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
divsum_count.py
#!/usr/bin/python
import sys
from subprocess import call
print "divsum_count.py ListOfDivsumFiles"
try:
files = sys.argv[1]
except:
files = raw_input("Introduce RepeatMasker's Divsum file: ")
files = open(files).readlines()
to_join = []
header = "Coverage for each repeat class and divergence (Kimura)\n"
for file in files:
file = file[:-1]
data = open(file).readlines()
matrix_start = data.index(header)
matrix = data[matrix_start+1:]
li= []
names_line = matrix[0]
info = names_line.split()
for fam in info:
li.append([fam])
info_len = len(li)
for line in matrix[1:]:
info = line.split()
for i in range(0,info_len):
li[i].append(info[i])
out = open(file+".counts","w")
for el in li:
numbers = el[1:]
numbers = [int(x) for x in numbers]
out.write(el[0]+"\t"+str(sum(numbers))+"\n")
out.close()
to_join.append(file+".counts")
call("join_multiple_lists.py %s" % (" ".join(to_join)), shell=True)