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mapping_blat_gs_nonormal.py
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#!/usr/bin/python
import sys, os
from subprocess import call
from commands import getstatusoutput
from os import listdir
from os.path import isfile, join
print "\nUsage: mapping_blat_gs.py ListOfSequences Reference NumberOfThreads [map/div/mapdiv/ssaha2/ssaha2div/nomap]\n"
try:
lista = sys.argv[1]
except:
lista = raw_input("Introduce list of fastq.gz files: ")
try:
reference = sys.argv[2]
except:
reference = raw_input("Introduce FASTA file with the refence: ")
try:
threads = sys.argv[3]
except:
threads = raw_input("Intruduce number of threads: ")
try:
map_question = sys.argv[4]
except:
pass
files = open(lista).readlines()
for n in range(0,len(files)/2):
file1 = files[n*2][:-1]
file2 = files[(n*2)+1][:-1]
w = open("tmp.list","w")
w.write(file1[:-3]+".fa\n")
w.write(file2[:-3]+".fa\n")
w.close()
# convert fq.gz to fasta
call("seqtk seq -a %s > %s" % (file1,file1[:-3]+".fa"),shell=True)
call("seqtk seq -a %s > %s" % (file2,file2[:-3]+".fa"),shell=True)
# run blat to find reads
call("blat_recursive.py %s %s %s" % (threads, "tmp.list", reference), shell=True)
# remove fasta and temp list
call("rm %s" % file1[:-3]+".fa", shell=True)
call("rm %s" % file2[:-3]+".fa", shell=True)
call("rm tmp.list", shell=True)
#get unique reads
call("awk {\047print $10\047} %s | uniq > uniq_1.txt" % (file1[:-3]+".fa.blat"), shell=True)
call("awk {\047print $10\047} %s | uniq > uniq_2.txt" % (file2[:-3]+".fa.blat"), shell=True)
call("cat uniq_1.txt uniq_2.txt > uniq_all.txt", shell=True)
# remove psl
call("rm %s" % file1[:-3]+".fa.blat", shell=True)
call("rm %s" % file2[:-3]+".fa.blat", shell=True)
# get read list
# reads_file = open("uniq_all.txt").readlines()
# trimmed_reads = open("uniq_trimmed.txt" ,"w")
# for read in reads_file:
# try:
# read = read[:-3]
# trimmed_reads.write(read+"\n")
# except:
# pass
# trimmed_reads.close()
call("sort %s | uniq > uniq_uniq.txt " % "uniq_all.txt", shell=True)
# w = open(file1[:-3]+".all.psl.list","w")
# uu = open("uniq_uniq.txt").readlines()
# for l in uu:
# w.write("%s\n%s\n" % (l[:-1]+"/1",l[:-1]+"/2"))
# w.close()
# remove uniq files
# call("rm uniq_1.txt uniq_2.txt uniq_all.txt uniq_trimmed.txt uniq_uniq.txt", shell=True)
call("rm uniq_1.txt uniq_2.txt uniq_all.txt", shell=True)
# get reads
call("seqtk subseq %s %s > %s" % (file1,"uniq_uniq.txt",file1[:-3]+".sel.fq"), shell=True)
call("seqtk subseq %s %s > %s" % (file2,"uniq_uniq.txt",file2[:-3]+".sel.fq"), shell=True)
#remove list
# call("rm %s" % (file1[:-3]+".all.psl.list"), shell=True)
call("rm uniq_uniq.txt", shell=True)
# remove FASTQ files
# call("rm %s" % file1+".fq",shell=True)
# call("rm %s" % file2+".fq",shell=True)
#RepeatMasker and Abundance/Divergence analysis
if map_question == "div" or map_question == "mapdiv":
call("seqtk seq -a %s > %s" % (file1[:-3]+".sel.fq", file1[:-3]+".sel.fa"), shell=True)
call("seqtk seq -a %s > %s" % (file2[:-3]+".sel.fq", file2[:-3]+".sel.fa"), shell=True)
call("shuffleSequences_fasta.pl %s %s %s" % (file1[:-3]+".sel.fa", file2[:-3]+".sel.fa", file1[:-3]+".all.fa"), shell=True)
n_nucs = getstatusoutput("""grep -v ">" %s | wc | awk '{print $3-$1}'""" % (file1[:-3]+".all.fa"))
n_nucs = int(n_nucs[1])
n_division = n_nucs/10**8
if n_division > 0:
call("faSplit sequence %s %s %s" % (file1[:-3]+".all.fa",str(n_division+1),file1[:-3]+".split.."), shell=True)
onlyfiles = [f for f in listdir(".") if isfile(join(".",f))]
splits = []
for f in onlyfiles:
if f.startswith(file1[:-3]+".split.") and f.endswith(".fa"):
splits.append(f)
splits.sort()
for n in range(0,len(splits)):
call("RepeatMasker -pa %s -a -nolow -no_is -lib %s %s" % (threads, reference, splits[n]), shell=True)
call("cat %s >> %s" % (splits[n]+".align",file1[:-3]+".all.fa.align"), shell=True)
elif n_division == 0:
call("RepeatMasker -pa %s -a -nolow -no_is -lib %s %s" % (threads, reference, file1[:-3]+".all.fa"), shell=True)
call("calcDivergenceFromAlign.pl -s %s %s" % (file1[:-3]+".all.fa.align.divsum", file1[:-3]+".all.fa.align"), shell=True)
# gsMapper
if map_question == "map" or map_question == "mapdiv":
call("runMapping -cpu %s -ref %s -read %s %s" % (threads, reference, file1[:-3]+".sel.fq", file2[:-3]+".sel.fq"), shell=True)
# change name
file_name = file1.split(".")
file_name = file_name[0]
ff = os.listdir(".")
fm = []
for f in ff:
if f.endswith("_runMapping"):
fm.append(f)
call("mv %s %s" % (fm[-1],file_name+"_mapping"), shell=True)
# Index bam file
call("samtools index %s_mapping/454Contigs.bam" % file_name, shell=True)
# SSAHA2
if map_question == "ssaha2" or map_question == "ssaha2div":
call("ls %s %s > ssaha2_list.txt" % (file1[:-3]+".sel.fq", file2[:-3]+".sel.fq"), shell=True)
call("ssaha2_run_multi.py ssaha2_list.txt %s %s" % (reference,threads), shell=True)
call("rm ssaha2_list.txt", shell=True)
if map_question == "ssaha2div":
file1_s = file1.split(".")
call("divnuc_bam.py %s %s" % (reference, file1_s[0]+"_mapped.bam"), shell=True)
#Nothing more happens
if map_question == "nomap":
pass