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_join_annot.py
#!/usr/bin/python
import sys
print "divsum_join_annot.py RepeatLandscapeFile AnnotationFile"
try:
rl_file = sys.argv[1]
except:
rl_file = raw_input("Introduce repeat landscape file: ")
try:
annot_file = sys.argv[2]
except:
annot_file = raw_input("Introduce anntation file")
rl = open(rl_file).readlines()
annot = open(annot_file).readlines()
annot_single = []
annot_dict = {}
rl_final = {}
fill = 71*"0"
zeros = []
for el in fill:
zeros.append(int(el))
for line in annot:
info = line.split()
annot_dict[info[0]] = info[1]
if info[1] not in annot_single:
annot_single.append(info[1])
rl_final[info[1]] = zeros
rl_db = []
header = rl[0]
header = header.split()
for el in header[1:]:
rl_db.append([el,[]])
for el in rl[1:]:
info = el.split()
info = info[1:]
for n in range(0,len(info)):
rl_db[n][1].append(int(info[n]))
for el in rl_db:
id = el[0]
name = annot_dict[id]
before = rl_final[name]
column = el[1]
suma = [before[i]+column[i] for i in range(len(before))]
rl_final[name] = suma
out = open("output.txt", "w")
for el in rl_final:
string = [str(i) for i in rl_final[el]]
out.write("%s\t%s\n" % (el, "\t".join(string)))
out.close()