Mercurial > repos > peterjc > fastq_pair_names
changeset 10:8ceccb6738de draft default tip
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names commit d67596914a7bbe183851437eaafe8c7305877e5a-dirty
| author | peterjc |
|---|---|
| date | Fri, 22 Feb 2019 10:14:11 -0500 |
| parents | 9e0212695094 |
| children | |
| files | tools/fastq_pair_names/fastq_pair_names.py tools/fastq_pair_names/tool_dependencies.xml |
| diffstat | 2 files changed, 15 insertions(+), 9 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/fastq_pair_names/fastq_pair_names.py Fri Nov 09 10:52:02 2018 -0500 +++ b/tools/fastq_pair_names/fastq_pair_names.py Fri Feb 22 10:14:11 2019 -0500 @@ -70,8 +70,12 @@ 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" +) count = 0 pairs = set() # Will this scale OK? @@ -99,7 +103,7 @@ # ============ # Forward read # ============ - template = name[:suffix.start()] + template = name[: suffix.start()] is_forward = True elif re_illumina_f.match(record.identifier): template = name # No suffix @@ -116,7 +120,7 @@ # ============ # Reverse read # ============ - template = name[:suffix.start()] + template = name[: suffix.start()] is_reverse = True elif re_illumina_r.match(record.identifier): template = name # No suffix @@ -136,5 +140,7 @@ out_pairs.close() out_nonpairs.close() -print("%i reads (%i forward, %i reverse, %i neither), %i pairs" % - (count, forward, reverse, neither, len(pairs))) +print( + "%i reads (%i forward, %i reverse, %i neither), %i pairs" + % (count, forward, reverse, neither, len(pairs)) +)
--- a/tools/fastq_pair_names/tool_dependencies.xml Fri Nov 09 10:52:02 2018 -0500 +++ b/tools/fastq_pair_names/tool_dependencies.xml Fri Feb 22 10:14:11 2019 -0500 @@ -1,6 +1,6 @@ -<?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> -</tool_dependency> +</tool_dependency> \ No newline at end of file