view SMART/Java/Python/GetFlanking.py @ 38:2c0c0a89fad7

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#! /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
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info".
# 
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
# 
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
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# same conditions as regards security.
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# The fact that you are presently reading this means that you have had
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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: "collinear"}
STRANDSTOSTR = {-1: "(-)", 0: "", 1: "(+)"}


def getOrderKey(transcript, direction, input):
	if direction == 1:
		if input == QUERY:
			return (transcript.getEnd(), -transcript.getStart())
		return (transcript.getStart(), -transcript.getEnd())
	if input == QUERY:
		return (-transcript.getStart(), transcript.getEnd())
	return (-transcript.getEnd(), transcript.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, transcriptQuery, transcriptRef, direction):
		#print "comparing", transcriptQuery, "with", transcriptRef, "on direction", direction
		if direction == 1 and transcriptRef.getEnd() < transcriptQuery.getStart():
			return False
		if direction == -1 and transcriptQuery.getEnd() < transcriptRef.getStart():
			return False
		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, chromosome, direction):
		if chromosome not in self.transcripts[REFERENCE]:
			return
		sortedTranscripts = dict([id, {}] for id in INPUTS)
		for id in INPUTS:
			sortedTranscripts[id] = sorted(self.transcripts[id][chromosome], key = lambda t: getOrderKey(t, direction, id))
		refIndex = 0
		progress = Progress(len(sortedTranscripts[QUERY]), "Reading chr %s %s" % (chromosome, STRANDSTOSTR[direction]), self.verbosity)
		for query in sortedTranscripts[QUERY]:
			#print "Q: ", query
			#print "R1: ", sortedTranscripts[REFERENCE][refIndex]
			while not self.match(query, sortedTranscripts[REFERENCE][refIndex], direction):
				refIndex += 1
				if refIndex == len(sortedTranscripts[REFERENCE]):
					progress.done()
					#print "done"
					return
				#print "R2: ", sortedTranscripts[REFERENCE][refIndex]
			self.flankings[query][direction] = sortedTranscripts[REFERENCE][refIndex]
			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*query.getDirection()]), refName)
		query.setTagValue("%s_%s%s" % (TAG_DISTANCE, self.tagName, TAGS_REGION[direction*query.getDirection()]), query.getDistance(reference))
		query.setTagValue("%s_%s" % (TAG_SENSE, self.tagName), TAGS_SENSE[query.getDirection() * reference.getDirection()])
		if direction == 0:
			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*query.getDirection()], tag), reference.getTagValue(tag))
		return query

	def write(self):
		progress = Progress(len(self.flankings.keys()), "Printing data", self.verbosity)
		for transcriptQuery in self.flankings.keys():
			if not self.flankings[transcriptQuery]:
				self.writer.addTranscript(transcriptQuery)
			elif self.directions:
				for direction in self.directions:
					#relativeDirection = direction if transcriptQuery.getDirection() == 1 else - direction
					relativeDirection = direction * transcriptQuery.getDirection()
					if relativeDirection in self.flankings[transcriptQuery]:
						transcriptRef = self.flankings[transcriptQuery][relativeDirection]
						transcriptQuery = self.setTags(transcriptQuery, transcriptRef, relativeDirection)
				self.writer.addTranscript(transcriptQuery)
			else:
				transcriptRef = sorted(self.flankings[transcriptQuery].values(), key = lambda transcriptRef: transcriptQuery.getDistance(transcriptRef))[0]
				self.writer.addTranscript(self.setTags(transcriptQuery, transcriptRef, 0))
			progress.inc()
		progress.done()

	def run(self):
		for chromosome in sorted(self.transcripts[QUERY].keys()):
			self.flankings = dict([query, {}] for query in self.transcripts[QUERY][chromosome])
			for direction in STRANDS:
				#print "comparison", chromosome, direction
				self.getFlanking(chromosome, direction)
			self.write()
		self.writer.close()

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()