root/galaxy-central/tools/fasta_tools/fasta_to_tabular.py

#!/usr/bin/env python
# This code exists in 2 places: ~/datatypes/converters and ~/tools/fasta_tools
"""
Input: fasta, int
Output: tabular
format convert: fasta to tabular
"""

import sys, os

def __main__():
    infile = sys.argv[1]
    outfile = sys.argv[2]
    keep_first = int( sys.argv[3] )
    fasta_title = fasta_seq = ''
    if keep_first == 0:
        keep_first = None
    else:
        keep_first += 1
    out = open( outfile, 'w' )
    for i, line in enumerate( open( infile ) ):
        line = line.rstrip( '\r\n' )
        if not line or line.startswith( '#' ):
            continue
        if line.startswith( '>' ):
            if i > 0:
                out.write('\n')
            out.write(line[1:keep_first])
            out.write('\t')
        else:
            out.write(line)
    if i > 0:
        out.write('\n')
    out.close()

if __name__ == "__main__" : __main__()