annotate smart_toolShed/SMART/Java/Python/GetFlanking.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2011
# 
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
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# "http://www.cecill.info".
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# modify and redistribute granted by the license, users are provided only
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from optparse import OptionParser
from commons.core.parsing.ParserChooser import ParserChooser
from commons.core.writer.TranscriptWriter import TranscriptWriter
from SMART.Java.Python.structure.Transcript import Transcript
from SMART.Java.Python.structure.Interval import Interval
from SMART.Java.Python.misc.Progress import Progress

QUERY        = 0
REFERENCE    = 1
INPUTS       = (QUERY, REFERENCE)
STRANDS      = (-1, 1)
TAG_DISTANCE = "distance_"
TAG_SENSE    = "_sense"
TAG_REGION   = "_region"
TAGS_REGION  = {-1: "_upstream", 0: "", 1: "_downstream"}
TAGS_RREGION = {-1: "upstream", 0: "overlapping", 1: "downstream"}
TAGS_SENSE   = {-1: "antisense", 0: "", 1: "colinear"}
STRANDSTOSTR = {-1: "(-)", 0: "", 1: "(+)"}


def getOrderKey(transcript, direction):
    if direction == 1:
        return transcript.getEnd()
    return - transcript.getStart()

def isInGoodRegion(transcriptRef, transcriptQuery, direction):
    if direction == 1:
        return transcriptQuery.getEnd() > transcriptRef.getEnd()
    return transcriptQuery.getStart() < transcriptRef.getStart()


class GetFlanking(object):

    def __init__(self, verbosity):
        self.verbosity   = verbosity
        self.transcripts = dict([id, {}] for id in INPUTS)
        self.directions  = []
        self.noOverlap   = False
        self.colinear    = False
        self.antisense   = False
        self.distance    = None
        self.minDistance = None
        self.maxDistance = None
        self.tagName     = "flanking"

    def setInputFile(self, fileName, format, id):
        chooser = ParserChooser(self.verbosity)
        chooser.findFormat(format)
        parser = chooser.getParser(fileName)
        for transcript in parser.getIterator():
            chromosome = transcript.getChromosome()
            if chromosome not in self.transcripts[id]:
                self.transcripts[id][chromosome] = []
            self.transcripts[id][chromosome].append(transcript)

    def setOutputFile(self, fileName):
        self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)

    def addUpstreamDirection(self, upstream):
        if upstream:
            self.directions.append(-1)

    def addDownstreamDirection(self, downstream):
        if downstream:
            self.directions.append(1)

    def setColinear(self, colinear):
        self.colinear = colinear

    def setAntisense(self, antisense):
        self.antisense = antisense

    def setNoOverlap(self, noOverlap):
        self.noOverlap = noOverlap

    def setMinDistance(self, distance):
        self.minDistance = distance

    def setMaxDistance(self, distance):
        self.maxDistance = distance

    def setNewTagName(self, tagName):
        self.tagName = tagName

    def match(self, transcriptRef, transcriptQuery, direction):
        if self.noOverlap and transcriptRef.overlapWith(transcriptQuery):
            return False
        if self.colinear and transcriptRef.getDirection() != transcriptQuery.getDirection():
            return False
        if self.antisense and transcriptRef.getDirection() == transcriptQuery.getDirection():
            return False
        if self.minDistance != None or self.maxDistance != None:
            distance = transcriptRef.getDistance(transcriptQuery)
            if self.minDistance != None and distance < self.minDistance:
                return False
            if self.maxDistance != None and distance > self.maxDistance:
                return False
        return True

    def getFlanking(self, direction):
        for chromosome in sorted(self.transcripts[REFERENCE].keys()):
            if chromosome not in self.transcripts[QUERY]:
                continue
            sortedTranscripts = dict([id, {}] for id in INPUTS)
            for id in INPUTS:
                sortedTranscripts[id] = sorted(self.transcripts[id][chromosome], key = lambda t: getOrderKey(t, direction))
            refIndex    = 0
            currentRefs = []
            outputs     = set()
            progress    = Progress(len(sortedTranscripts[QUERY]), "Reading chr %s %s" % (chromosome, STRANDSTOSTR[direction]), self.verbosity)
            for query in sortedTranscripts[QUERY]:
                while refIndex < len(sortedTranscripts[REFERENCE]) and isInGoodRegion(sortedTranscripts[REFERENCE][refIndex], query, direction):
                    currentRefs.append(sortedTranscripts[REFERENCE][refIndex])
                    refIndex += 1
                nextCurrentRefs = []
                for currentRef in currentRefs:
                    if self.match(currentRef, query, direction):
                        if currentRef not in self.flankings:
                            self.flankings[currentRef] = {}
                        self.flankings[currentRef][direction * currentRef.getDirection()] = query
                    else:
                        nextCurrentRefs.append(currentRef)
                currentRefs = nextCurrentRefs
                progress.inc()
            progress.done()

    def setTags(self, query, reference, direction):
        refName = reference.getTagValue("ID")
        if refName == None:
            refName = reference.getName()
        if refName == None:
            refName = reference.__str__()
        query.setTagValue("%s%s" % (self.tagName, TAGS_REGION[direction]), refName)
        query.setTagValue("%s_%s%s" % (TAG_DISTANCE, self.tagName, TAGS_REGION[direction]), query.getDistance(reference))
        if direction == 0:
            query.setTagValue("%s_%s" % (TAG_SENSE, self.tagName), TAGS_SENSE[query.getDirection() * reference.getDirection()])
            query.setTagValue("%s_%s" % (TAG_REGION, self.tagName), TAGS_RREGION[cmp(query.getRelativeDistance(reference), 0)])
        for tag in reference.getTagNames():
            if tag not in ("quality", "feature"):
                query.setTagValue("%s%s_%s" % (self.tagName, TAGS_REGION[direction], tag), reference.getTagValue(tag))
        return query

    def write(self):
        outputs   = set()
        progress  = Progress(len(self.flankings.keys()), "Printing data", self.verbosity)
        for transcriptRef in self.flankings.keys():
            if self.directions:
                for direction in self.directions:
                    if direction in self.flankings[transcriptRef]:
                        query = self.flankings[transcriptRef][direction]
                        outputs.add(self.setTags(query, transcriptRef, direction))
            else:
                if self.flankings[transcriptRef]:
                    query = sorted(self.flankings[transcriptRef].values(), key = lambda query: query.getDistance(transcriptRef))[0]
                    outputs.add(self.setTags(query, transcriptRef, 0))
            progress.inc()
        for transcript in sorted(list(outputs), key = lambda flanking: (flanking.getChromosome(), flanking.getStart(), flanking.getEnd())):
            self.writer.addTranscript(transcript)
        self.writer.close()
        progress.done()

    def run(self):
        self.flankings = {}
        for direction in STRANDS:
            self.getFlanking(direction)
        self.write()

if __name__ == "__main__":
    
    description = "Get Flanking v1.0.1: Get the flanking regions of a set of reference. [Category: Data Selection]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input1",      dest="inputFileName1", action="store",                          type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
    parser.add_option("-f", "--format1",     dest="format1",        action="store",                          type="string", help="format of previous file [compulsory] [format: transcript file format]")
    parser.add_option("-j", "--input2",      dest="inputFileName2", action="store",                          type="string", help="reference input file [compulsory] [format: file in transcript format given by -g]")
    parser.add_option("-g", "--format2",     dest="format2",        action="store",                          type="string", help="format of previous file [compulsory] [format: transcript file format]")
    parser.add_option("-5", "--upstream",    dest="upstream",       action="store_true", default=False,                     help="output upstream elements [format: boolean] [default: False]")
    parser.add_option("-3", "--downstream",  dest="downstream",     action="store_true", default=False,                     help="output downstream elements [format: boolean] [default: False]")
    parser.add_option("-c", "--colinear",    dest="colinear",       action="store_true", default=False,                     help="find first colinear element [format: boolean] [default: False]")
    parser.add_option("-a", "--antisense",   dest="antisense",      action="store_true", default=False,                     help="find first anti-sense element [format: boolean] [default: False]")
    parser.add_option("-e", "--noOverlap",   dest="noOverlap",      action="store_true", default=False,                     help="do not consider elements which are overlapping reference elements [format: boolean] [default: False]")
    parser.add_option("-d", "--minDistance", dest="minDistance",    action="store",      default=None,       type="int",    help="minimum distance between 2 elements [format: int]")
    parser.add_option("-D", "--maxDistance", dest="maxDistance",    action="store",      default=None,       type="int",    help="maximum distance between 2 elements [format: int]")
    parser.add_option("-t", "--tag",         dest="tagName",        action="store",      default="flanking", type="string", help="name of the new tag [format: string] [default: flanking]")
    parser.add_option("-o", "--output",      dest="outputFileName", action="store",                          type="string", help="output file [format: output file in GFF3 format]")
    parser.add_option("-v", "--verbosity",   dest="verbosity",      action="store",      default=1,          type="int",    help="trace level [format: int]")
    (options, args) = parser.parse_args()

    gf = GetFlanking(options.verbosity)
    gf.setInputFile(options.inputFileName1, options.format1, QUERY)
    gf.setInputFile(options.inputFileName2, options.format2, REFERENCE)
    gf.setOutputFile(options.outputFileName)
    gf.addUpstreamDirection(options.upstream)
    gf.addDownstreamDirection(options.downstream)
    gf.setColinear(options.colinear)
    gf.setAntisense(options.antisense)
    gf.setNoOverlap(options.noOverlap)
    gf.setMinDistance(options.minDistance)
    gf.setMaxDistance(options.maxDistance)
    gf.setNewTagName(options.tagName)
    gf.run()