Orders a multi fasta genome file by chromosome name in karyotypic order. I.e., after chr1 follows chr2, and not chr10.

fasta_order_genome_karyotypically.py

#!/usr/local/bin/python
# File created by Tabea Kischka at Thu May 19 15:24:59 CEST 2016
# This script orders the sequence in a multi fasta file by the chromosome name in
# karyotypic oder, and not lexicographically.
# I.e., it creates this order: chr1, chr2, chr10, ...
# instead of the order chr1, chr10, chr2


import sys


def yield_fasta(fh):
    """
    Yields a tuple of the name
    and sequence of each entry
    """
    from itertools import groupby
    faiter = (x[1] for x in groupby(fh, lambda line: line[0] == ">"))
    for header in faiter:
        # drop the ">"
        header = header.next()[1:].strip()
        # join all sequence lines to one.
        seq = "".join(s.strip() for s in faiter.next())
        yield header, seq

fh = open(sys.argv[1], 'r')
seqs = {}
for header, seq in yield_fasta(fh):
    seqs[header.replace(">chr","")] = seq

karyo_ordered = {}
unordered = seqs.keys()
unordered_temp = []

max_chrom = 0

for i, elem in enumerate(seqs.keys()):
    elemshort = elem.replace("chr", "")
    try:
      karyo_ordered[elem]=int(elemshort)
      if int(elemshort) > max_chrom: max_chrom=int(elemshort)
    except ValueError:
      continue


for i, elem in enumerate(seqs.keys()):
    if elem in karyo_ordered: continue
    elemshort = elem.split('_')[0].replace("chr","")
    try:
      karyo_ordered[elem]=int(elemshort)+max_chrom
    except ValueError:
      continue

karyo_ordered_sorted = sorted(karyo_ordered.items(), key=operator.itemgetter(1))

for fullname, order in karyo_ordered_sorted:
    print ">%s\n%s" % (fullname, seqs[fullname])