Source code for galaxy.datatypes.converters.fasta_to_len

#!/usr/bin/env python
"""
Input: fasta, int
Output: tabular
Return titles with lengths of corresponding seq
"""
import sys

assert sys.version_info[:2] >= (2, 4)


[docs]def compute_fasta_length(fasta_file, out_file, keep_first_char, keep_first_word=False):

    infile = fasta_file
    keep_first_char = int(keep_first_char)

    fasta_title = ''
    seq_len = 0

    # number of char to keep in the title
    if keep_first_char == 0:
        keep_first_char = None
    else:
        keep_first_char += 1

    first_entry = True

    with open(out_file, 'w') as out:
        with open(infile) as fh:
            for line in fh:
                line = line.strip()
                if not line or line.startswith('#'):
                    continue
                if line[0] == '>':
                    if first_entry is False:
                        if keep_first_word:
                            fasta_title = fasta_title.split()[0]
                        out.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
                    else:
                        first_entry = False
                    fasta_title = line
                    seq_len = 0
                else:
                    seq_len += len(line)

        # last fasta-entry
        if keep_first_word:
            fasta_title = fasta_title.split()[0]
        out.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))


if __name__ == "__main__" :
    compute_fasta_length(sys.argv[1], sys.argv[2], sys.argv[3], True)