########################################################################### # # # 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)