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
novoplasty_run.py
#!/usr/bin/python2
import sys
from subprocess import call
try:
li = sys.argv[1]
except:
li = raw_input("Introduce list of input files: NAME REF FASTQ1 FASTQ2")
try:
co = sys.argv[2]
except:
co = raw_input("Introduce configuration file")
novo_path = "/home/fruano/private/src/NOVOPlasty4/NOVOPlasty4.3.1.pl"
li = open(li).readlines()
co = open(co).readlines()
co_dict = {"name":0, "ref":0, "fq1":0, "fq2":0}
i = -1
for line in co:
i += 1
if line.startswith("Project name"):
co_dict["name"] = i
elif line.startswith("Seed Input"):
co_dict["ref"] = i
elif line.startswith("Forward reads"):
co_dict["fq1"] = i
elif line.startswith("Reverse reads"):
co_dict["fq2"] = i
elif line.startswith("Output path"):
print line
out = line.split()
print out
try:
call("mkdir " + out[-1], shell=True)
except:
pass
for line in li:
line = line.split()
print line
n = line[0]
r = line[1]
f1 = line[2]
f2 = line[3]
i = -1
w = open("config_mod.txt", "w")
for line in co:
i += 1
if i == co_dict["name"]:
line = line[:-1]+n+"\n"
elif i == co_dict["ref"]:
line = line[:-1]+r+"\n"
elif i == co_dict["fq1"]:
line = line[:-1]+f1+"\n"
elif i == co_dict["fq2"]:
line = line[:-1]+f2+"\n"
w.write(line)
print line
w.close()
print n
print "%s -c config_mod.txt" % novo_path
call("%s -c config_mod.txt" % novo_path, shell=True)