A script to deinterleave phylip-formatted sequence files.

PhylipDeinterleaver.py

#!/usr/bin/env python

import sys

try:
    stream = open(sys.argv[1], 'r')
except:
    stream = sys.stdin

is_header = True
is_first_row = True
lines = []
for l in stream:
    if is_header:
        print l[:-1]
        is_header = False
    else:
        if l.lstrip() == '':
            is_first_row = False
            i = 0
        else:
            if is_first_row:
                lines.append(l[:-1])
            else:
                lines[i] += ' ' + l[:-1].lstrip()
                i += 1

if stream is not sys.stdin:
    stream.close()

for l in lines: print l

Hi! Some programs like TCS do not tolerate spaces in sequences. Therefore the last line may be substituted with something like:

for l in lines: print l[0:10]+l[11:-1].replace(" ","")

cheers