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from __future__ import print_function
from optparse import OptionParser
import sys
import os
import re
import random
import numpy
def createMirna(string):
cols = string.split("[")
idx = 0
obj=mirna()
for c in cols[1:]:
idx += 1
c=c.replace("]","")
p=c.split(":")
chrom=p[0]
p=p[1].split("-")
start=int(p[0])
end=int(p[1])
if idx == 1:
obj.addp5(chrom,start,end)
else:
obj.addp3(chrom,start,end)
return obj
class pos:
def __init__(self,n,s,e):
self.s=s
self.e=e
self.id=n
class mirna:
def __init__(self):
self.p5=0
self.p3=0
def addp5(self,n,s,e):
#print("adding p5")
self.p5=pos(n,s,e)
#print(self.p5)
def addp3(self,n,s,e):
self.p3=pos(n,s,e)
usagetxt = "usage: %prog -f precurso.fa -m miRNA.str -n 10 -s hsa"
parser = OptionParser(usage=usagetxt, version="%prog 1.0")
parser.add_option("-f", "--fa", dest="fasta",
help="", metavar="FILE")
parser.add_option("-m", "--ma", dest="strfile",
help="", metavar="FILE")
parser.add_option("-n", "--num", dest="numsim",
help="")
parser.add_option("-s", "--species", dest="species",
help="", metavar="FILE")
parser.add_option("-e", "--exp", dest="exp", action="store_true",
help="give expression", default=False)
parser.add_option("-p", "--prefix", help="output name")
if len(sys.argv)<4:
parser.print_help()
sys.exit(1)
(options, args) = parser.parse_args()
species=options.species
out_fa = "%s.fa" % options.prefix
out_fq = "%s.fq" % options.prefix
pos_mirna=open(options.strfile,'r')
listmirna={}
for line in pos_mirna:
if line.find("[")>0:
line = line.strip()
name = line.split(" ")
name = name[0].replace(">","")
listmirna[name]=createMirna(line)
pos_mirna.close()
data = {}
fas = open(options.fasta, 'r')
fout = open(out_fa, 'w')
fqout = open(out_fq, 'w')
name = ""
seq = ""
nt = ['A', 'T', 'G', 'C']
for line in fas:
line = line.strip()
if (line.find(">")>=0):
if (len(name)!=0):
mir=listmirna[name].p5
if mir!=0 and name.find(species)>=0:
for rand in range(int(options.numsim)):
randS=random.randint(mir.s-2,mir.s+2)+1
randE=random.randint(mir.e-2,mir.e+2)+1
if randS<1:
randS=1
if randE>mir.e:
randE=mir.e-1
randSeq=seq[randS-1:randE]
randName=name+"_"+mir.id+"_"+str(randS)+":"+str(randE)
randName=randName+"_"+str(randS-mir.s)+":"+str(randE-mir.e)
isMut=random.randint(0,3)
mut_tag = "_mut:null"
if isMut==3:
ntMut=random.randint(0,3)
posMut=random.randint(0,len(randSeq)-1)
tempList=list(randSeq)
if tempList[posMut] == nt[ntMut]:
ntMut -= 1
if ntMut < 0 :
ntMut +=2
tempList[posMut]=nt[ntMut]
randSeq=''.join(tempList)
mut_tag="_mut:"+str(posMut+1)+nt[ntMut]
randName+=mut_tag
isAdd=random.randint(0,2)
add_tag = "_add:null"
if isAdd==2:
posAdd=random.randint(1,3)
randAdd=""
add_tag="_add:"
for numadd in range(posAdd):
ntAdd=random.randint(0,1)
randSeq+=nt[ntAdd]
add_tag+=nt[ntAdd]
randName+=add_tag
exp = ""
if not data.has_key(randSeq):
if options.exp:
trial =random.randint(1, 100)
p = random.randint(1, 50) / 50.0
exp = "_x%s" % numpy.random.negative_binomial(trial, p, 1)[0]
print("@%s%s" % (randName, exp), file=fqout, end="")
print("%s" % randSeq, file=fqout, end="")
print("+\n%s" % "".join(["I"] * len(randSeq)), file=fqout, end="")
print(">%s%s" % (randName, exp), file=fout, end="")
print("%s" % randSeq, file=fout, end="")
data[randSeq]=1
name = line.split(" ")
name = name[0].replace(">","")
seq=""
else:
seq+=line.replace("U","T")
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