Mercurial > repos > artbio > blast_unmatched
changeset 2:dfcdac284538 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 830e10a94c2afc178f4078609842cd93808df1b4
| author | artbio |
|---|---|
| date | Thu, 05 Oct 2017 05:11:01 -0400 |
| parents | 50c1fa95a076 |
| children | fffdb903f2d1 |
| files | blast_unmatched.py blast_unmatched.xml |
| diffstat | 2 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- a/blast_unmatched.py Tue Oct 03 12:41:53 2017 -0400 +++ b/blast_unmatched.py Thu Oct 05 05:11:01 2017 -0400 @@ -1,7 +1,7 @@ #!/usr/bin/env python3 import optparse - +import re def parse_options(): """ @@ -36,10 +36,13 @@ """ output_file_handle = open(output_file, 'w') unmatched = False + end = re.compile(".+\W$") with open(fasta_file, 'r') as infile: for line in infile: if line.startswith('>'): - subline = line[1:100].rstrip() #qid are 100chars long in blast + subline = line[1:].rstrip() #qid are 100chars long in blast + while end.match(subline) != None: + subline = subline[:-1] if subline not in matched: output_file_handle.write(line) unmatched = True
--- a/blast_unmatched.xml Tue Oct 03 12:41:53 2017 -0400 +++ b/blast_unmatched.xml Thu Oct 05 05:11:01 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="blast_unmatched" name="Blast Unmatched" version="0.2.0"> +<tool id="blast_unmatched" name="Blast Unmatched" version="0.4.0"> <description>get query sequences that didn't get a match during a blast</description> <requirements> </requirements>