Mercurial > repos > devteam > tabular_to_fasta
comparison tabular_to_fasta.py @ 0:0b4e36026794 draft
Imported from capsule None
| author | devteam |
|---|---|
| date | Mon, 19 May 2014 12:34:07 -0400 |
| parents | |
| children | 0a7799698fe5 |
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| -1:000000000000 | 0:0b4e36026794 |
|---|---|
| 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__() |