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YAPDemux.py
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YAPDemux.py
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########################################################################################
## This file is a part of YAP package of scripts. https://github.com/shpakoo/YAP
## Distributed under the MIT license: http://www.opensource.org/licenses/mit-license.php
## Copyright (c) 2011-2013 Sebastian Szpakowski
########################################################################################
#################################################
## A pipeline for cleaning up sff files
#################################################
import sys
from optparse import OptionParser, OptionGroup
from StepsLibrary import *
from StepsLibrary_EXP import *
from collections import defaultdict
from Queue import Queue
_author="Sebastian Szpakowski"
_date="2012/08/27"
_version="Version 1"
#################################################
## Classes
##
#################################################
### Iterator over input file.
### every line is converted into a dictionary with variables referred to by their
### header name
class GeneralPurposeParser:
def __init__(self, file, skip=0, sep="\t"):
self.filename = file
self.fp = open(self.filename, "rU")
self.sep = sep
self.linecounter = 0
self.currline=""
def __iter__(self):
return (self)
def next(self):
otpt = dict()
for currline in self.fp:
currline = currline.strip().split(self.sep)
self.currline = currline
self.linecounter = self.linecounter + 1
return(currline)
raise StopIteration
def __str__(self):
return "%s [%s]\n\t%s" % (self.filename, self.linecounter, self.currline)
class InfoParser:
def __init__(self, filename):
self.filename = filename
self.info = GeneralPurposeParser(filename, sep=",")
self.store = defaultdict(list)
for line in self.info:
if line[0].endswith("/"):
line[0] = line[0][:-1]
path = "%s/%s" % (line[0].strip("\""),line[1].strip("\""))
self.store[path].append(line[2:])
self.primers = set()
def makeOligoFile(self, x):
tmp=defaultdict(list)
### group barcodes and primers
for line in self.store[x]:
barcode = line[0].strip().strip("\"")
forward = line[1].strip().strip("\"")
reverse = line[2].strip().strip("\"")
use = line[3].upper().strip().strip("\"")
needTwoPrimers = line[4].upper().strip().strip("\"")
sampleID =line[5].strip().strip("\"")
if needTwoPrimers in ("Yes", "yes", "Y", "YES"):
if forward == "" or reverse =="":
print "%s: two primers needed, only one supplied F:'%s'-R:'%s' %s\n check %s " % (x, forward, reverse, self.name)
sys.exit(2)
bin = "B-%s-%s" % (forward, reverse)
tmp[bin].append((barcode, sampleID))
elif use in ("N", "NONE"):
bin ="N-none"
tmp[bin].append((barcode, sampleID))
else:
if forward != "" and "F" in use:
bin ="F-%s" % (forward)
tmp[bin].append((barcode, sampleID))
elif forward == "" and "F" in use:
print "%s: demultiplexing using forward primer requested but primer sequence not specified" % (x)
sys.exit(3)
if reverse != "" and "R" in use:
bin ="R-%s" % (reverse)
tmp[bin].append((barcode, sampleID))
elif reverse == "" and "R" in use:
print "%s: demultiplexing using reverse primer requested but primer sequence not specified" % (x)
sys.exit(4)
oligofiles=list()
for bin in tmp:
otpt=""
fn_otpt=""
if bin.startswith("B"):
fn_otpt = "%s.B.%s.%s.oligos" % (x.split("/")[-1], F, R)
T, F, R = bin.strip().split("-")
otpt += "forward\t%s\n" % (F)
otpt += "reverse\t%s\n" % (R)
otpt += "# %s both primers\n"
elif bin.startswith("N"):
fn_otpt = "%s.N.oligos" % (x.split("/")[-1])
otpt += "# no primers\n"
else:
D, P = bin.strip().split("-")
if D == "F":
fn_otpt = "%s.F.%s.oligos" % (x.split("/")[-1], P)
otpt += "forward\t%s\n" % (P)
otpt += "# %s this is the FORWARD primer\n" % (x)
else:
fn_otpt = "%s.R.%s.oligos" % (x.split("/")[-1], P)
otpt += "forward\t%s\n" % (P)
otpt += "# %s this is the REVERSE primer\n" % (x)
for barcode, sampleID in tmp[bin]:
if bin.startswith("N"):
otpt+= "barcode\t%s\t%s\n" % (revComp(barcode), sampleID)
otpt+= "barcode\t%s\t%s\n" % (barcode, sampleID)
otptfile = open(fn_otpt, "w")
otptfile.write(otpt)
otptfile.close()
oligofiles.append(fn_otpt)
return (oligofiles)
def removeNonFiles(self, x):
return x != "path/file"
def getFiles(self):
return (filter(self.removeNonFiles, self.store.keys()))
def getPrimerFilename(self):
primerfilename = "primers.fasta"
if len(self.primers)>4:
print "The annotation file has more than 2 primers !"
for p in self.primers:
print "%s" % (p.strip())
sys.exit(5)
primerfile = open(primerfilename , "w")
for p in self.primers:
primerfile.write(p)
primerfile.close()
return (primerfilename)
#################################################
## Functions
##
################################################
### Read in a file and return a list of lines
###
def loadLines(x):
try:
fp = open(x, "rU")
cont=fp.readlines()
fp.close()
#print "%s line(s) loaded." % (len(cont))
except:
cont=""
#print "%s cannot be opened, does it exist? " % ( x )
return cont
def getOligoFlip(filename):
if filename.find(".R.")>-1:
return "T"
else:
return "F"
def demultiplex():
forprocessing = InfoParser(options.fn_info)
DEMUX = list()
if options.strictlevel==2:
bdiffs="0"
pdiffs="1"
elif options.strictlevel==3:
bdiffs="0"
pdiffs="2"
elif options.strictlevel==4:
bdiffs="1"
pdiffs="2"
else:
bdiffs="0"
pdiffs="0"
for file in forprocessing.getFiles():
oligos = forprocessing.makeOligoFile(file)
sffinputs = {"sff": ["%s" % (file)]}
print oligos
# #### extract fasta and qual files
if options.useflows:
A = MothurStep("sffinfo", options.nodesize, sffinputs, {"flow":"T"}, list())
else:
D = SFFInfoStep(sffinputs, dict(), list())
for oligofile in oligos:
oligoinputs = {"oligos": ["../%s" % (oligofile)]}
if options.useflows:
args = {
"bdiffs": bdiffs,
"pdiffs": pdiffs,
"maxhomop":"7",
"maxhomop":"7",
"minflows":"360",
"maxflows":"720"
}
B = MothurStep("trim.flows", options.nodesize, oligoinputs, args, [A])
C = MothurSHHH([B])
D = FileMerger("fasta,name,qfile", [C])
#### deconvolution
args = { "flip":getOligoFlip(oligofile),
"bdiffs": bdiffs,
"pdiffs": pdiffs,
"minlength": "%s" % (options.minlength),
"maxlength": "2500",
"qtrim": "F",
"maxambig":"0",
"maxhomop":"7"
}
if options.useflows:
args["force"] = "name,fasta,oligos"
E = MothurStep("trim.seqs", options.nodesize, oligoinputs, args, [D])
if options.useflows:
DEMUX.append(E)
else:
#### generate trimming coordinates using LUCY
F = LUCYcheck(options.nodesize, [E])
#### trim the reads using LUCY-generated coordinates
G = LUCYtrim([F])
DEMUX.append(G)
A1 = FileMerger("fasta,name,group,qfile", DEMUX)
A2 = MatchGroupsToFasta(dict(), [A1])
args = {"mingroupmembers": options.mingroupmembers,
"report": "failing"}
A3 = GroupRetriever(args, A2)
args = {
"force" : "fasta,name,group",
"find": "groups"
}
A4 = MothurStep("remove.groups", options.nodesize, dict(), args, [A3])
return ([A4, forprocessing.getPrimerFilename()])
#################################################
## Arguments
##
parser = OptionParser()
group = OptionGroup(parser, "Required", description="Will not run without these !")
group.add_option("-P", "--PROJECT", dest="project", default="",
help="project code", metavar="#")
group.add_option("-E", "--EMAIL", dest="email", default="",
help="e-mail address", metavar="@")
group.add_option("-i", "--info", dest="fn_info", default="",
help="mapping: file, barcode, primer, sample information. File should be in CSV format", metavar="allinfo.csv")
parser.add_option_group(group)
group = OptionGroup(parser, "Optional Configuration", description="parameters to alter if necessary")
group.add_option("-a", "--annotations", dest="dir_anno", default="/usr/local/devel/ANNOTATION/sszpakow/ANNOTATION/",
help="directory that stores auxilliary files\n[%default]", metavar="annotations")
group.add_option("-m", "--minlen", dest="minlength", default=220, type="int",
help="what is the minimum length of reads to process\n[%default]", metavar="#")
group.add_option("-g", "--mingroupsize", dest="mingroupmembers", default=100, type="int",
help="after demultiplexing, discard groups with fewer reads than #\n[%default]", metavar="#")
group.add_option("-x", "--strict", dest="strictlevel", default=2, type="int",
help="""how strict to be at demultiplexing:
1 very strict (barcode no mismatches, primer no mismatches)
2 less strict (barcode no mismatches, primer 1 mismatch allowed)
3 even less strict (barcode no mismatches, primer 2 mismatches allowed)
4 last resort (barcode 1 mismatch, primer 2 mismatches allowed)
[%default]""", metavar="#")
group.add_option("-F", "--useFlows", dest="useflows", action="store_true", default=False,
help="""if specified flows will be used and pyronoise will be employed. Otherwise qual values will be used with LUCY""", metavar="#")
parser.add_option_group(group)
group = OptionGroup(parser, "Technical", description="could be useful sometimes")
group.add_option("-C", "--NODESIZE", dest="nodesize", default=30,
help="maximum number of grid node's CPUs to use\n[%default]", metavar="#")
parser.add_option_group(group)
(options, args) = parser.parse_args()
#################################################
## Begin
##
if options.fn_info == "" or options.email == "" or options.project =="":
parser.print_help()
sys.exit(1)
init(options.project, options.email)
############################
supplementary = list()
READY, primerfile = demultiplex()
OutputStep("DEMUX", "groupstats,fasta,group,name,list,pdf,svg,tiff,taxsummary,globalsummary,localsummary", [READY])
gs = GroupSplit({}, {}, [READY])
OutputStep("GROUPSPLIT", "fasta", [gs])
##########################################################################
#
#################################################
## Finish
#################################################