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
bwa_mem_protocol.py
#!/usr/bin/python
import sys
from subprocess import call
print "\nUsage: bwa_protocol.py ListOfReads Reference Threads [noreduce/reduce]\n"
try:
data = sys.argv[1]
except:
data = raw_input("List of reads: ")
try:
ref = sys.argv[2]
except:
ref = raw_input("FASTA reference file: ")
try:
threads = sys.argv[3]
except:
threads = raw_input("Number of threads: ")
try:
reduce = sys.argv[4]
except:
reduce = raw_input("Reduce or not reduce: ")
files = open(data).readlines()
l_files = []
for f in range(0,(len(files)/2)):
l_files.append([files[f*2][:-1],files[(f*2)+1][:-1]])
try:
open(ref+".pac")
open(ref+".ann")
open(ref+".amb")
open(ref+".bwt")
open(ref+".sa")
except:
call("bwa index -a bwtsw %s" % ref, shell=True)
for pair in l_files:
name = pair[0]
name = name.split(".")
name = name[0][:-2]
call("bwa mem -t %s %s %s %s | samtools view -bS - > %s_fastq.bam" % (threads, ref, pair[0], pair[1], name), shell=True)
call("samtools sort -T aln.sorted %s_fastq.bam -o %s_sort.bam" % (name, name), shell=True)
call("rm %s_fastq.bam" % (name), shell=True)
call("samtools index %s_sort.bam" % (name), shell=True)
call("samtools flagstat %s_sort.bam > %s_sort.flagstat" % (name, name), shell=True)
if reduce == "reduce":
call("reduce_bam.py %s_sort.bam && rm %s_sort.bam" % (name, name), shell=True)
call("rm %s_sort.bam.bai" % (name), shell=True)