Mercurial > repos > peterjc > fastq_paired_unpaired
changeset 25:7bb90baebdf5 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired commit d67596914a7bbe183851437eaafe8c7305877e5a-dirty
| author | peterjc |
|---|---|
| date | Fri, 22 Feb 2019 10:14:56 -0500 |
| parents | f9dd4ba8c8a6 |
| children | 680343171dbb |
| files | tools/fastq_paired_unpaired/fastq_paired_unpaired.py tools/fastq_paired_unpaired/tool_dependencies.xml |
| diffstat | 2 files changed, 33 insertions(+), 15 deletions(-) [+] |
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--- a/tools/fastq_paired_unpaired/fastq_paired_unpaired.py Fri Nov 09 10:53:10 2018 -0500 +++ b/tools/fastq_paired_unpaired/fastq_paired_unpaired.py Fri Feb 22 10:14:56 2019 -0500 @@ -122,8 +122,12 @@ re_illumina_r = re.compile(r"^[a-zA-Z0-9_:-]+ 2:.*$") assert re_illumina_f.match("HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA") assert re_illumina_r.match("HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA") -assert not re_illumina_f.match("HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA") -assert not re_illumina_r.match("HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA") +assert not re_illumina_f.match( + "HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA" +) +assert not re_illumina_r.match( + "HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA" +) FASTQ_TEMPLATE = "@%s\n%s\n+\n%s\n" @@ -147,7 +151,7 @@ # ============ # Forward read # ============ - template = name[:suffix.start()] + template = name[: suffix.start()] is_forward = True elif re_illumina_f.match(title): template = name # No suffix @@ -172,7 +176,7 @@ # ============ # Reverse read # ============ - template = name[:suffix.start()] + template = name[: suffix.start()] is_reverse = True elif re_illumina_r.match(title): template = name # No suffix @@ -226,12 +230,26 @@ pairs_r_handle.close() if neither: - print("%i reads (%i forward, %i reverse, %i neither), %i in pairs, %i as singles" - % (count, forward, reverse, neither, pairs, singles)) + print( + "%i reads (%i forward, %i reverse, %i neither), %i in pairs, %i as singles" + % (count, forward, reverse, neither, pairs, singles) + ) else: - print("%i reads (%i forward, %i reverse), %i in pairs, %i as singles" - % (count, forward, reverse, pairs, singles)) + print( + "%i reads (%i forward, %i reverse), %i in pairs, %i as singles" + % (count, forward, reverse, pairs, singles) + ) -assert count == pairs + singles == forward + reverse + neither, \ - "%i vs %i+%i=%i vs %i+%i+%i=%i" \ - % (count, pairs, singles, pairs + singles, forward, reverse, neither, forward + reverse + neither) +assert count == pairs + singles == forward + reverse + neither, ( + "%i vs %i+%i=%i vs %i+%i+%i=%i" + % ( + count, + pairs, + singles, + pairs + singles, + forward, + reverse, + neither, + forward + reverse + neither, + ) +)
--- a/tools/fastq_paired_unpaired/tool_dependencies.xml Fri Nov 09 10:53:10 2018 -0500 +++ b/tools/fastq_paired_unpaired/tool_dependencies.xml Fri Feb 22 10:14:56 2019 -0500 @@ -1,9 +1,9 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <tool_dependency> <package name="galaxy_sequence_utils" version="1.0.1"> - <repository changeset_revision="c38bd3fe9da6" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c38bd3fe9da6" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"/> </package> <package name="biopython" version="1.67"> - <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu"/> </package> -</tool_dependency> +</tool_dependency> \ No newline at end of file