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pathtype.py
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pathtype.py
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#!/usr/bin/python
from __future__ import division
import sys
import re
import glob
import subprocess
from random import randrange
import math
r2=str(randrange(10000))
#Theo Allnutt, 2016
#Find E. coli virulence genes using local version of CGE database (https://cge.cbs.dtu.dk/services/VirulenceFinder/)
#Usage:
#python pathtype.py in/ vir_ecoli 95 80 blastn
#'in' is folder of assemblies in fasta format
#vir_ecoli is a blast db of virulence genes
#95 is min %ID of hit
#80 is min % length of hit
#see vir_matchtype.py in order to attach gene names to db entries before building with makeblastdb
def tokenize(filename):
digits = re.compile(r'(\d+)')
return tuple(int(token) if match else token
for token, match in((fragment, digits.search(fragment))
for fragment in digits.split(filename)))
#nb the database annotation must be in the sequence id after a " " e.g. >seq1 rage_proteinXF5
folder = sys.argv[1]
filelist=glob.glob(folder+"/*")
filelist.sort(key=tokenize)
#print filelist
db = sys.argv[2] #ref db to blast against
g= sys.argv[3]
pid =int(sys.argv[4]) #%id threshold
plen=int(sys.argv[5]) #%of subject length threshold
blast_type=sys.argv[6]
# 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore'
out = "temp%s.blast" %r2
data={}
names=[]
genes=[]
b=(0,0)
c=0
for f in filelist:
name=f.split("/")[-1].split(".")[0]
data[name]={}
names.append(name)
loci=[]
print f,blast_type
if blast_type == "blastp":
p1= subprocess.Popen("blastp -query %s -db %s -out %s -outfmt '6 qseqid sseqid pident length slen qstart qend sstart send evalue bitscore stitle' -num_threads 24 -evalue 1e-10" %(f,db,out), shell=True).wait()
if blast_type == "blastn":
p1= subprocess.Popen("blastn -task blastn -query %s -db %s -out %s -outfmt '6 qseqid sseqid pident length slen qstart qend sstart send evalue bitscore stitle' -num_threads 24 -evalue 1e-10" %(f,db,out), shell=True).wait()
if blast_type == "mega":
p1= subprocess.Popen("blastn -query %s -db %s -out %s -outfmt '6 qseqid sseqid pident length slen qstart qend sstart send evalue bitscore stitle' -num_threads 24 -evalue 1e-10" %(f,db,out), shell=True).wait()
if blast_type == "blastx":
p1= subprocess.Popen("blastx -query %s -db %s -out %s -outfmt '6 qseqid sseqid pident length slen qstart qend sstart send evalue bitscore stitle' -num_threads 24 -evalue 1e-10" %(f,db,out), shell=True).wait()
result = open(out,'r')
c=0
result.seek(0)
new_range=0
#p1.wait()
for i in result:
k=i.split("\t")
start = int(k[5])
end=int(k[6])
if start >end:
z=end
end=start
start=z
b=(start,end)
info=k[-1].rstrip("\n")
gene=k[1]+" "+info#.split("|")[0]
locus=k[0]
pchit=float(k[2])
pclen=float(float(k[3])/float(k[4]))*100
#print gene, pclen
if locus not in data[name].keys() and pchit>=pid and pclen>= plen:
loci_ranges=[]
loci_ranges.append(b)
loci.append(locus)
data[name][locus]=[]
data[name][locus].append(gene)
data[name][locus].append(pchit)
data[name][locus].append(pclen)
data[name][locus].append(start)
data[name][locus].append(end)
data[name][locus].append(info)
genes.append(gene)
c=0
if locus in data[name] and pchit>=pid and pclen>= plen:
#test loci range:
for t in loci_ranges:
if start>t[1] or end<t[0]:
new_range=1
else:
new_range=0
break
if new_range==1:
loci_ranges.append(b)
c=c+1
locus=locus+"_"+str(c)
loci.append(locus)
data[name][locus]=[]
data[name][locus].append(gene)
data[name][locus].append(pchit)
data[name][locus].append(pclen)
data[name][locus].append(start)
data[name][locus].append(end)
data[name][locus].append(info)
genes.append(gene)
new_range=0
genes=list(set(genes))
genes.sort(key=tokenize)
#write detail files
for n in names:
outfile=open(g+"/"+n+".txt",'w')
outfile.write("Contig\tGene\t%Identity\t%Length\tStart\tEnd\tProtein\n")
for i in data[n].keys():
outfile.write("%s\t%s\n" %(i,"\t".join(str(p) for p in data[n][i])))
print genes
#write summary table
h=open(g+"/"+db.split("/")[-1]+"_"+"summary.txt",'w')
h.write("\t"+"\t".join(str(p) for p in genes)+"\n")
hit=0
for i in names:
h.write(i)
for j in genes:
for x in data[i].keys():
if data[i][x][0]==j:
#proportion of matched bases of whole gene
pchit2=data[i][x][1]/100 * data[i][x][2]/100
hit=1
break
else:
hit=0
if hit==0:
h.write("\t0")
else:
h.write("\t"+str(pchit2))
hit=0
h.write("\n")
p5= subprocess.Popen("rm temp%s.blast" %r2, shell=True).wait()