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58 lines
1.9 KiB
Python
58 lines
1.9 KiB
Python
#!/usr/bin/env python
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# This code exists in 2 places: ~/datatypes/converters and ~/tools/fasta_tools
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"""
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Input: fasta (input file), tabular (output file), int (truncation of id), int (columns from description)
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Output: tabular
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format convert: fasta to tabular
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"""
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import sys, os
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def stop_err( msg ):
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sys.stderr.write( msg )
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sys.exit()
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def __main__():
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if len(sys.argv) != 5:
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stop_err("Wrong number of argument. Expect four (fasta, tabular, truncation, columns)")
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infile = sys.argv[1]
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outfile = sys.argv[2]
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keep_first = int( sys.argv[3] )
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descr_split = int( sys.argv[4] )
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fasta_title = fasta_seq = ''
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if keep_first == 0:
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keep_first = None
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elif descr_split == 1:
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#Added one for the ">" character
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#(which is removed if using descr_split > 1)
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keep_first += 1
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if descr_split < 1:
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stop_err("Bad description split value (should be 1 or more)")
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out = open( outfile, 'w' )
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for i, line in enumerate( open( infile ) ):
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line = line.rstrip( '\r\n' )
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if not line or line.startswith( '#' ):
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continue
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if line.startswith( '>' ):
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#Don't want any existing tabs to trigger extra columns:
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line = line.replace('\t', ' ')
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if i > 0:
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out.write('\n')
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if descr_split == 1:
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out.write(line[1:keep_first])
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else:
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words = line[1:].split(None, descr_split-1)
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#apply any truncation to first word (the id)
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words[0] = words[0][0:keep_first]
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#pad with empty columns if required
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words += [""]*(descr_split-len(words))
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out.write("\t".join(words))
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out.write('\t')
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else:
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out.write(line)
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if i > 0:
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out.write('\n')
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out.close()
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if __name__ == "__main__" : __main__()
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