https://github.com/fjruizruano/ngs-protocols
Tip revision: 39a091d1fa569a7fc717ac73c4b3de07f0a1204d authored by fjruizruano on 03 August 2023, 11:48:27 UTC
adding gfa2fas.py and extract_gfa.py
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()