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_analysis.py
#!/usr/bin/python
import sys
print "divsum_analysis.py DivsumFile NumberOfNucleotides"
try:
file = sys.argv[1]
except:
file = raw_input("Introduce RepeatMasker's Divsum file: ")
try:
nucs = sys.argv[2]
except:
nucs = raw_input("Introduce number of analysed nucleotides: ")
nucs = int(nucs)
data = open(file).readlines()
s_matrix = data.index("Coverage for each repeat class and divergence (Kimura)\n")
matrix = []
elements = data[s_matrix+1]
elements = elements.split()
for element in elements[1:]:
matrix.append([element,[]])
n_el = len(matrix)
for line in data[s_matrix+2:]:
# print line
info = line.split()
info = info[1:]
for n in range(0,n_el):
matrix[n][1].append(int(info[n]))
abs = open(file+".abs", "w")
rel = open(file+".rel", "w")
for n in range(0,n_el):
abs.write("%s\t%s\n" % (matrix[n][0], sum(matrix[n][1])))
rel.write("%s\t%s\n" % (matrix[n][0], round(1.0*sum(matrix[n][1])/nucs,100)))