Mercurial > repos > artbio > blast_unmatched

comparison blast_unmatched.py @ 1:50c1fa95a076 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit be082f72c8d8c1eebe3f5643da1a73ab0ac9e4b3
author artbio
date Tue, 03 Oct 2017 12:41:53 -0400
parents f3b63b59a1ea
children dfcdac284538
comparison
equal deleted inserted replaced
0:f3b63b59a1ea 1:50c1fa95a076
21 def get_matched(blast_file): 21 def get_matched(blast_file):
22 """ 22 """
23 Get a dictionary of all the queries that got a match 23 Get a dictionary of all the queries that got a match
24 """ 24 """
25 matched = dict() 25 matched = dict()
26 blast_file_handle = open(blast_file, 'r') 26 with open(blast_file, 'r') as infile:
27 for line in blast_file_handle.readlines(): 27 for line in infile:
28 fields = line.split("\t") 28 fields = line.split("\t")
29 query_id = fields[0] 29 query_id = fields[0]
30 matched[query_id] = 1 30 matched[query_id] = 1
31 blast_file_handle.close()
32 return matched 31 return matched
33 32
34 def get_unmatched(output_file, fasta_file, matched): 33 def get_unmatched(output_file, fasta_file, matched):
35 """ 34 """
36 Compares matched queries to query fasta file and print unmatched to ouput 35 Compares matched queries to query fasta file and print unmatched to ouput
37 """ 36 """
38 output_file_handle = open(output_file, 'w') 37 output_file_handle = open(output_file, 'w')
39 fasta_file_handle = open(fasta_file, 'r')
40 unmatched = False 38 unmatched = False
41 for line in fasta_file_handle.readlines(): 39 with open(fasta_file, 'r') as infile:
42 if line.startswith('>'): 40 for line in infile:
43 subline = line[1:100].rstrip() #qid are 100chars long in blast 41 if line.startswith('>'):
44 if subline not in matched: 42 subline = line[1:100].rstrip() #qid are 100chars long in blast
43 if subline not in matched:
44 output_file_handle.write(line)
45 unmatched = True
46 else:
47 unmatched = False
48 elif unmatched:
45 output_file_handle.write(line) 49 output_file_handle.write(line)
46 unmatched = True
47 else:
48 unmatched = False
49 elif unmatched:
50 output_file_handle.write(line)
51 fasta_file_handle.close()
52 output_file_handle.close() 50 output_file_handle.close()
53 51
54 def __main__(): 52 def __main__():
55 opts = parse_options() 53 opts = parse_options()
56 matched = get_matched(opts.blast_file) 54 matched = get_matched(opts.blast_file)