Mercurial > repos > bgruening > find_subsequences
changeset 7:99f356eeba15 draft
planemo upload commit 7ff6d582464c6b7183e1acd421272167f8a2433f
| author | bgruening |
|---|---|
| date | Tue, 05 Apr 2016 15:26:05 -0400 |
| parents | 53c20f28562e |
| children | e614ec7a43b8 |
| files | .shed.yml find_subsequences.py find_subsequences.xml tool_dependencies.xml |
| diffstat | 4 files changed, 4 insertions(+), 6 deletions(-) [+] |
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--- a/.shed.yml Fri Apr 10 06:47:42 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -# repository published to https://toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences -owner: bgruening -name: find_subsequences
--- a/find_subsequences.py Fri Apr 10 06:47:42 2015 -0400 +++ b/find_subsequences.py Tue Apr 05 15:26:05 2016 -0400 @@ -34,7 +34,7 @@ Simple regular expression search. This is way faster than the complex search. """ bed_template = '%s\t%s\t%s\t%s\t%s\t%s\n' - for match in re.finditer( str(pattern), str(sequence.seq) ): + for match in re.finditer( str(pattern), str(sequence.seq), re.IGNORECASE ): outfile.write(bed_template % (sequence.id, match.start(), match.end(), sequence.description, '', strand))
--- a/find_subsequences.xml Fri Apr 10 06:47:42 2015 -0400 +++ b/find_subsequences.xml Tue Apr 05 15:26:05 2016 -0400 @@ -1,6 +1,7 @@ -<tool id="bg_find_subsequences" name="Nucleotide subsequence search" version="0.1"> +<tool id="bg_find_subsequences" name="Nucleotide subsequence search" version="0.2"> <description>providing regions in BED format</description> <requirements> + <!-- Contains also the Conda dependency, see https://anaconda.org/anaconda/biopython --> <requirement type="package" version="1.65">biopython</requirement> </requirements> <command interpreter="python">
--- a/tool_dependencies.xml Fri Apr 10 06:47:42 2015 -0400 +++ b/tool_dependencies.xml Tue Apr 05 15:26:05 2016 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="biopython" version="1.65"> - <repository changeset_revision="f8d72690eeae" name="package_biopython_1_65" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b3a791f6e3ba" name="package_biopython_1_65" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>