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https://github.com/fjruizruano/ngs-protocols
05 April 2024, 22:19:15 UTC
Revision 09d12f8d08a94a91a3e992a50c5791ae72070afe authored by Paquillo on 11 February 2021, 22:58:53 UTC, committed by Paquillo on 11 February 2021, 22:58:53 UTC 
adding rm_getseq_stats.py
1 parent a948c24
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Tip revision: 09d12f8d08a94a91a3e992a50c5791ae72070afe authored by Paquillo on 11 February 2021, 22:58:53 UTC
adding rm_getseq_stats.py
Tip revision: 09d12f8
sat_subfam2fam_multi_support.py 
#!/usr/bin/python

import sys
from subprocess import call

print "sat_subfam2fam.py AlignFile PatternFile"

try:
    dat = sys.argv[1]
except:
    dat = raw_input("Introduce align file: ")

try:
    pat = sys.argv[2]
except:
    pat = raw_input("Introduce pattern file: ")

pat = open(pat).readlines()

patterns = {}

for line in pat:
    info = line.split()
    patterns[info[0]] = info[1]

data = open(dat).readlines()

w = open(dat+".fam", "w")

for line in data:
    for el in patterns:
        line = line.replace(el,patterns[el])
    w.write(line)

w.close()
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