--- /dev/null
+###########################################################################
+# #
+# C O P Y R I G H T N O T I C E #
+# Copyright (c) 2003-10 by: #
+# * California Institute of Technology #
+# #
+# All Rights Reserved. #
+# #
+# Permission is hereby granted, free of charge, to any person #
+# obtaining a copy of this software and associated documentation files #
+# (the "Software"), to deal in the Software without restriction, #
+# including without limitation the rights to use, copy, modify, merge, #
+# publish, distribute, sublicense, and/or sell copies of the Software, #
+# and to permit persons to whom the Software is furnished to do so, #
+# subject to the following conditions: #
+# #
+# The above copyright notice and this permission notice shall be #
+# included in all copies or substantial portions of the Software. #
+# #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, #
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF #
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND #
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS #
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN #
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN #
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE #
+# SOFTWARE. #
+###########################################################################
+#
+# This class contains the core code for visualizing sequences from several of the experiments.
+
+from cistematic.core.motif import Motif
+from cistematic.core.geneinfo import geneinfoDB
+import math, random
+
+pilPresent = False
+
+try:
+ import Image, ImageDraw, ImageFont
+ pilPresent = True
+except:
+ pass
+
+
+class Draw:
+ """ The Draw class contains the code used to visualize the location of motifs in their
+ genomic neighborhood. It is meant to be used as the parent of other classes,
+ such as the orthology classes. It relies on the python imaging library, and saves
+ PNG images.
+ """
+ drawable = False
+ maxWidth = 1200
+ leftMargin = 100
+ rightMargin = 50
+ lineHeight = 110
+
+ if pilPresent:
+ theFont = ImageFont.load_default()
+ drawable = True
+ else:
+ print "Draw: python image library missing - will not be able to draw on this system"
+
+
+ def draw(self, picName, geneList=[], motifList=[], excludeGeneList=[], excludeMotifList=[],
+ showHeader=True, showFooter=True, maxOccurences=100, skipSanity=False):
+ """ Draws an image of motifs on the sequences. Can specifically list or exclude genes and/or motifs.
+ Options showHeader will add experiment information while showFooter will add a motif key.
+ This function will not show motifs that occur more than maxOccurences in the dataset.
+ """
+ if not self.drawable:
+ return
+
+ limitGenes = False
+ limitMotifs = False
+ if len(geneList) > 0:
+ limitGenes = True
+
+ if len(motifList) > 0:
+ limitMotifs = True
+
+ idb = geneinfoDB()
+ bound = ""
+ if self.boundToNextGene:
+ bound = "up to "
+
+ expResults = self.getResults()
+ (up, cds, down) = self.getSeqParameters()
+ hasORF = "NO"
+ if cds > 0:
+ hasORF = "YES"
+
+ if cds > 1:
+ hasORF = "MASKED"
+
+ motColor = {}
+ motConsensus = {}
+ motNumber = {}
+ maxLength = 1
+ geneLength = {}
+ adjustedMotLength = {}
+ datasetIDs = self.getDatasetNames()
+ orthologyList = []
+ if len(datasetIDs) > 0:
+ for datasetName in datasetIDs:
+ dataset = self.getSetting(datasetName)
+ theList = eval(dataset[0])
+ for gene in theList:
+ if limitGenes and gene not in geneList:
+ continue
+
+ if gene not in excludeGeneList and gene not in orthologyList:
+ orthologyList.append(gene)
+ else:
+ for gene in self.genepool:
+ if limitGenes and gene not in geneList:
+ continue
+
+ if gene not in excludeGeneList and gene not in orthologyList:
+ orthologyList.append(gene)
+
+ for geneID in orthologyList:
+ geneLength[geneID] = len(self.genepool[geneID])
+ if maxLength < geneLength[geneID]:
+ maxLength = geneLength[geneID]
+
+ seqScaler = float(self.maxWidth) / float(maxLength)
+ for mot in expResults:
+ if limitMotifs and mot.tagID not in motifList:
+ continue
+
+ if mot.tagID in excludeMotifList:
+ continue
+
+ if len(self.motifToGene(mot.tagID)) >= maxOccurences:
+ continue
+
+ if not skipSanity and not mot.isSane():
+ continue
+
+ motConsensus[mot.tagID] = mot.buildConsensus()
+ currentRed = random.randint(5, 240)
+ currentGreen = random.randint(5, 240)
+ currentBlue = random.randint(5, 240)
+ motColor[mot.tagID] = (currentRed, currentGreen, currentBlue)
+
+ motKeys = motConsensus.keys()
+ motKeys.sort()
+ motKeysLen = len(motKeys)
+ for tagID in motKeys:
+ motNumber[tagID] = 0
+ adjustedMotLength[tagID] = int(math.ceil(len(self.findMotif(tagID)) * seqScaler))
+
+ numLines = len(orthologyList)
+ if showHeader:
+ numLines += 1
+
+ footerLines = motKeysLen / 3
+ if motKeysLen % 3:
+ footerLines += 1
+
+ imsize = (self.maxWidth + self.leftMargin + self.rightMargin, int(round((numLines + footerLines/2.) * self.lineHeight)))
+ image = Image.new("RGB", imsize, color="#ffffff")
+ draw = ImageDraw.Draw(image)
+ currentHeight = 0
+ if showHeader:
+ line1 = "Experiment: %s in %s Type: %s Analysis: %s" % (self.experimentID, self.expFile, self.experimentType, self.analysisID)
+ draw.text([10, 10], line1, font=self.theFont, fill=0)
+ draw.line((10, 30, self.maxWidth + self.leftMargin + self.rightMargin - 10, 30), fill=0)
+ line2 = "Upstream: %s%s ORF: %s Downstream: %s%s" % (bound, up, hasORF, bound, down)
+ draw.text([10, 40], line2, font=self.theFont, fill=0)
+ draw.line((10, 60, self.maxWidth + self.leftMargin + self.rightMargin - 10, 60), fill=0)
+ currentHeight = self.lineHeight
+
+ for geneID in orthologyList:
+ geneNames = ""
+ seqLength = geneLength[geneID]
+ try:
+ res = idb.geneIDSynonyms(geneID)
+ for entry in res[1:]:
+ geneNames += "%s " % str(entry)
+ except:
+ pass
+
+ motList = self.geneToMotif(geneID)
+ draw.text([5, currentHeight+45], str(geneID[0]), font=self.theFont, fill=0)
+ draw.text([5, currentHeight+55], str(geneID[1]), font=self.theFont, fill=0)
+ draw.text([5, currentHeight+65], geneNames, font=self.theFont, fill=0)
+ adjustedSeqLength = seqLength * seqScaler
+ seqStart = self.leftMargin + int(self.maxWidth) - adjustedSeqLength
+ features = self.getFeatures(geneID)
+ for (ftype, fstart, fstop, forientation) in features:
+ if ftype != "CDS":
+ continue
+
+ if float(fstop) < float(fstart):
+ fstart = fstop
+ fstop = fstart
+
+ start = int(math.floor(float(fstart) * seqScaler))
+ consLength = int(math.ceil((fstop - fstart) * seqScaler))
+ if start + consLength > adjustedSeqLength:
+ consLength = adjustedSeqLength - start
+
+ start += seqStart
+ draw.rectangle([start, currentHeight + 51, start + consLength, currentHeight + 64], fill="#aaaaaa")
+
+ draw.rectangle([seqStart, currentHeight + 35, seqStart + adjustedSeqLength, currentHeight + 65], outline=0)
+ tagIndex = 0
+ tagPosList = []
+ for (tagID, (pos, sense)) in motList:
+ if tagID not in motKeys:
+ continue
+
+ tagIndex += 1
+ motNumber[tagID] += 1
+ start = 0
+ top = 0
+ bottom = 0
+ start = int(math.floor(float(pos) * seqScaler)) + seqStart
+ if sense == "F":
+ top = 12
+ if tagIndex % 2:
+ textHeight = 0
+ else:
+ textHeight = 70
+ else:
+ top = 35
+ bottom = 18
+ if tagIndex % 2:
+ textHeight = 15
+ else:
+ textHeight = 85
+
+ for (prevStart, prevHeight) in tagPosList:
+ if abs(prevStart - start) <= 7 and abs(prevHeight - textHeight) <= 7:
+ if textHeight < 50:
+ textHeight -= 7
+ else:
+ textHeight += 7
+
+ tagPosList.append((start, textHeight))
+ draw.rectangle([start, currentHeight + top, start + adjustedMotLength[tagID], currentHeight + 65 + bottom], fill=motColor[tagID])
+ if tagID.count("-") == 2:
+ tagIDlist = tagID.split("-")
+ tempID = tagIDlist[0] + tagIDlist[1][0] + tagIDlist[2]
+ else:
+ tempID = tagID
+
+ draw.text([start - 5, currentHeight + textHeight], tempID, font=self.theFont, fill=motColor[tagID])
+
+ conservedWindows = []
+ try:
+ conservedWindows = self.getConservedSequenceWindows(geneID)
+ except:
+ pass
+
+ for (location, cLength, criteria) in conservedWindows:
+ start = int(math.floor(float(location) * seqScaler)) + seqStart
+ consLength = int(math.ceil(float(cLength) * seqScaler))
+ draw.rectangle([start, currentHeight + 38, start + consLength, currentHeight + 50], fill ='#ff0000')
+
+ for location in range(0, seqLength, 1000):
+ start = int(math.floor(float(location) * seqScaler)) + seqStart
+ draw.rectangle([start, currentHeight + 60, start + 1, currentHeight + 65], fill = '#000000')
+
+ draw.text([self.leftMargin + self.maxWidth + 5, currentHeight + 45], str(seqLength), font=self.theFont, fill=0)
+ currentHeight += self.lineHeight
+
+ motNum = 0
+ if showFooter:
+ for motID in motKeys:
+ x = self.leftMargin + (self.maxWidth / 3) * (motNum % 3)
+ x = self.leftMargin + (self.maxWidth / 3) * (motNum % 3)
+ y1 = currentHeight + ((self.lineHeight/2) * (motNum/3))+ 5
+ y2 = currentHeight + ((self.lineHeight/2) * (motNum/3))+ 15
+ y3 = currentHeight + ((self.lineHeight/2) * (motNum/3))+ 25
+ draw.text([x, y1], motID, font=self.theFont, fill=motColor[motID])
+ draw.text([x, y2], motConsensus[motID], font=self.theFont, fill=0)
+ draw.text([x, y3], str(motNumber[motID]) + " matches", font=self.theFont, fill=0)
+ motNum +=1
+
+ del draw
+ image.save(picName, "PNG")
+
+
+ def drawMotifs(self, picName, motifList, geneList=[], excludeGeneList=[], showHeader=True,
+ showFooter=True, maxOccurences=100, genesWithMotifOnly=True, skipSanity=False):
+ """ Draws an image of one or more motifs on the sequences. Can specifically list or exclude genes.
+ Options showHeader will add experiment information while showFooter will add a motif key.
+ This function will not show motifs that occur more than maxOccurences in the dataset, and will
+ only show sequences with the motif by default.
+ """
+ restrictedGeneList = []
+ if genesWithMotifOnly:
+ for motID in motifList:
+ matches = self.motifToGene(motID)
+ for (loc, pos) in matches:
+ if loc not in restrictedGeneList and loc not in excludeGeneList:
+ restrictedGeneList.append(loc)
+ else:
+ restrictedGeneList = geneList
+
+ self.draw(picName, restrictedGeneList, motifList, excludeGeneList, [], showHeader, showFooter, maxOccurences, skipSanity)
+
+
+ def drawGenes(self, picName, geneList, motifList=[], excludeMotifList=[], showHeader=True,
+ showFooter=True, maxOccurences=100, includeHomologs=False, motifsOnGeneOnly=True,
+ skipSanity=False):
+ """ Draws an image of one or more motifs on the sequences. Can specifically list or exclude motif.
+ Options showHeader will add experiment information while showFooter will add a motif key.
+ This function will not show motifs that occur more than maxOccurences in the dataset, and will
+ only show motifs on the sequence by default in the footer.
+ """
+ restrictedMotifList = []
+ theGeneList = []
+ if includeHomologs:
+ for geneID in geneList:
+ if geneID not in theGeneList:
+ theGeneList.append(geneID)
+ try:
+ hgenes = self.returnHomologs(geneID)
+ for gID in hgenes:
+ if gID in self.genepool and gID not in theGeneList:
+ theGeneList.append(gID)
+ except:
+ pass
+ else:
+ theGeneList = geneList
+
+ if motifsOnGeneOnly:
+ for geneID in theGeneList:
+ matches = self.geneToMotif(geneID)
+ for (motID, pos) in matches:
+ if motID not in restrictedMotifList and motID not in excludeMotifList:
+ restrictedMotifList.append(motID)
+ else:
+ restrictedMotifList = motifList
+
+ self.draw(picName, theGeneList, restrictedMotifList, [], excludeMotifList, showHeader, showFooter, maxOccurences, skipSanity)
\ No newline at end of file
projects / erange.git / blobdiff