diff smart_toolShed/commons/core/parsing/GffParser.py @ 0:e0f8dcca02ed

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/parsing/GffParser.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,149 @@
+#
+# Copyright INRA-URGI 2009-2010
+# 
+# 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.
+#
+import re
+import sys
+from SMART.Java.Python.structure.Interval import Interval
+from SMART.Java.Python.structure.Transcript import Transcript
+from commons.core.parsing.TranscriptListParser import TranscriptListParser
+
+
+class GffParser(TranscriptListParser):
+	"""A class that parses a GFF file and create a transcript list"""
+
+
+	def __init__(self, fileName, verbosity = 0):
+		super(GffParser, self).__init__(fileName, verbosity)
+
+
+	def __del__(self):
+		super(GffParser, self).__del__()
+
+
+	def getFileFormats():
+		return ["gff", "gff2", "gff3"]
+	getFileFormats = staticmethod(getFileFormats)
+
+
+	def skipFirstLines(self):
+		pass
+
+
+	def getInfos(self):
+		self.chromosomes = set()
+		self.nbTranscripts = 0
+		self.size = 0
+		self.reset()
+		if self.verbosity >= 10:
+			print "Getting information on %s." % (self.fileName)
+		self.reset()
+		for line in self.handle:
+			line = line.strip()
+			if line == "" or line[0] == "#":
+				continue
+			parts = line.split("\t")
+			if len(parts) != 9:
+				raise Exception("Error! Line '%s' has %d tab-separated fields instead of 9!" % (line, len(parts)))
+			self.chromosomes.add(parts[0])
+			if parts[8].find("Parent") == -1:
+				self.nbTranscripts += 1
+			else:
+				self.size += max(int(parts[3]), int(parts[4])) - min(int(parts[3]), int(parts[4])) + 1
+			if self.verbosity >= 10 and self.nbTranscripts % 100000 == 0:
+				sys.stdout.write("	%d transcripts read\r" % (self.nbTranscripts))
+				sys.stdout.flush()
+		self.reset()
+		if self.verbosity >= 10:
+			print "	%d transcripts read" % (self.nbTranscripts)
+			print "Done."
+
+
+	def parseLine(self, line):
+		if not line or line[0] == "#":
+			return None
+		m = re.search(r"^\s*(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+([+-.])\s+(\S+)\s+(\S.*)$", line)
+		if m == None:
+			raise Exception("\nLine %d '%s' does not have a GFF format\n" % (self.currentLineNb, line))
+		interval = Interval()
+		interval.setChromosome(m.group(1))
+		interval.setName("unnamed transcript")
+		interval.setStart(min(int(m.group(4)), int(m.group(5))))
+		interval.setEnd(max(int(m.group(4)), int(m.group(5))))
+		if m.group(7) == ".":
+			interval.setDirection("+")
+		else:
+			interval.setDirection(m.group(7))
+		interval.setTagValue("feature", m.group(3))
+		if m.group(6).isdigit():
+			interval.setTagValue("score", m.group(6))
+
+		remainings = m.group(9).split(";")
+		for remaining in remainings:
+			remaining = remaining.strip()
+			if remaining == "":
+				continue
+			posSpace = remaining.find(" ")
+			posEqual = remaining.find("=")
+			if posEqual != -1 and (posEqual < posSpace or posSpace == -1):
+				parts = remaining.split("=")
+			else:
+				parts = remaining.split()
+			field = parts[0].strip()
+			value = " ".join(parts[1:]).strip(" \"")
+			if field in ("Name", "name", "Sequence", "TE", "SAT"):
+				interval.setName(value)
+			else:
+				try:
+					intValue = int(value)
+					interval.setTagValue(field, intValue)
+				except ValueError:
+					interval.setTagValue(field, value)
+
+		self.currentTranscriptAddress = self.previousTranscriptAddress
+		if "Parent" in interval.getTagNames():
+			if self.currentTranscript == None:
+				raise Exception("GFF file does not start with a transcript! First line is '%s'." % (line.strip()))
+			if interval.getTagValue("Parent") != self.currentTranscript.getTagValue("ID"):
+				raise Exception("Exon '%s' is not right after its transcript in GFF file!" % (interval))
+			self.currentTranscript.addExon(interval)
+			if interval.name == None:
+				interval.name = self.currentTranscript.name
+			return None
+		
+		transcript = self.currentTranscript
+		self.currentTranscript = Transcript()
+		self.currentTranscript.copy(interval)
+		self.previousTranscriptAddress = self.currentAddress
+
+		if transcript != None and transcript.name.startswith("unnamed"):
+			if "ID" in transcript.getTagNames():
+				transcript.name = transcript.getTagValue("ID")
+			else:
+				transcript.name = "unnamed transcript %s" % (self.currentLineNb)
+		return transcript