCTCCTTTGGGGCAACGACGGTTTCAAACCAGGATTTTGTGT\n+TTTTTCGTTccccccacccgcccccAGCAGATGGAAAGAAAGCACCTGTTTTTACAAATT\n+CttttttttttttttttttttttttttttGCTGGTGTCTGAGCTTCAGTATAAAAGACAA\n+AACTTCCTGTTTGTGGAACAAAATTTCGAAAGAAAAAACCAAA\n+>ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds\n+CCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAGCATTCTTGGGTGGGAGCAGC\n+CACGGGTCAGCCACAAGGGCCACAGCCATGAATGGCACAGAAGGCCCTAACTTCTACGTG\n+CCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTG\n+GCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGC\n+TTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCT\n+CTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTC\n+ACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAAT\n+TTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTG\n+GCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAAC\n+CATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCA\n+CTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTAC\n+TACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCAC\n+TTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAG\n+GAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACC\n+CGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTG\n+GCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCA\n+GCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAG\n+CAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGAT\n+GAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTG\n+CCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACA\n+GCCATCCCACCAG\n' |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c test-data/dustmasker_three_human.maskinfo-asn1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dustmasker_three_human.maskinfo-asn1 Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -0,0 +1,64 @@ +Blast-db-mask-info ::= { + algo-id 2, + algo-program dust, + algo-options "window=64; level=20; linker=1", + masks { + masks { + packed-int { + { + from 1447, + to 1495, + id local id 1 + }, + { + from 1540, + to 1552, + id local id 1 + }, + { + from 1886, + to 1892, + id local id 1 + }, + { + from 2278, + to 2284, + id local id 1 + }, + { + from 4409, + to 4415, + id local id 1 + }, + { + from 4635, + to 4653, + id local id 1 + }, + { + from 4726, + to 4734, + id local id 1 + } + }, + packed-int { + { + from 139, + to 219, + id local id 2 + }, + { + from 4569, + to 4584, + id local id 2 + }, + { + from 4621, + to 4648, + id local id 2 + } + } + }, + more FALSE + } +} |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c test-data/dustmasker_three_human.maskinfo-asn1-binary |
| b |
| Binary file test-data/dustmasker_three_human.maskinfo-asn1-binary has changed |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c test-data/tblastn_four_human_vs_rhodopsin.html --- a/test-data/tblastn_four_human_vs_rhodopsin.html Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Tue Oct 08 05:08:26 2013 -0400 |
| b |
| b'@@ -3,7 +3,7 @@\n <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">\n <PRE>\n \n-<b>TBLASTN 2.2.26+</b>\n+<b>TBLASTN 2.2.27+</b>\n \n \n <b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44\n@@ -20,12 +20,12 @@\n \n \n \n-Lambda K H\n- 0.347 0.182 0.684 \n+Lambda K H a alpha\n+ 0.347 0.182 0.684 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 127710\n \n@@ -45,12 +45,12 @@\n \n \n \n-Lambda K H\n- 0.347 0.182 0.684 \n+Lambda K H a alpha\n+ 0.347 0.182 0.684 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 127710\n \n@@ -70,12 +70,12 @@\n \n \n \n-Lambda K H\n- 0.347 0.182 0.684 \n+Lambda K H a alpha\n+ 0.347 0.182 0.684 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 127710\n \n@@ -95,12 +95,12 @@\n \n \n \n-Lambda K H\n- 0.347 0.182 0.684 \n+Lambda K H a alpha\n+ 0.347 0.182 0.684 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 127710\n \n@@ -120,12 +120,12 @@\n \n \n \n-Lambda K H\n- 0.347 0.182 0.684 \n+Lambda K H a alpha\n+ 0.347 0.182 0.684 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 127710\n \n@@ -145,12 +145,12 @@\n \n \n \n-Lambda K H\n- 0.347 0.182 0.684 \n+Lambda K H a alpha\n+ 0.347 0.182 0.684 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 127710\n \n@@ -169,12 +169,12 @@\n \n \n \n-Lambda K H\n- 0.334 0.170 0.615 \n+Lambda K H a alpha\n+ 0.334 0.170 0.615 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 370988\n \n@@ -194,12 +194,12 @@\n \n \n \n-Lambda K H\n- 0.334 0.170 0.615 \n+Lambda K H a alpha\n+ 0.334 0.170 0.615 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 370988\n \n@@ -219,12 +219,12 @@\n \n \n \n-Lambda K H\n- 0.334 0.170 0.615 \n+Lambda K H a alpha\n+ 0.334 0.170 0.615 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 370988\n \n@@ -244,12 +244,12 @@\n \n \n \n-Lambda K H\n- 0.334 0.170 0.615 \n+Lambda K H a alpha\n+ 0.334 0.170 0.615 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.2'..b'bda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 441350\n \n@@ -368,12 +368,12 @@\n \n \n \n-Lambda K H\n- 0.346 0.180 0.700 \n+Lambda K H a alpha\n+ 0.346 0.180 0.700 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 441350\n \n@@ -393,12 +393,12 @@\n \n \n \n-Lambda K H\n- 0.346 0.180 0.700 \n+Lambda K H a alpha\n+ 0.346 0.180 0.700 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 441350\n \n@@ -418,12 +418,12 @@\n \n \n \n-Lambda K H\n- 0.346 0.180 0.700 \n+Lambda K H a alpha\n+ 0.346 0.180 0.700 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 441350\n \n@@ -443,12 +443,12 @@\n \n \n \n-Lambda K H\n- 0.346 0.180 0.700 \n+Lambda K H a alpha\n+ 0.346 0.180 0.700 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 441350\n \n@@ -492,12 +492,12 @@\n \n \n \n-Lambda K H\n- 0.351 0.182 0.707 \n+Lambda K H a alpha\n+ 0.351 0.182 0.707 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 109230\n \n@@ -542,12 +542,12 @@\n \n \n \n-Lambda K H\n- 0.351 0.182 0.707 \n+Lambda K H a alpha\n+ 0.351 0.182 0.707 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 109230\n \n@@ -616,12 +616,12 @@\n \n \n \n-Lambda K H\n- 0.351 0.182 0.707 \n+Lambda K H a alpha\n+ 0.351 0.182 0.707 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 109230\n \n@@ -666,12 +666,12 @@\n \n \n \n-Lambda K H\n- 0.351 0.182 0.707 \n+Lambda K H a alpha\n+ 0.351 0.182 0.707 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 109230\n \n@@ -716,12 +716,12 @@\n \n \n \n-Lambda K H\n- 0.351 0.182 0.707 \n+Lambda K H a alpha\n+ 0.351 0.182 0.707 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 109230\n \n@@ -766,12 +766,12 @@\n \n \n \n-Lambda K H\n- 0.351 0.182 0.707 \n+Lambda K H a alpha\n+ 0.351 0.182 0.707 0.522 1.92 \n \n Gapped\n-Lambda K H\n- 0.299 0.0710 0.270 \n+Lambda K H a alpha sigma\n+ 0.299 0.0710 0.270 1.10 13.8 14.5 \n \n Effective search space used: 109230\n \n' |
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| diff -r aecdffbc08fc -r 5ec998a3530c test-data/tblastn_four_human_vs_rhodopsin.xml --- a/test-data/tblastn_four_human_vs_rhodopsin.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Tue Oct 08 05:08:26 2013 -0400 |
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| @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>tblastn</BlastOutput_program> - <BlastOutput_version>TBLASTN 2.2.26+</BlastOutput_version> + <BlastOutput_version>TBLASTN 2.2.27+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> |
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| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/README.rst Tue Oct 08 05:08:26 2013 -0400 |
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| @@ -53,6 +53,7 @@ <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" /> + <tool file="ncbi_blast_plus/ncbi_dustmasker_wrapper.xml" /> <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" /> <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" /> <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" /> @@ -62,7 +63,9 @@ You will also need to install 'blast_datatypes' from the Tool Shed. This defines the BLAST XML file format ('blastxml') and protein and nucleotide -BLAST databases composite file formats ('blastdbp' and 'blastdbn'). +BLAST databases composite file formats ('blastdbp' and 'blastdbn'): + +* http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes As described above for an automated installation, you must also tell Galaxy about any system level BLAST databases using the tool-data/blastdb*.loc files. @@ -117,6 +120,13 @@ - Adopted standard MIT License. - Development moved to GitHub, https://github.com/peterjc/galaxy_blast - Updated citation information (Cock et al. 2013). +v0.0.21 - Use macros to simplify the XML wrappers. + - Added wrapper for dustmasker + - Enabled masking for makeblastdb + - Requires 'maskinfo-asn1' and 'maskinfo-asn1-binary' datatypes + defined in updated blast_datatypes on Galaxy ToolShed. + - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26 + - Now depends on package_blast_plus_2_2_27 in ToolShed ======= ====================================================================== |
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| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,46 +1,19 @@ -<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.6"> +<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.21"> <description>Show BLAST database information from blastdbcmd</description> <requirements> <requirement type="binary">blastdbcmd</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> + <requirement type="package" version="2.2.27">blast+</requirement> </requirements> <version_command>blastdbcmd -version</version_command> + <macros> + <import>ncbi_macros.xml</import> + </macros> <command> blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- Suspect blastdbcmd sometimes fails to set error level --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + <expand macro="stdio" /> <inputs> - <conditional name="db_opts"> - <param name="db_type" type="select" label="Type of BLAST database"> - <option value="nucl" selected="True">Nucleotide</option> - <option value="prot">Protein</option> - </param> - <when value="nucl"> - <param name="database" type="select" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - </when> - <when value="prot"> - <param name="database" type="select" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - </when> - </conditional> + <expand macro="input_conditional_choose_db_type" /> </inputs> <outputs> <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> |
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| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Tue Oct 08 05:08:26 2013 -0400 |
| [ |
| @@ -1,10 +1,13 @@ -<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.6"> +<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.21"> <description>Extract sequence(s) from BLAST database</description> <requirements> <requirement type="binary">blastdbcmd</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> + <requirement type="package" version="2.2.27">blast+</requirement> </requirements> <version_command>blastdbcmd -version</version_command> + <macros> + <import>ncbi_macros.xml</import> + </macros> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -47,39 +50,9 @@ | sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq" #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- Suspect blastdbcmd sometimes fails to set error level --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + <expand macro="stdio" /> <inputs> - <conditional name="db_opts"> - <param name="db_type" type="select" label="Type of BLAST database"> - <option value="nucl" selected="True">Nucleotide</option> - <option value="prot">Protein</option> - </param> - <when value="nucl"> - <param name="database" type="select" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - </when> - <when value="prot"> - <param name="database" type="select" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - </when> - </conditional> + <expand macro="input_conditional_choose_db_type" /> <conditional name="id_opts"> <param name="id_type" type="select" label="Type of identifier list"> <option value="file">From file</option> |
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| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,12 +1,15 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.20"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.21"> <description>Search nucleotide database with nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> <requirements> <requirement type="binary">blastn</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> + <requirement type="package" version="2.2.27">blast+</requirement> </requirements> <version_command>blastn -version</version_command> + <macros> + <import>ncbi_macros.xml</import> + </macros> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -48,44 +51,14 @@ ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + + <expand macro="stdio" /> + <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">Locally installed BLAST database</option> - <option value="histdb">BLAST database from your history</option> - <option value="file">FASTA file from your history (see warning note below)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> - </when> - </conditional> + + <expand macro="input_conditional_nucleotide_db" /> + <param name="blast_type" type="select" display="radio" label="Type of BLAST"> <option value="megablast">megablast</option> <option value="blastn">blastn</option> @@ -97,20 +70,7 @@ --> </param> <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> + <expand macro="input_out_format" /> <conditional name="adv_opts"> <param name="adv_opts_selector" type="select" label="Advanced Options"> <option value="basic" selected="True">Hide Advanced Options</option> @@ -141,15 +101,7 @@ </inputs> <outputs> <data name="output1" format="tabular" label="${blast_type.value_label} on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + <expand macro="output_change_format" /> </data> </outputs> <tests> |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,12 +1,15 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.20"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.21"> <description>Search protein database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> <requirements> <requirement type="binary">blastp</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> + <requirement type="package" version="2.2.27">blast+</requirement> </requirements> <version_command>blastp -version</version_command> + <macros> + <import>ncbi_macros.xml</import> + </macros> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -46,63 +49,20 @@ ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + + <expand macro="stdio" /> + <inputs> <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">Locally installed BLAST database</option> - <option value="histdb">BLAST database from your history</option> - <option value="file">FASTA file from your history (see warning note below)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> - </when> - </conditional> + + <expand macro="input_conditional_protein_db" /> + <param name="blast_type" type="select" display="radio" label="Type of BLAST"> <option value="blastp">blastp</option> <option value="blastp-short">blastp-short</option> </param> <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> + <expand macro="input_out_format" /> <conditional name="adv_opts"> <param name="adv_opts_selector" type="select" label="Advanced Options"> <option value="basic" selected="True">Hide Advanced Options</option> @@ -112,16 +72,9 @@ <when value="advanced"> <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> - <param name="matrix" type="select" label="Scoring matrix"> - <option value="BLOSUM90">BLOSUM90</option> - <option value="BLOSUM80">BLOSUM80</option> - <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> - <option value="BLOSUM50">BLOSUM50</option> - <option value="BLOSUM45">BLOSUM45</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> - </param> + + <expand macro="input_scoring_matrix" /> + <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> <validator type="in_range" min="0" /> @@ -142,15 +95,7 @@ </inputs> <outputs> <data name="output1" format="tabular" label="${blast_type.value_label} on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + <expand macro="output_change_format" /> </data> </outputs> <tests> |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,12 +1,15 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.19"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.21"> <description>Search protein database with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> <requirements> <requirement type="binary">blastx</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> + <requirement type="package" version="2.2.27">blast+</requirement> </requirements> <version_command>blastx -version</version_command> + <macros> + <import>ncbi_macros.xml</import> + </macros> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -46,80 +49,18 @@ ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + + <expand macro="stdio" /> + <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">Locally installed BLAST database</option> - <option value="histdb">BLAST database from your history</option> - <option value="file">FASTA file from your history (see warning note below)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> - </when> - </conditional> - <param name="query_gencode" type="select" label="Query genetic code"> - <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> - <option value="1" select="True">1. Standard</option> - <option value="2">2. Vertebrate Mitochondrial</option> - <option value="3">3. Yeast Mitochondrial</option> - <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> - <option value="5">5. Invertebrate Mitochondrial</option> - <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> - <option value="9">9. Echinoderm Mitochondrial</option> - <option value="10">10. Euplotid Nuclear</option> - <option value="11">11. Bacteria and Archaea</option> - <option value="12">12. Alternative Yeast Nuclear</option> - <option value="13">13. Ascidian Mitochondrial</option> - <option value="14">14. Flatworm Mitochondrial</option> - <option value="15">15. Blepharisma Macronuclear</option> - <option value="16">16. Chlorophycean Mitochondrial Code</option> - <option value="21">21. Trematode Mitochondrial Code</option> - <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> - <option value="23">23. Thraustochytrium Mitochondrial Code</option> - <option value="24">24. Pterobranchia mitochondrial code</option> - </param> + + <expand macro="input_conditional_protein_db" /> + <expand macro="input_query_gencode" /> <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> + + <expand macro="input_out_format" /> + <conditional name="adv_opts"> <param name="adv_opts_selector" type="select" label="Advanced Options"> <option value="basic" selected="True">Hide Advanced Options</option> @@ -134,16 +75,9 @@ <option value="-strand plus">Plus (forward)</option> <option value="-strand minus">Minus (reverse complement)</option> </param> - <param name="matrix" type="select" label="Scoring matrix"> - <option value="BLOSUM90">BLOSUM90</option> - <option value="BLOSUM80">BLOSUM80</option> - <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> - <option value="BLOSUM50">BLOSUM50</option> - <option value="BLOSUM45">BLOSUM45</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> - </param> + + <expand macro="input_scoring_matrix" /> + <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> <validator type="in_range" min="0" /> @@ -159,15 +93,7 @@ </inputs> <outputs> <data name="output1" format="tabular" label="blastx on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + <expand macro="output_change_format" /> </data> </outputs> <tests> |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -0,0 +1,115 @@ +<tool id="ncbi_dustmasker_wrapper" name="NCBI dustmasker" version="0.0.21"> + <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo --> + <description>masks low complexity regions</description> + <requirements> + <requirement type="binary">dustmasker</requirement> + <requirement type="package" version="2.2.27">blast+</requirement> + </requirements> + <version_command>dustmasker -version-full</version_command> + <macros> + <import>ncbi_macros.xml</import> + </macros> + <command> +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +dustmasker +#if $db_opts.db_opts_selector == "db": + -in "${db_opts.database.fields.path}" -infmt blastdb +#elif $db_opts.db_opts_selector == "histdb": + -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb +#else: + -in "$subject" -infmt fasta +#end if +-out "$outfile" +-window $window -level $level -linker $linker -outfmt $outformat + </command> + <expand macro="stdio" /> + <inputs> + <expand macro="input_conditional_nucleotide_db" /> + <param name="window" type="integer" value="64" label="DUST window length" /> + <param name="level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" /> + <param name="linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" /> + <param name="outformat" type="select" label="Output format"> +<!-- acclist and maskinfo_xml are listed as possible output formats in + "dustmasker -help", but were not recognized by NCBI BLAST up to + release 2.2.27+. Fixed in BLAST 2.2.28+. + seqloc_* formats are not very useful --> +<!-- <option value="acclist">acclist</option>--> + <option value="fasta">FASTA</option> + <option value="interval" selected="true">interval</option> + <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> + <option value="maskinfo_asn1_text">maskinfo ASN.1 text</option> +<!-- <option value="maskinfo_xml">maskinfo_xml</option> + <option value="seqloc_asn1_bin">seqloc_asn1_bin</option> + <option value="seqloc_asn1_text">seqloc_asn1_text</option> + <option value="seqloc_xml">seqloc_xml</option>--> + </param> + </inputs> + <outputs> + <data name="outfile" format="interval" label="DUST Masked File"> + <change_format> + <when input="outformat" value="fasta" format="fasta" /> + <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> + <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="window" value="64" /> + <param name="level" value="20" /> + <param name="linker" value="1" /> + <param name="outformat" value="fasta" /> + <output name="outfile" file="dustmasker_three_human.fasta" /> + </test> + <test> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="window" value="64" /> + <param name="level" value="20" /> + <param name="linker" value="1" /> + <param name="outformat" value="maskinfo_asn1_bin" /> + <output name="outfile" file="dustmasker_three_human.maskinfo-asn1-binary" /> + </test> + <test> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="window" value="64" /> + <param name="level" value="20" /> + <param name="linker" value="1" /> + <param name="outformat" value="maskinfo_asn1_text" /> + <output name="outfile" file="dustmasker_three_human.maskinfo-asn1" /> + </test> + </tests> + <help> +**What it does** + +This tool identifies and masks out low complexity regions of a nucleotide database (or sequences in FASTA format) by using the symmetric DUST algorithm. + +If you select *maskinfo ASN.1* (binary or text) as output format, the output file can be used as masking data for NCBI BLAST+ makeblastdb tool. + +More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_. + +.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers (a more specific paper covering this wrapper is planned): + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus + </help> +</tool> |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| b'@@ -0,0 +1,220 @@\n+<macros>\n+ <macro name="output_change_format">\n+\n+ <change_format>\n+ <when input="out_format" value="0" format="txt"/>\n+ <when input="out_format" value="0 -html" format="html"/>\n+ <when input="out_format" value="2" format="txt"/>\n+ <when input="out_format" value="2 -html" format="html"/>\n+ <when input="out_format" value="4" format="txt"/>\n+ <when input="out_format" value="4 -html" format="html"/>\n+ <when input="out_format" value="5" format="blastxml"/>\n+ </change_format>\n+\n+ </macro>\n+ <macro name="input_out_format">\n+ <param name="out_format" type="select" label="Output format">\n+ <option value="6">Tabular (standard 12 columns)</option>\n+ <option value="ext" selected="True">Tabular (extended 24 columns)</option>\n+ <option value="5">BLAST XML</option>\n+ <option value="0">Pairwise text</option>\n+ <option value="0 -html">Pairwise HTML</option>\n+ <option value="2">Query-anchored text</option>\n+ <option value="2 -html">Query-anchored HTML</option>\n+ <option value="4">Flat query-anchored text</option>\n+ <option value="4 -html">Flat query-anchored HTML</option>\n+ <!--\n+ <option value="-outfmt 11">BLAST archive format (ASN.1)</option>\n+ -->\n+ </param>\n+ </macro>\n+ <macro name="input_scoring_matrix">\n+ <param name="matrix" type="select" label="Scoring matrix">\n+ <option value="BLOSUM90">BLOSUM90</option>\n+ <option value="BLOSUM80">BLOSUM80</option>\n+ <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>\n+ <option value="BLOSUM50">BLOSUM50</option> \n+ <option value="BLOSUM45">BLOSUM45</option>\n+ <option value="PAM250">PAM250</option>\n+ <option value="PAM70">PAM70</option>\n+ <option value="PAM30">PAM30</option>\n+ </param>\n+ </macro>\n+ <macro name="stdio">\n+ <stdio>\n+ <!-- Anything other than zero is an error -->\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ <!-- In case the return code has not been set propery check stderr too -->\n+ <regex match="Error:" />\n+ <regex match="Exception:" />\n+ </stdio>\n+ </macro>\n+ <macro name="input_query_gencode">\n+ <param name="query_gencode" type="select" label="Query genetic code">\n+ <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->\n+ <option value="1" select="True">1. Standard</option>\n+ <option value="2">2. Vertebrate Mitochondrial</option>\n+ <option value="3">3. Yeast Mitochondrial</option>\n+ <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>\n+ <option value="5">5. Invertebrate Mitochondrial</option>\n+ <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>\n+ <option value="9">9. Echinoderm Mitochondrial</option>\n+ <option value="10">10. Euplotid Nuclear</option>\n+ <option value="11">11. Bacteria and Archaea</option>\n+ <option value="12">12. Alternative Yeast Nuclear</option>\n+ <option value="13">13. Ascidian Mitochondrial</option>\n+ <option value="14">14. Flatworm Mitochondrial</option>\n+ <option value="15">15. Blepharisma Macronuclear</option>\n+ <option value="16">16. Chlorophycean Mitochondrial Code</option>\n+ <option value="21">21. Trematode Mitochondrial Code</option>\n+ <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>\n+ <option value="23">23. Thraustochytrium Mitochondrial Code</option>\n+ <option value="24">24. Pterobranchia mitochondrial code</option>\n+ '..b'se</option>\n+ <option value="histdb">BLAST database from your history</option>\n+ <option value="file">FASTA file from your history (see warning note below)</option>\n+ </param>\n+ <when value="db">\n+ <param name="database" type="select" label="Protein BLAST database">\n+ <options from_file="blastdb_p.loc">\n+ <column name="value" index="0"/>\n+ <column name="name" index="1"/>\n+ <column name="path" index="2"/>\n+ </options>\n+ </param>\n+ <param name="histdb" type="hidden" value="" />\n+ <param name="subject" type="hidden" value="" />\n+ </when>\n+ <when value="histdb">\n+ <param name="database" type="hidden" value="" />\n+ <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" />\n+ <param name="subject" type="hidden" value="" />\n+ </when>\n+ <when value="file">\n+ <param name="database" type="hidden" value="" />\n+ <param name="histdb" type="hidden" value="" />\n+ <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> \n+ </when>\n+ </conditional>\n+ </macro>\n+\n+ <macro name="input_conditional_pssm">\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)">\n+ <option value="db" selected="True">Locally installed BLAST database</option>\n+ <!-- TODO - define new datatype\n+ <option value="histdb">BLAST protein domain database from your history</option>\n+ -->\n+ </param>\n+ <when value="db">\n+ <param name="database" type="select" label="Protein domain database">\n+ <options from_file="blastdb_d.loc">\n+ <column name="value" index="0"/>\n+ <column name="name" index="1"/>\n+ <column name="path" index="2"/>\n+ </options>\n+ </param>\n+ <param name="histdb" type="hidden" value="" />\n+ <param name="subject" type="hidden" value="" />\n+ </when>\n+ <!-- TODO - define new datatype\n+ <when value="histdb">\n+ <param name="database" type="hidden" value="" />\n+ <param name="histdb" type="data" format="blastdbd" label="Protein domain database" />\n+ <param name="subject" type="hidden" value="" />\n+ </when>\n+ -->\n+ </conditional>\n+ </macro>\n+\n+ <macro name="input_conditional_choose_db_type">\n+ <conditional name="db_opts">\n+ <param name="db_type" type="select" label="Type of BLAST database">\n+ <option value="nucl" selected="True">Nucleotide</option>\n+ <option value="prot">Protein</option>\n+ </param>\n+ <when value="nucl">\n+ <param name="database" type="select" label="Nucleotide BLAST database">\n+ <options from_file="blastdb.loc">\n+ <column name="value" index="0"/>\n+ <column name="name" index="1"/>\n+ <column name="path" index="2"/>\n+ </options>\n+ </param>\n+ </when>\n+ <when value="prot">\n+ <param name="database" type="select" label="Protein BLAST database">\n+ <options from_file="blastdb_p.loc">\n+ <column name="value" index="0"/>\n+ <column name="name" index="1"/>\n+ <column name="path" index="2"/>\n+ </options>\n+ </param>\n+ </when>\n+ </conditional>\n+ </macro>\n+\n+\n+</macros>\n' |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,10 +1,13 @@ -<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.5"> +<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.21"> <description>Make BLAST database</description> <requirements> <requirement type="binary">makeblastdb</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> + <requirement type="package" version="2.2.27">blast+</requirement> </requirements> <version_command>makeblastdb -version</version_command> + <macros> + <import>ncbi_macros.xml</import> + </macros> <command> makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}" $parse_seqids @@ -24,30 +27,29 @@ -title "BLAST Database" #end if -dbtype $dbtype -## #set $sep = '-mask_data ' -## #for $i in $mask_data -## $sep${i.file} -## #set $set = ', ' -## #end for +#set $mask_string = '' +#set $sep = '-mask_data ' +#for $i in $mask_data +#set $mask_string += $sep + str($i.file) +#set $sep = ',' +#end for +$mask_string +## #set $gi_mask_string = '' ## #set $sep = '-gi_mask -gi_mask_name ' ## #for $i in $gi_mask -## $sep${i.file} -## #set $set = ', ' -## #end for +## #set $gi_mask_string += $sep + str($i.file) +## #set $sep = ',' +## #end for +## $gi_mask_string ## #if $tax.select == 'id': ## -taxid $tax.id ## #else if $tax.select == 'map': ## -taxid_map $tax.map ## #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + + <expand macro="stdio" /> + <inputs> <param name="dbtype" type="select" display="radio" label="Molecule type of input"> <option value="prot">protein</option> @@ -66,10 +68,10 @@ <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values." help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." /> <!-- SEQUENCE MASKING OPTIONS --> + <repeat name="mask_data" title="Masking data file"> + <param name="file" type="data" format="maskinfo-asn1,maskinfo-asn1-binary" label="ASN.1 file containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> + </repeat> <!-- TODO - <repeat name="mask_data" title="Provide one or more files containing masking data"> - <param name="file" type="data" format="asnb" label="File containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> - </repeat> <repeat name="gi_mask" title="Create GI indexed masking data"> <param name="file" type="data" format="asnb" label="Masking data output file" /> </repeat> |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,12 +1,15 @@ -<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.0.4"> +<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.0.21"> <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> <requirements> <requirement type="binary">rpsblast</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> + <requirement type="package" version="2.2.27">blast+</requirement> </requirements> <version_command>rpsblast -version</version_command> + <macros> + <import>ncbi_macros.xml</import> + </macros> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -40,57 +43,18 @@ ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + + <expand macro="stdio" /> + <inputs> <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)"> - <option value="db" selected="True">Locally installed BLAST database</option> - <!-- TODO - define new datatype - <option value="histdb">BLAST protein domain database from your history</option> - --> - </param> - <when value="db"> - <param name="database" type="select" label="Protein domain database"> - <options from_file="blastdb_d.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <!-- TODO - define new datatype - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbd" label="Protein domain database" /> - <param name="subject" type="hidden" value="" /> - </when> - --> - </conditional> + + <expand macro="input_conditional_pssm" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> + + <expand macro="input_out_format" /> + <conditional name="adv_opts"> <param name="adv_opts_selector" type="select" label="Advanced Options"> <option value="basic" selected="True">Hide Advanced Options</option> @@ -114,15 +78,9 @@ </inputs> <outputs> <data name="output1" format="tabular" label="rpsblast on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + + <expand macro="output_change_format" /> + </data> </outputs> <help> |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,12 +1,15 @@ -<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.4"> +<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.21"> <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> <requirements> <requirement type="binary">rpstblastn</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> + <requirement type="package" version="2.2.27">blast+</requirement> </requirements> <version_command>rpstblastn -version</version_command> + <macros> + <import>ncbi_macros.xml</import> + </macros> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -41,57 +44,16 @@ ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + <expand macro="stdio" /> <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)"> - <option value="db" selected="True">Locally installed BLAST database</option> - <!-- TODO - define new datatype - <option value="histdb">BLAST protein domain database from your history</option> - --> - </param> - <when value="db"> - <param name="database" type="select" label="Protein domain database"> - <options from_file="blastdb_d.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <!-- TODO - define new datatype - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbd" label="Protein domain database" /> - <param name="subject" type="hidden" value="" /> - </when> - --> - </conditional> + + <expand macro="input_conditional_pssm" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> + + <expand macro="input_out_format" /> + <conditional name="adv_opts"> <param name="adv_opts_selector" type="select" label="Advanced Options"> <option value="basic" selected="True">Hide Advanced Options</option> @@ -115,15 +77,7 @@ </inputs> <outputs> <data name="output1" format="tabular" label="rpstblastn on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + <expand macro="output_change_format" /> </data> </outputs> <help> |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| b'@@ -1,12 +1,15 @@\n-<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.20">\n+<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.21">\n <description>Search translated nucleotide database with protein query sequence(s)</description>\n <!-- If job splitting is enabled, break up the query file into parts -->\n <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>\n <requirements>\n <requirement type="binary">tblastn</requirement>\n- <requirement type="package" version="2.2.26+">blast+</requirement>\n+ <requirement type="package" version="2.2.27">blast+</requirement>\n </requirements>\n <version_command>tblastn -version</version_command>\n+ <macros>\n+ <import>ncbi_macros.xml</import>\n+ </macros>\n <command>\n ## The command is a Cheetah template which allows some Python based syntax.\n ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces\n@@ -46,59 +49,16 @@\n ## End of advanced options:\n #end if\n </command>\n- <stdio>\n- <!-- Anything other than zero is an error -->\n- <exit_code range="1:" />\n- <exit_code range=":-1" />\n- <!-- In case the return code has not been set propery check stderr too -->\n- <regex match="Error:" />\n- <regex match="Exception:" />\n- </stdio>\n+\n+ <expand macro="stdio" />\n+\n <inputs>\n <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> \n- <conditional name="db_opts">\n- <param name="db_opts_selector" type="select" label="Subject database/sequences">\n- <option value="db" selected="True">Locally installed BLAST database</option>\n- <option value="histdb">BLAST database from your history</option>\n- <option value="file">FASTA file from your history (see warning note below)</option>\n- </param>\n- <when value="db">\n- <param name="database" type="select" label="Nucleotide BLAST database">\n- <options from_file="blastdb.loc">\n- <column name="value" index="0"/>\n- <column name="name" index="1"/>\n- <column name="path" index="2"/>\n- </options>\n- </param>\n- <param name="histdb" type="hidden" value="" />\n- <param name="subject" type="hidden" value="" />\n- </when>\n- <when value="histdb">\n- <param name="database" type="hidden" value="" />\n- <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" />\n- <param name="subject" type="hidden" value="" />\n- </when>\n- <when value="file">\n- <param name="database" type="hidden" value="" />\n- <param name="histdb" type="hidden" value="" />\n- <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> \n- </when>\n- </conditional>\n+\n+ <expand macro="input_conditional_nucleotide_db" />\n+ <expand macro="input_out_format" />\n <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />\n- <param name="out_format" type="select" label="Output format">\n- <option value="6">Tabular (standard 12 columns)</option>\n- <option value="ext" selected="True">Tabular (extended 24 columns)</option>\n- <option value="5">BLAST XML</option>\n- <option value="0">Pairwise text</option>\n- <option value="0 -html">Pairwise HTML</option>\n- <option value="2">Query-anchored text</option>\n- <option value="2 -html">Query-anchored HTML</option>\n- <option value="4">Flat query-anchored text</option>\n- '..b'Hide Advanced Options</option>\n@@ -106,39 +66,14 @@\n </param>\n <when value="basic" />\n <when value="advanced">\n- <param name="db_gencode" type="select" label="Database/subject genetic code">\n- <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->\n- <option value="1" select="True">1. Standard</option>\n- <option value="2">2. Vertebrate Mitochondrial</option>\n- <option value="3">3. Yeast Mitochondrial</option>\n- <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>\n- <option value="5">5. Invertebrate Mitochondrial</option>\n- <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>\n- <option value="9">9. Echinoderm Mitochondrial</option>\n- <option value="10">10. Euplotid Nuclear</option>\n- <option value="11">11. Bacteria and Archaea</option>\n- <option value="12">12. Alternative Yeast Nuclear</option>\n- <option value="13">13. Ascidian Mitochondrial</option>\n- <option value="14">14. Flatworm Mitochondrial</option>\n- <option value="15">15. Blepharisma Macronuclear</option>\n- <option value="16">16. Chlorophycean Mitochondrial Code</option>\n- <option value="21">21. Trematode Mitochondrial Code</option>\n- <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>\n- <option value="23">23. Thraustochytrium Mitochondrial Code</option>\n- <option value="24">24. Pterobranchia mitochondrial code</option>\n- </param>\n+\n+ <expand macro="input_db_gencode" />\n+\n <!-- Could use a select (yes, no, other) where other allows setting \'window locut hicut\' -->\n <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />\n- <param name="matrix" type="select" label="Scoring matrix">\n- <option value="BLOSUM90">BLOSUM90</option>\n- <option value="BLOSUM80">BLOSUM80</option>\n- <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>\n- <option value="BLOSUM50">BLOSUM50</option> \n- <option value="BLOSUM45">BLOSUM45</option>\n- <option value="PAM250">PAM250</option>\n- <option value="PAM70">PAM70</option>\n- <option value="PAM30">PAM30</option>\n- </param>\n+\n+ <expand macro="input_scoring_matrix" />\n+\n <!-- Why doesn\'t optional override a validator? I want to accept an empty string OR a non-negative integer -->\n <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">\n <validator type="in_range" min="0" />\n@@ -159,15 +94,7 @@\n </inputs>\n <outputs>\n <data name="output1" format="tabular" label="tblastn on ${on_string}">\n- <change_format>\n- <when input="out_format" value="0" format="txt"/>\n- <when input="out_format" value="0 -html" format="html"/>\n- <when input="out_format" value="2" format="txt"/>\n- <when input="out_format" value="2 -html" format="html"/>\n- <when input="out_format" value="4" format="txt"/>\n- <when input="out_format" value="4 -html" format="html"/>\n- <when input="out_format" value="5" format="blastxml"/>\n- </change_format>\n+ <expand macro="output_change_format" />\n </data>\n </outputs>\n <tests>\n' |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| b'@@ -1,12 +1,15 @@\n-<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.20">\n+<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.21">\n <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>\n <!-- If job splitting is enabled, break up the query file into parts -->\n <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>\n <requirements>\n <requirement type="binary">tblastx</requirement>\n- <requirement type="package" version="2.2.26+">blast+</requirement>\n+ <requirement type="package" version="2.2.27">blast+</requirement>\n </requirements>\n <version_command>tblastx -version</version_command>\n+ <macros>\n+ <import>ncbi_macros.xml</import>\n+ </macros>\n <command>\n ## The command is a Cheetah template which allows some Python based syntax.\n ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces\n@@ -46,80 +49,18 @@\n ## End of advanced options:\n #end if\n </command>\n- <stdio>\n- <!-- Anything other than zero is an error -->\n- <exit_code range="1:" />\n- <exit_code range=":-1" />\n- <!-- In case the return code has not been set propery check stderr too -->\n- <regex match="Error:" />\n- <regex match="Exception:" />\n- </stdio>\n+\n+ <expand macro="stdio" />\n+\n <inputs>\n <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> \n- <conditional name="db_opts">\n- <param name="db_opts_selector" type="select" label="Subject database/sequences">\n- <option value="db" selected="True">Locally installed BLAST database</option>\n- <option value="histdb">BLAST database from your history</option>\n- <option value="file">FASTA file from your history (see warning note below)</option>\n- </param>\n- <when value="db">\n- <param name="database" type="select" label="Nucleotide BLAST database">\n- <options from_file="blastdb.loc">\n- <column name="value" index="0"/>\n- <column name="name" index="1"/>\n- <column name="path" index="2"/>\n- </options>\n- </param>\n- <param name="histdb" type="hidden" value="" />\n- <param name="subject" type="hidden" value="" />\n- </when>\n- <when value="histdb">\n- <param name="database" type="hidden" value="" />\n- <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" />\n- <param name="subject" type="hidden" value="" />\n- </when>\n- <when value="file">\n- <param name="database" type="hidden" value="" />\n- <param name="histdb" type="hidden" value="" />\n- <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> \n- </when>\n- </conditional>\n- <param name="query_gencode" type="select" label="Query genetic code">\n- <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->\n- <option value="1" select="True">1. Standard</option>\n- <option value="2">2. Vertebrate Mitochondrial</option>\n- <option value="3">3. Yeast Mitochondrial</option>\n- <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>\n- <option value="5">5. Invertebrate Mitochondrial</option>\n- <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>\n- <option value="9">9. Echinoderm Mitochondrial</option>\n- <option value="10">10. Euplotid Nuclear</option>\n- '..b'wprintgc.cgi for details -->\n- <option value="1" select="True">1. Standard</option>\n- <option value="2">2. Vertebrate Mitochondrial</option>\n- <option value="3">3. Yeast Mitochondrial</option>\n- <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>\n- <option value="5">5. Invertebrate Mitochondrial</option>\n- <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>\n- <option value="9">9. Echinoderm Mitochondrial</option>\n- <option value="10">10. Euplotid Nuclear</option>\n- <option value="11">11. Bacteria and Archaea</option>\n- <option value="12">12. Alternative Yeast Nuclear</option>\n- <option value="13">13. Ascidian Mitochondrial</option>\n- <option value="14">14. Flatworm Mitochondrial</option>\n- <option value="15">15. Blepharisma Macronuclear</option>\n- <option value="16">16. Chlorophycean Mitochondrial Code</option>\n- <option value="21">21. Trematode Mitochondrial Code</option>\n- <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>\n- <option value="23">23. Thraustochytrium Mitochondrial Code</option>\n- <option value="24">24. Pterobranchia mitochondrial code</option>\n- </param>\n+\n+ <expand macro="input_db_gencode" />\n+\n <!-- Could use a select (yes, no, other) where other allows setting \'window locut hicut\' -->\n <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />\n <param name="strand" type="select" label="Query strand(s) to search against database/subject">\n@@ -155,16 +78,7 @@\n <option value="-strand plus">Plus (forward)</option>\n <option value="-strand minus">Minus (reverse complement)</option>\n </param>\n- <param name="matrix" type="select" label="Scoring matrix">\n- <option value="BLOSUM90">BLOSUM90</option>\n- <option value="BLOSUM80">BLOSUM80</option>\n- <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>\n- <option value="BLOSUM50">BLOSUM50</option> \n- <option value="BLOSUM45">BLOSUM45</option>\n- <option value="PAM250">PAM250</option>\n- <option value="PAM70">PAM70</option>\n- <option value="PAM30">PAM30</option>\n- </param>\n+ <expand macro="input_scoring_matrix" />\n <!-- Why doesn\'t optional override a validator? I want to accept an empty string OR a non-negative integer -->\n <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">\n <validator type="in_range" min="0" />\n@@ -179,15 +93,7 @@\n </inputs>\n <outputs>\n <data name="output1" format="tabular" label="tblastx on ${on_string}">\n- <change_format>\n- <when input="out_format" value="0" format="txt"/>\n- <when input="out_format" value="0 -html" format="html"/>\n- <when input="out_format" value="2" format="txt"/>\n- <when input="out_format" value="2 -html" format="html"/>\n- <when input="out_format" value="4" format="txt"/>\n- <when input="out_format" value="4 -html" format="html"/>\n- <when input="out_format" value="5" format="blastxml"/>\n- </change_format>\n+ <expand macro="output_change_format" />\n </data>\n </outputs>\n <tests>\n' |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/repository_dependencies.xml --- a/tools/ncbi_blast_plus/repository_dependencies.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/repository_dependencies.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> - <repository changeset_revision="a44a7a5456e1" name="blast_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="7ceb2ae30ff4" name="blast_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories> |
| b |
| diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/tool_dependencies.xml --- a/tools/ncbi_blast_plus/tool_dependencies.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Tue Oct 08 05:08:26 2013 -0400 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="blast+" version="2.2.26+"> - <repository changeset_revision="c85236cd100d" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <package name="blast+" version="2.2.27"> + <repository changeset_revision="eab09bc4d63e" name="package_blast_plus_2_2_27" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |