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rna_qc_cov.py
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#!/usr/bin/env python
import argparse
from collections import defaultdict
import subprocess
import os
parser = argparse.ArgumentParser(description="Calculate average coverage across features")
parser.add_argument("f1", help="Input BED file")
parser.add_argument("--norna", default=False, action="store_true", help="Don't run SortMeRNA")
parser.add_argument("--nomap", default=False, action="store_true", help="Don't do mapping")
parser.add_argument("--nocov", default=False, action="store_true", help="Don't do coverage mapping")
parser.add_argument("--local", default=False, action="store_true", help="Local alignment with Bowtie2")
parser.add_argument("--bwa", default=False, action="store_true", help="Alignment with BWA")
parser.add_argument("--strain", default=False, action="store_true", help="Strain level")
parser.add_argument("--db", default="RDP", choices=["barcodes","RDP","genbank","unite","unite_big","clete","ena500","ena100"], help="RNA database to use")
parser.add_argument("--cpu", default="6", help="CPUs to use")
args = parser.parse_args()
#RUN SORTMERNA AND BLAST THE RNADB
cpu = args.cpu
read_file = args.f1
sortmerna_path = "/home/jacek/software/assembly_reads/sortmerna-2.0-linux-64/"
sortmerna_path = "/home/jacek/software/assembly_reads/sortmerna-2.1-linux-64/"
if args.norna == False:
ret = subprocess.call([sortmerna_path+"sortmerna","--ref",sortmerna_path+"rRNA_databases/"+args.db+".fasta,"+sortmerna_path+"rRNA_databases/"+args.db+"_db","--reads",read_file,"--fastx","--aligned",read_file+"_rRNA","-m","8192","-a",cpu], stdout=None, stderr=subprocess.STDOUT)
if args.nomap == False:
FNULL = open(os.devnull, 'w')
loc="--end-to-end"
if args.local == True:
loc="--local "
#print read_file
if args.bwa == False:
if read_file.find(".fq") != -1 or read_file.find(".fastq") != -1:
ret = subprocess.call(["/home/jacek/software/assembly_reads/bowtie2-2.2.6/bowtie2",loc,"--very-sensitive","-N","1","-x",sortmerna_path+"rRNA_databases/"+args.db+"_db","-U",read_file+"_rRNA."+read_file.split(".")[-1],"-S",read_file+"_rRNA.sam","-p",cpu], stdout=None, stderr=subprocess.STDOUT)
elif read_file.find(".fa") != -1 or read_file.find(".fasta") != -1:
ret = subprocess.call(["/home/jacek/software/assembly_reads/bowtie2-2.2.6/bowtie2",loc,"--very-sensitive","-N","1","-x",sortmerna_path+"rRNA_databases/RDP_db","-U",read_file+"_rRNA."+read_file.split(".")[-1],"-f","-S",read_file+"_rRNA.sam","-p",cpu], stdout=None, stderr=subprocess.STDOUT)
else:
out_f = open(read_file+"_rRNA.sai",'w')
ret = subprocess.call(["/home/jacek/software/assembly_reads/bwa/bwa","aln",sortmerna_path+"rRNA_databases/RDP_db.fasta",read_file+"_rRNA.fasta"], stdout=out_f)
out_f.close()
out_f = open(read_file+"_rRNA.sam",'w')
ret = subprocess.call(["/home/jacek/software/assembly_reads/bwa/bwa","samse",sortmerna_path+"rRNA_databases/RDP_db.fasta",read_file+"_rRNA.sai",read_file], stdout=out_f)
out_f.close()
ret = subprocess.call(["/home/jacek/software/assembly_reads/samtools-1.2/samtools","view","-Shbo",read_file+"_rRNA_temp1.bam",read_file+"_rRNA.sam"], stdout=None, stderr=subprocess.STDOUT)
#ret = subprocess.call(["/home/jacek/software/samtools-1.2/samtools","view","-Shbq","1","-o",read_file+"_rRNA_temp1.bam",read_file+"_rRNA.sam"], stdout=None, stderr=subprocess.STDOUT)
ret = subprocess.call(["/home/jacek/software/assembly_reads/samtools-1.2/samtools","sort","-@",cpu,read_file+"_rRNA_temp1.bam",read_file+"_rRNA_temp2"], stdout=None, stderr=subprocess.STDOUT)
ret = subprocess.call(["/home/jacek/software/assembly_reads/samtools-1.2/samtools","rmdup",read_file+"_rRNA_temp2.bam",read_file+"_rRNA.bam"], stdout=FNULL, stderr=FNULL)#subprocess.STDOUT)
ret = subprocess.call(["/home/jacek/software/assembly_reads/samtools-1.2/samtools","index",read_file+"_rRNA.bam"], stdout=None, stderr=subprocess.STDOUT)
out_f = open(read_file+"_rRNA_cov.txt","w")
ret = subprocess.call(["bedtools","genomecov","-ibam",read_file+"_rRNA.bam","-g",sortmerna_path+"rRNA_databases/RDP_db.fasta"], stdout=out_f, stderr=subprocess.STDOUT)
out_f.close()
if args.nocov == False:
cov = defaultdict(list)
#READ COVERAGE DATA
with open(read_file+"_rRNA_cov.txt","r") as f:
for l in f:
cov[l.split()[0]].append([int(l.split()[1]),int(l.split()[2])])
if args.db.find("unite") == -1:
#CALCULATE MEAN COVERAGE AND CUMULATIVE COVERAGE PER SPECIES
cov_max = ["",0]
final_cov = defaultdict(float)
final_cov_species = defaultdict(list)
for g in cov:
if g != "genome":
avg = 0
total = 0
for h in cov[g]:
avg += h[0]*h[1]
total += h[1]
if float(avg)/float(total) > cov_max[1]:
cov_max = [g,float(avg)/float(total)]
final_cov[g]=float(avg)/float(total)
if args.db == "RDP" or args.db == "genbank":
final_cov_species["_".join([ g.split("_")[1],g.split("_")[2].rstrip(";")])].append(float(avg)/float(total))
elif args.db.find("ena") != -1:
final_cov_species["_".join(g.split("|")[2].split("_")[:2])].append(float(avg)/float(total))
elif args.db == "clete":
final_cov_species[g].append(float(avg)/float(total))
elif args.db == "barcodes":
final_cov_species[g.split("|")[1]].append(float(avg)/float(total))
final_cov_species2 = defaultdict(float)
for s in final_cov_species:
#print s, final_cov_species[s]
final_cov_species2[s] = sum(final_cov_species[s])#/len(final_cov_species[s])
if args.strain == True:
for k in sorted(final_cov, key=final_cov.get, reverse=True):
print k,final_cov[k]
else:
for k in sorted(final_cov_species2, key=final_cov_species2.get, reverse=True):
print k,final_cov_species2[k]
else:
if args.db == "unite":
with open(sortmerna_path+"rRNA_databases/unite_tax.txt") as tax_f:
tax_db = {}
for l in tax_f:
unite_id = l.strip().split("\t")[0]
unite_species = l.strip().split("\t")[1].split(";")[-1][3:]
tax_db[unite_id] = unite_species
cov_max = ["",0]
final_cov = defaultdict(float)
final_cov_species = defaultdict(list)
for g in cov:
if g != "genome":
avg = 0
total = 0
for h in cov[g]:
avg += h[0]*h[1]
total += h[1]
if float(avg)/float(total) > cov_max[1]:
cov_max = [g,float(avg)/float(total)]
final_cov[g]=float(avg)/float(total)
final_cov_species[tax_db[g]].append(float(avg)/float(total))
final_cov_species2 = defaultdict(float)
for s in final_cov_species:
final_cov_species2[s] = sum(final_cov_species[s])#/len(final_cov_species[s])
for k in sorted(final_cov_species2, key=final_cov_species2.get, reverse=True):
print k,final_cov_species2[k]
elif args.db == "unite_big":
cov_max = ["",0]
final_cov = defaultdict(float)
final_cov_species = defaultdict(list)
for g in cov:
if g != "genome":
avg = 0
total = 0
for h in cov[g]:
avg += h[0]*h[1]
total += h[1]
if float(avg)/float(total) > cov_max[1]:
cov_max = [g,float(avg)/float(total)]
final_cov[g]=float(avg)/float(total)
sp = g.strip().split(";")[-1][3:].split("|")[0]
final_cov_species[sp].append(float(avg)/float(total))
final_cov_species2 = defaultdict(float)
for s in final_cov_species:
final_cov_species2[s] = sum(final_cov_species[s])
for k in sorted(final_cov_species2, key=final_cov_species2.get, reverse=True):
print k,final_cov_species2[k]