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