def getfiltseqs(fname):
fpathnoext, fext = os.path.splitext(fname)
if fext in [".bam",".sam"]:
filt_seqs = [(record.query_name,str(record.seq)) for record in openxam(fname)]
else:
fpathnoext,fext,ftype,fh = openfastx(fname)
filt_seqs = [(record.id,str(record.seq)) for record in SeqIO.parse(fh,ftype)]
return(set(filt_seqs))
def gettargetseqs(fname):
fpathnoext, fext = os.path.splitext(fname)
if fext in [".bam",".sam"]:
return openxam(fname,"r")
else:
fpathnoext,fext,ftype,fh = openfastx(fname)
return SeqIO.parse(fh,ftype)
return(set(filt_seqs))
ifpathnoext, ifext = os.path.splitext(args["INFNAME"])
ofpathnoext, ofext = os.path.splitext(args["OUTFNAME"])
if not isxam(ifext) and isxam(ofext):
raise TypeError("ERROR: cannot output BAM from a FASTX input")
if isxam(ifext):
infile = pysam.AlignmentFile(args["INFNAME"])
if isxam(ofext):
outfile = pysam.AlignmentFile(args["OUTFNAME"], mode="wb", template=infile)
for aln in filteralignments(infile,lengths,reqnts,args["nmism"],args["nmaps"],args["endtoend"]):
outfile.write(aln)
else:
ofpathnoext,ofext,oftype,ofh = openfastx(args["OUTFNAME"],mode="wt")
for aln in filteralignments(infile,lengths,reqnts,args["nmism"],args["nmaps"],args["endtoend"]):
seq = Seq(aln.seq)
seq.name = seq.id = seq.description = aln.query_name
if aln.is_reverse:
seq = seq.reverse_complement()
record = SeqRecord(seq,id=aln.query_name,description="")
SeqIO.write(record,ofh,oftype)
ofh.close()
else:
fpathnoext,fext,ftype,fh = openfastx(args["INFNAME"])
infile = SeqIO.parse(fh,ftype)
ofpathnoext,ofext,oftype,ofh = openfastx(args["OUTFNAME"],mode="wt")
if record.is_reverse:
seq = seq.reverse_complement()
target_seqs.append((record.query_name,str(seq)))
except TypeError:
seq = str(record.seq)
target_seqs.append((record.id,str(seq)))
filter_seqs = getfiltseqs(ffilters)
return filterseqs(target_seqs,filter_seqs)
if __name__ == "__main__":
args = parsearguments()
if not args["OUTFNAME"].endswith(".fasta"):
args["OUTFNAME"] += ".fasta"
matched_target_seqs,matching_filter_seqs = filterseqs_from_files(args["TARGETS"],args["FILTERS"])
if args["output_targets"]:
ofpathnoext,ofext,oftype,ofh = openfastx("targets_" + args["OUTFNAME"],mode="wt")
for id,seq in matched_target_seqs:
ofh.write(">{}\n{}\n".format(id,seq))
ofh.close()
if args["output_filters"]:
ofpathnoext,ofext,oftype,ofh = openfastx("filters_" + args["OUTFNAME"],mode="wt")
for id,seq in matching_filter_seqs:
ofh.write(">{}\n{}\n".format(id,seq))
ofh.close()
return(vars(parser.parse_args()))
if __name__ == "__main__":
import argparse,sys,collections,os
from tstk.io import openfastx,parsefastx
from tstk.common import revcomp
import pysam
args = parsearguments()
fpathnoext, fext = os.path.splitext(args["INFNAME"])
if fext in [".bam",".sam"]:
entries = [entry for entry in pysam.AlignmentFile(args["INFNAME"],"rb") if dict(entry.get_tags())["HI"] == 1]# only get the first entry in case of multi-mappers
entries = [revcomp(str(e.seq)) if e.is_reverse else str(e.seq) for e in entries]
counter = collections.Counter(entries) #only include one hit from the multi mappers
else:
fpathnoext,fext,ftype,fh = openfastx(args["INFNAME"])
seqs = [str(seq) for name,seq,qual in parsefastx(fh)]
counter = collections.Counter(seqs)
fh.close()
ofpathnoext,ofext,oftype,ofh = openfastx(args["OUTFNAME"].replace("fastq","fasta"),mode='wt')
seqid = 1
for seq in counter.most_common():
ofh.write(">{}-{}\n{}\n".format(seqid,seq[1],seq[0]))
seqid += 1
ofh.close()
def getcounts(SEQFILE,minlength=18,maxlength=33,uncollapse=False,normfw=None,normrv=None,normnreads=False,stranded=False,noN=False,c3p=False,chrnames=None,nmaps=1,t2u=False,rvonly=False,fwonly=False):
from tstk.io import openfastx
from Bio import SeqIO
from Bio.Seq import Seq
import numpy as np
import sys,os,re
fpath = SEQFILE
ext = os.path.splitext(fpath)[1]
lengths = np.arange(minlength,maxlength+1)
if stranded:
lengths_rv = np.arange(minlength,maxlength+1)
counts = {}
if noN:
counts = {key: {"A":0,"C":0,"T":0,"G":0} for key in lengths}
counts_rv = {key: {"A":0,"C":0,"T":0,"G":0} for key in lengths}
else:
counts = {key: {"A":0,"C":0,"T":0,"G":0,"N":0} for key in lengths}
counts_rv = {key: {"A":0,"C":0,"T":0,"G":0,"N":0} for key in lengths}
if c3p:
nucpos = -1
else:
nucpos = 0
nrecords = 0
if ext == ".bam":
import pysam
bamfile = pysam.AlignmentFile(fpath)
if chrnames:
reads = []
for chrname in chrnames:
reads += bamfile.fetch(chrname)
else:
reads = bamfile.fetch()
for read in reads:
tags = dict(read.get_tags())
if "NH" not in tags or tags["NH"] <= nmaps:
if read.is_reverse:
seq = Seq(read.seq)
seq = seq.reverse_complement()
else:
seq = read.seq
firstnuc = seq[nucpos]
if not noN or firstnuc != "N":
if len(seq) in lengths:
if stranded and read.is_reverse:
counts_rv[len(seq)][firstnuc] += 1
else:
counts[len(seq)][firstnuc] += 1
if normnreads:
if chrnames:
nrecords = 0
for chrname in chrnames:
nrecords += sum(1 for r in pysam.AlignmentFile(fpath).fetch(chrname) if dict(r.get_tags())["HI"] == 1)
else:
nrecords = sum(1 for r in pysam.AlignmentFile(fpath) if dict(r.get_tags())["HI"] == 1)
else:
checkheader = True
fpathnoext,fext,ftype,fh = openfastx(fpath)
for record in SeqIO.parse(fh,ftype):
if uncollapse:
if checkheader:
reid = re.compile("^\d+-\d+$")
if not reid.match(record.id):
print("WARNING: the fasta header doesn't seem to match the 'id-count' format. Ignoring uncollapse request.")
uncollapse = False
checkheader = False
if ftype == "fastq":
print("WARNING: file format is fastq, ignoring uncollapse request")
uncollapse = False
count = 1
else:
count = int(record.id.split("-")[1])
else:
count = 1
nrecords += count
firstnuc = record.seq[nucpos]
if not noN or firstnuc != "N":
if len(record.seq) in lengths:
counts[len(record.seq)][firstnuc] += count
normfactor_fw = None
normfactor_rv = None
if normnreads:
normfactor_fw = nrecords
normfactor_rv = nrecords
if normfw:
if normnreads:
print("WARNING: normalisation to library size specified together with specific normalisation factor. Using the specific factor for FW reads")
normfactor_fw = normfw
if normrv:
if normnreads:
print("WARNING: normalisation to library size specified together with specific normalisation factor. Using the specific factor for RV reads")
normfactor_rv = normrv
if normfactor_fw:
for l in counts:
for n in counts[l]:
counts[l][n] = counts[l][n] / normfactor_fw
if stranded and normfactor_rv:
for l in counts_rv:
for n in counts_rv[l]:
counts_rv[l][n] = counts_rv[l][n] / normfactor_rv
try:
fh.close()
except NameError:
pass
if t2u:
for l in counts:
counts[l]["U"] = counts[l].pop("T")
for l in counts_rv:
counts_rv[l]["U"] = counts_rv[l].pop("T")
counts = {"fw":counts,"rv":counts_rv}
return counts
