--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/GetFlanking.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,233 @@
+#! /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
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+# 
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+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()