comparison fasta_to_tabular.py @ 0:ae709fd50581 draft

Imported from capsule None
author devteam
date Mon, 19 May 2014 11:00:01 -0400
parents
children ff4751ce764d
comparison
equal deleted inserted replaced
-1:000000000000 0:ae709fd50581
1 #!/usr/bin/env python
2 # This code exists in 2 places: ~/datatypes/converters and ~/tools/fasta_tools
3 """
4 Input: fasta (input file), tabular (output file), int (truncation of id), int (columns from description)
5 Output: tabular
6 format convert: fasta to tabular
7 """
8
9 import sys, os
10
11 def stop_err( msg ):
12 sys.stderr.write( msg )
13 sys.exit()
14
15 def __main__():
16 if len(sys.argv) != 5:
17 stop_err("Wrong number of argument. Expect four (fasta, tabular, truncation, columns)")
18 infile = sys.argv[1]
19 outfile = sys.argv[2]
20 keep_first = int( sys.argv[3] )
21 descr_split = int( sys.argv[4] )
22 fasta_title = fasta_seq = ''
23 if keep_first == 0:
24 keep_first = None
25 elif descr_split == 1:
26 #Added one for the ">" character
27 #(which is removed if using descr_split > 1)
28 keep_first += 1
29 if descr_split < 1:
30 stop_err("Bad description split value (should be 1 or more)")
31 out = open( outfile, 'w' )
32 for i, line in enumerate( open( infile ) ):
33 line = line.rstrip( '\r\n' )
34 if not line or line.startswith( '#' ):
35 continue
36 if line.startswith( '>' ):
37 #Don't want any existing tabs to trigger extra columns:
38 line = line.replace('\t', ' ')
39 if i > 0:
40 out.write('\n')
41 if descr_split == 1:
42 out.write(line[1:keep_first])
43 else:
44 words = line[1:].split(None, descr_split-1)
45 #apply any truncation to first word (the id)
46 words[0] = words[0][0:keep_first]
47 #pad with empty columns if required
48 words += [""]*(descr_split-len(words))
49 out.write("\t".join(words))
50 out.write('\t')
51 else:
52 out.write(line)
53 if i > 0:
54 out.write('\n')
55 out.close()
56
57 if __name__ == "__main__" : __main__()