File: run_parse_alignment.py

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#!/usr/bin/python3
import sys
import os
import subprocess
from parse_read import *
from parse_alignment import *

filename = sys.argv[1]
readarg = sys.argv[2]


stream = subprocess.Popen(["LAshow", filename , filename ,readarg],
                                  stdout=subprocess.PIPE, bufsize=1)

alignments = parse_alignment(stream.stdout) # generator

for alignment in alignments:
    print(alignment)