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#!/usr/bin/python
from __future__ import print_function
def get_alignments(infile):
alignment = None
last_sample = None
with open(infile, 'r') as infilestream:
for line in infilestream:
m = re.match("Sample (\d+)\s+Alignment:\s+(.*)$",line)
if m is not None:
current_sample = int(m.group(1))
a = m.group(2)
# when starting a new group, yield the last alignment and start a new one
if last_sample != current_sample:
if alignment is not None:
yield alignment
alignment = []
last_sample = current_sample
alignment.append(a)
# Since we only yield an alignment when we start a new one,
# the last one must be handled separately
yield alignment
def print_alignment(alignment):
for line in alignment:
print(line)
if __name__ == '__main__':
import codecs
import re
import sys
import os
infile = sys.argv[1]
num = 0
for alignment in get_alignments(infile):
num += 1
print_alignment(alignment)
print("\n\n")
sys.stderr.write("Read {} alignments.\n".format(num))
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