https://github.com/fjruizruano/ngs-protocols
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Tip revision: 39a091d1fa569a7fc717ac73c4b3de07f0a1204d authored by fjruizruano on 03 August 2023, 11:48:27 UTC
adding gfa2fas.py and extract_gfa.py
Tip revision: 39a091d
extract_reads_blat.py
#!/usr/bin/python

import sys

try:
    file = sys.argv[1]
except:
    file = raw_input("Blat output file: ")

data = open(file).readlines()
reads = []

for line in data[5:]:
    line = line.split()
    reads.append(line[9][:-1])

reads_set = set(reads)

w = open(file+".list", "w")

for r in reads_set:
    w.write("%s\n%s\n" % (r+"1", r+"2"))

w.close()
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