Mercurial > repos > xuebing > sharplabtool

comparison tools/fasta_tools/tabular_to_fasta.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2 """
3 Input: fasta, minimal length, maximal length
4 Output: fasta
5 Return sequences whose lengths are within the range.
6 """
7 import sys, os
8
9 assert sys.version_info[:2] >= ( 2, 4 )
10
11 def stop_err( msg ):
12 sys.stderr.write( msg )
13 sys.exit()
14
15 def __main__():
16 infile = sys.argv[1]
17 title_col = sys.argv[2]
18 seq_col = sys.argv[3]
19 outfile = sys.argv[4]
20
21 if title_col == None or title_col == 'None' or seq_col == None or seq_col == 'None':
22 stop_err( "Columns not specified." )
23 try:
24 seq_col = int( seq_col ) - 1
25 except:
26 stop_err( "Invalid Sequence Column: %s." %str( seq_col ) )
27
28 title_col_list = title_col.split( ',' )
29 out = open( outfile, 'w' )
30 skipped_lines = 0
31 first_invalid_line = 0
32 invalid_line = ""
33 i = 0
34
35 for i, line in enumerate( open( infile ) ):
36 error = False
37 line = line.rstrip( '\r\n' )
38 if line and not line.startswith( '#' ):
39 fields = line.split( '\t' )
40 fasta_title = []
41 for j in title_col_list:
42 try:
43 j = int( j ) - 1
44 fasta_title.append( fields[j] )
45 except:
46 skipped_lines += 1
47 if not invalid_line:
48 first_invalid_line = i + 1
49 invalid_line = line
50 error = True
51 break
52 if not error:
53 try:
54 fasta_seq = fields[seq_col]
55 if fasta_title[0].startswith( ">" ):
56 fasta_title[0] = fasta_title[0][1:]
57 print >> out, ">%s\n%s" % ( "_".join( fasta_title ), fasta_seq )
58 except:
59 skipped_lines += 1
60 if not invalid_line:
61 first_invalid_line = i + 1
62 invalid_line = line
63 out.close()
64
65 if skipped_lines > 0:
66 print 'Data issue: skipped %d blank or invalid lines starting at #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
67
68 if __name__ == "__main__" : __main__()