changeset 3:fffdb903f2d1 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 1db05fc1c4849528c99b149d482eb34d3a80f22e

--- a/blast_unmatched.py	Thu Oct 05 05:11:01 2017 -0400
+++ b/blast_unmatched.py	Sun Oct 15 19:30:10 2017 -0400
@@ -3,21 +3,24 @@
 import optparse
 import re
 
+
 def parse_options():
     """
     Parse the options guiven to the script
     """
     parser = optparse.OptionParser(description='Get unmatched blast queries')
-    parser.add_option('-f','--fasta', dest='fasta_file', help='Query fasta file\
-used during blast')
-    parser.add_option('-b','--blast', dest='blast_file', help='Blast tabular\
-output (queries in 1rst column)')
-    parser.add_option('-o','--output', dest='output_file', help='Output file name')
+    parser.add_option('-f', '--fasta', dest='fasta_file',
+                      help='Query fasta file used during blast')
+    parser.add_option('-b', '--blast', dest='blast_file',
+                      help='Blast tabular output (queries in 1rst column)')
+    parser.add_option('-o', '--output', dest='output_file',
+                      help='Output file name')
     (options, args) = parser.parse_args()
     if len(args) > 0:
         parser.error('Wrong number of arguments')
     return options
 
+
 def get_matched(blast_file):
     """
     Get a dictionary of all the queries that got a match
@@ -30,6 +33,7 @@
             matched[query_id] = 1
     return matched
 
+
 def get_unmatched(output_file, fasta_file, matched):
     """
     Compares matched queries to query fasta file and print unmatched to ouput
@@ -40,8 +44,8 @@
     with open(fasta_file, 'r') as infile:
         for line in infile:
             if line.startswith('>'):
-                subline = line[1:].rstrip() #qid are 100chars long in blast
-                while end.match(subline) != None:
+                subline = line[1:].rstrip()  # qid are 100chars long in blast
+                if end.match(subline) is not None:
                     subline = subline[:-1]
                 if subline not in matched:
                     output_file_handle.write(line)
@@ -52,10 +56,12 @@
                 output_file_handle.write(line)
     output_file_handle.close()
 
+
 def __main__():
     opts = parse_options()
     matched = get_matched(opts.blast_file)
     get_unmatched(opts.output_file, opts.fasta_file, matched)
 
+
 if __main__():
     __main__()

--- a/blast_unmatched.xml	Thu Oct 05 05:11:01 2017 -0400
+++ b/blast_unmatched.xml	Sun Oct 15 19:30:10 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="blast_unmatched" name="Blast Unmatched" version="0.4.0">
+<tool id="blast_unmatched" name="Blast Unmatched" version="0.5.0">
     <description>get query sequences that didn't get a match during a blast</description>
     <requirements>
     </requirements>