s_mart: SMART/Java/Python/structure/Mapping.py comparison

comparison SMART/Java/Python/structure/Mapping.py @ 6:769e306b7933

Change the repository level.

author	yufei-luo
date	Fri, 18 Jan 2013 04:54:14 -0500
parents
children

comparison

equal deleted inserted replaced

-:ea3082881bf8
+:769e306b7933
+#
+# 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.
+#
+from SMART.Java.Python.structure.SubMapping import SubMapping
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.structure.Interval import Interval
+class Mapping(object):
+"""A class that represents a mapping"""
+def __init__(self):
+self.targetInterval = None
+self.queryInterval  = None
+self.subMappings    = []
+self.size           = None
+self.transcript     = None
+self.tags           = {}
+def copy(self, mapping):
+for subMapping in mapping.subMappings:
+newSubMapping = SubMapping(subMapping)
+self.addSubMapping(newSubMapping)
+self.targetInterval = Interval(mapping.targetInterval)
+self.queryInterval  = Interval(mapping.queryInterval)
+self.size           = mapping.size
+self.tags           = {}
+for tag in mapping.tags:
+self.tags[tag] = mapping[tag]
+self.transcript.copy(mapping.transcript)
+def setTargetInterval(self, interval):
+self.targetInterval = Interval(interval)
+if self.queryInterval != None:
+self.setDirection(self.targetInterval.getDirection() * self.queryInterval.getDirection())
+def setQueryInterval(self, interval):
+self.queryInterval = Interval(interval)
+if self.targetInterval != None:
+self.setDirection(self.targetInterval.getDirection() * self.queryInterval.getDirection())
+def getQueryInterval(self):
+return self.queryInterval
+def addSubMapping(self, subMapping):
+subMappingCopy = SubMapping(subMapping)
+self.subMappings.append(subMappingCopy)
+if self.targetInterval:
+self.targetInterval.setStart(min(self.targetInterval.getStart(), subMapping.targetInterval.getStart()))
+self.targetInterval.setEnd(max(self.targetInterval.getEnd(),     subMapping.targetInterval.getEnd()))
+else:
+self.setTargetInterval(subMapping.targetInterval)
+if self.queryInterval:
+self.queryInterval.setStart(min(self.queryInterval.getStart(), subMapping.queryInterval.getStart()))
+self.queryInterval.setEnd(max(self.queryInterval.getEnd(),     subMapping.queryInterval.getEnd()))
+else:
+self.setQueryInterval(subMapping.queryInterval)
+if self.getDirection() != 0:
+subMapping.setDirection(self.getDirection())
+if self.size == None:
+self.size = 0
+if "identity" in subMapping.getTagNames() and "identity" not in self.getTagNames():
+self.setTagValue("identity", subMapping.getTagValue("identity"))
+elif "identity" in subMapping.getTagNames() and subMapping.size != None:
+self.setTagValue("identity", (self.getTagValue("identity") * self.size + subMapping.getTagValue("identity") * subMapping.size) / (self.size + subMapping.size))
+if subMapping.size != None:
+self.size += subMapping.size
+if "nbMismatches" in subMapping.getTagNames() and "nbMismatches" not in self.getTagNames():
+self.setTagValue("nbMismatches", subMapping.getTagValue("nbMismatches"))
+elif "nbMismatches" in subMapping.getTagNames():
+self.setTagValue("nbMismatches", self.getTagValue("nbMismatches") + subMapping.getTagValue("nbMismatches"))
+if "nbGaps" in subMapping.getTagNames() and "nbGaps" not in self.getTagNames():
+self.setTagValue("nbGaps", subMapping.getTagValue("nbGaps"))
+elif "nbGaps" in subMapping.getTagNames():
+self.setTagValue("nbGaps", self.getTagValue("nbGaps") + subMapping.getTagValue("nbGaps"))
+def setDirection(self, direction):
+for subMapping in self.subMappings:
+subMapping.setDirection(direction)
+def getDirection(self):
+if not self.subMappings:
+raise Exception("Error! Mapping '%s' has no submapping" % (self))
+return self.subMappings[0].getDirection()
+def setSize(self, size):
+self.size = size
+if "identity" in self.getTagNames():
+self.setTagValue("nbMismatches", self.size - round(self.size * self.getTagValue("identity") / 100.0))
+def setTagValue(self, name, value):
+self.tags[name] = value
+self.transcript = None
+def getTagValue(self, name):
+return self.tags[name]
+def getTagNames(self):
+return self.tags.keys()
+def setIdentity(self, identity):
+self.setTagValue("identity", identity)
+if self.size != None and "nbMismatches" not in self.getTagNames():
+nbMismatches = 0 if self.size == 0 else self.size - round(self.size * self.getTagValue("identity") / 100.0)
+self.setTagValue("nbMismatches", nbMismatches)
+def setNbOccurrences(self, nbOccurrences):
+self.setTagValue("nbOccurrences", nbOccurrences)
+def setNbMismatches(self, nbMismatches):
+self.setTagValue("nbMismatches", nbMismatches)
+if self.size != None and "identity" not in self.getTagNames():
+identity = 100 if self.size == 0 else (self.size - self.getTagValue("nbMismatches")) / float(self.size) * 100
+self.setTagValue("identity", identity)
+def setNbGaps(self, nbGaps):
+self.setTagValue("nbGaps", nbGaps)
+def setRank(self, rank):
+self.setTagValue("rank", rank)
+def setEvalue(self, evalue):
+self.setTagValue("evalue", evalue)
+def setOccurrence(self, occurrence):
+self.setTagValue("occurrence", occurrence)
+def setBestRegion(self, bestRegion):
+self.setTagValue("bestRegion", bestRegion)
+def mergeExons(self, distance):
+previousSubMapping = None
+subMappings        = []
+for subMapping in self.subMappings:
+if previousSubMapping == None:
+subMappings.append(subMapping)
+previousSubMapping = subMapping
+else:
+targetDistance = subMapping.targetInterval.getDistance(previousSubMapping.targetInterval)
+queryDistance  = subMapping.queryInterval.getDistance(previousSubMapping.queryInterval)
+if targetDistance <= distance:
+self.setTagValue("nbGaps", self.getTagValue("nbGaps") + queryDistance)
+previousSubMapping.merge(subMapping)
+else:
+subMappings.append(subMapping)
+previousSubMapping = subMapping
+self.subMappings = subMappings
+def getTranscript(self):
+"""
+Extract a transcript from this mapping
+@return: a transcript
+"""
+if self.transcript != None:
+return self.transcript
+self.transcript = Transcript()
+self.transcript.copy(self.targetInterval)
+self.transcript.setDirection(self.getDirection())
+self.transcript.setName(self.queryInterval.getName())
+self.transcript.removeExons()
+if len(self.subMappings) > 1:
+for subMapping in self.subMappings:
+self.transcript.addExon(subMapping.targetInterval)
+cpt = 1
+for exon in self.transcript.exons:
+exon.setDirection(self.transcript.getDirection())
+exon.setName("%s-exon%d" % (self.transcript.getName(), cpt))
+exon.setChromosome(self.transcript.getChromosome())
+cpt += 1
+self.transcript.setDirection(self.getDirection())
+self.transcript.sortExons()
+for tag in self.tags:
+if "bestRegion" not in self.getTagNames():
+self.transcript.setTagValue("bestRegion", "(self)")
+self.transcript.setTagValue(tag, self.getTagValue(tag))
+return self.transcript
+def getChromosome(self):
+if not self.subMappings:
+raise Exception("Error! Mapping '%s' has no submapping" % (self))
+return self.subMappings[0].targetInterval.getChromosome()
+def getErrorScore(self):
+return self.getTagValue("nbGaps") * 3 + self.getTagValue("nbMismatches") + (len(self.subMappings) - 1) * 0.1
+def printGBrowseReference(self):
+return self.getTranscript().printGBrowseReference()
+def printGBrowseLine(self):
+return self.getTranscript().printGBrowseLine()
+def printGBrowse(self):
+return self.getTranscript().printGBrowse()
+def printBed(self):
+return self.getTranscript().printBed()
+def __str__(self):
+return "%s     ----     %s" % (str(self.getTranscript()), ", ". join([str(submapping) for submapping in self.subMappings]))

Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/structure/Mapping.py @ 6:769e306b7933