gistfile1.txt

from BCBio import GFF
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
import os
import pickle
import string
from pprint import pprint


def split_file():
    """takes the 20g file with all 5 chromosomes of all 81 ecotypes
    and splits it into 5 separate files (one for each chromosome).
    In the process it strips all tabs from the file and removes the
    first two columns."""
    f = open('TAIR9_genome_matrix_2010_10_18.txt')
    t = None
    count = 1
    current = None
    for line in f:
        parts = line.strip().split('\t')
        c = parts.pop(0)
        n = parts.pop(0)
        n = int(n.strip())
        if c != current:
            if t != None:
                t.close()
            print 'Next Chromosome', c, n, count-1
            t = open('%s.txt' % c, 'w')
            current = c
            count = 1
        if n != count:
            diff = n - count
            print 'Inserting %s empty rows after %i' % (diff, count - 1)
            count += diff
            for i in xrange(diff):
                t.write('-' * 81 + '\n')
        t.write(''.join(parts) + '\n')
        count += 1