Python parse_read Beispiele

Beispiel #1

def get_all_reads(filename):
    stream = subprocess.Popen(["DBshow", filename],
                              stdout=subprocess.PIPE,
                              bufsize=1)
    reads = parse_read(stream.stdout)  # generator
    return reads

Beispiel #2

Datei: get_draft_path.py Projekt: Debian/HINGE

#for node in in_graph.nodes():
#    print node

#for edge in in_graph.edges():
#    print len(in_graph.edge[edge[0]][edge[1]])

reads = sorted(
    list(set([int(x.split("_")[0].lstrip("B")) for x in in_graph.nodes()])))

dbshow_reads = ' '.join([str(x + 1) for x in reads])

DBshow_cmd = "DBshow " + filedir + '/' + filename + ' ' + dbshow_reads
stream = subprocess.Popen(DBshow_cmd.split(),
                          stdout=subprocess.PIPE,
                          bufsize=1)
reads_queried = parse_read(stream.stdout)
read_dict = {}
for read_id, read in itertools.izip(reads, reads_queried):
    rdlen = len(read[1])
    #     print read
    read_dict[read_id] = read

# to simulate reads

# read_dict = {}
# for vertex in in_graph.nodes():
#     read_dict[int(vertex.split('_')[0])] = ['A','A'*50000]

complement = {
    'A': 'T',
    'C': 'G',

Beispiel #3

def get_reads(filename, readlist):
    stream = subprocess.Popen(["DBshow", filename] + map(str, readlist),
                              stdout=subprocess.PIPE,
                              bufsize=1)
    reads = parse_read(stream.stdout)  # generator
    return reads

Beispiel #4

Datei: get_draft_annotation.py Projekt: fxia22/HINGE

import itertools

NCTCname = sys.argv[1]
filename = '/data/pacbio_assembly/pb_data/NCTC/'+NCTCname+'/'+NCTCname
graphml_path = sys.argv[2]

in_graph = nx.read_graphml(graphml_path)

reads = sorted(list(set([int(x.split("_")[0].lstrip("B")) for x in in_graph.nodes()])))

dbshow_reads = ' '.join([str(x+1) for x in reads])

DBshow_cmd = "DBshow "+filename+' '+dbshow_reads
stream = subprocess.Popen(DBshow_cmd.split(),
                                  stdout=subprocess.PIPE,bufsize=1)
reads_queried = parse_read(stream.stdout)
read_dict = {}
for read_id,read in itertools.izip(reads,reads_queried):
    rdlen = len(read[1])
#     print read
    read_dict[read_id] = read

complement = {'A':'T','C': 'G','T':'A', 'G':'C','a':'t','t':'a','c':'g','g':'c'}

def reverse_complement(string):
    return "".join(map(lambda x:complement[x],reversed(string)))

def get_string(path):
    #print path
    ret_str = ''
    for itm in path:

Beispiel #5

Datei: run_parse_read.py Projekt: pythseq/HINGE

#!/usr/bin/env python

import sys
import os
import subprocess
from parse_read import *

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

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

reads = parse_read(stream.stdout)  # generator

for read in reads:
    print read

#print result

Beispiel #6

Datei: run_parse_read.py Projekt: fxia22/HINGE

#!/usr/bin/env python

import sys
import os
import subprocess
from parse_read import *

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


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

reads = parse_read(stream.stdout) # generator

for read in reads:
    print read

#print result

Beispiel #7

Datei: interface_utils.py Projekt: fxia22/HINGE

def get_all_reads(filename):
    stream = subprocess.Popen(["DBshow", filename],
                                      stdout=subprocess.PIPE,bufsize=1)
    reads = parse_read(stream.stdout) # generator
    return reads

Beispiel #8

Datei: interface_utils.py Projekt: fxia22/HINGE

def get_reads(filename, readlist):
    stream = subprocess.Popen(["DBshow", filename] + map(str,readlist),
                                      stdout=subprocess.PIPE,bufsize=1)
    reads = parse_read(stream.stdout) # generator
    return reads