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
fastq_edit_ids.py
#!/usr/bin/python
import sys
from subprocess import call
from commands import getstatusoutput
print "Usage: fastq_edit_ids.py ListOfFastqFiles [GZ]"
print "\nFormat of the list: cosa_1.fastq(.gz) cosa_2.fastq.gz"
print "GZ: Optionally con write GZ if you prefer a .gz file as output instead of a .fastq file\n"
try:
file = sys.argv[1]
except:
file = raw_input("Introduce FASTQ(.GZ) list name: ")
try:
compress = sys.argv[2]
except:
compress = "NONE"
ext = file.split(".")
extension = ext[-1]
data = open(file).readlines()
#li = open("list_checked.txt","w")
for line in data:
line = line[:-1]
print line
ext = line.split(".")
extension = ext[-1]
if extension == "fq" or extension == "fastq":
firstline = getstatusoutput("head -n 1 %s" % line)
side = ext[-2][-1]
name = "".join(ext[0:-1])
name = name[:-2] + "_checked" + name[-2:] + "." + extension
elif extension == "gz":
firstline = getstatusoutput("gzip -cd %s | head -n 1" % line)
side = ext[-3][-1]
name = "".join(ext[0:-2])
name = name[:-2] + "_checked" + name[-2:] + "." + ext[-2]
id = firstline[1]
id = id.split("\n")
id = id[0]
sp = id.find(" ")
identifier = id.split(":")
identifier = identifier[0]
if sp != -1:
print line+" with uncorrect format, editing ids."
awk_cmd1 = """awk '{ if (NR%4==1) { print $1"/"""
awk_cmd2 = """" } else { print } }' """
if extension == "fq" or extension == "fastq":
if compress != "GZ":
call(awk_cmd1+side+awk_cmd2+ "%s > %s" % (line, name), shell=True)
elif compress == "GZ":
call(awk_cmd1+side+awk_cmd2+line+" | gzip > "+name+".gz", shell=True)
elif extension == "gz":
if compress != "GZ":
call("zcat " +line+ " | " +awk_cmd1+side+awk_cmd2 +"> "+ name, shell=True )
elif compress == "GZ":
call("zcat " +line+ " | " +awk_cmd1+side+awk_cmd2 +"| gzip > "+name+".gz", shell=True )
# li.write(name+"\n")
elif id[-2:] == "/%s" % side:
call("ln -sf %s %s" % (line, name), shell=True)
print line+" with the correct format, nothing happens."
# li.write(name+"\n")
else:
print line+": Something wrong happens, check file."
#li.close()