Python parse_alignment Exemples

Exemple #1

def get_alignments(filename, readlist):
    stream = subprocess.Popen(["LAshow", filename, filename] +
                              map(str, readlist),
                              stdout=subprocess.PIPE,
                              bufsize=1)
    alignments = parse_alignment(stream.stdout)  # generator
    return alignments

Exemple #2

Fichier : interface_utils.py Projet : fxia22/HINGE

def get_all_alignments(filename):
    stream = subprocess.Popen(["LAshow", filename, filename ],
                                      stdout=subprocess.PIPE,bufsize=1)
    alignments = parse_alignment(stream.stdout) # generator
    return alignments

Exemple #3

Fichier : run_parse_alignment.py Projet : fxia22/HINGE

#!/usr/bin/env python
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

Exemple #4

#!/usr/bin/env python
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