#!/usr/bin/python # Originally written by Daofeng (/bar/dli/pyScript/trackDbParser.py) import sys sys.path.append('/apps/lib/python2.7/site-package') # import MySQLdb class dupKeyError(Exception): def __init__(self, key, line): self.key = key self.line = line def __str__(self): return repr(self.key) + ' from ' + repr(self.line) tkColor = { 'Input':'0,0,200', 'MeDIPInput':'0,0,200', #0,0,200 'H3K4me1':'0,133,66', # active 'H3K4me2':'0,82,41', 'H3K4me3':'0,117,0', 'H3K36me3':'33,97,11', 'H3K9ac':'46,92,0', 'H3K9me1':'150,0,0', 'H3K9me3':'159,0,72', # repressive 'H3K27me3':'180,0,0', 'H3K27ac':'140,97,0', 'p300':'158,84,0', 'NR2F1':'51,102,190', 'TFAP2A':'0,148,64', 'H2AK5ac':'140,97,0', 'H2AK9ac':'158,84,0', 'H2A.Z':'51,102,190', 'H2BK120ac':'0,148,64', 'H2BK12ac':'0,0,175', 'H2BK15ac':'180,0,0', 'H2BK5ac':'0,120,110', 'H2BK20ac':'40,100,20', 'H3K14ac':'0,0,200', 'H3K18ac':'150,0,0', 'H3K23ac':'0,150,0', 'H3K23me2':'0,110,120', 'H3K27ac':'0,0,150', 'H3K4ac':'113,113,0', 'H3K56ac':'0,149,149', 'H3K79me1':'185,0,185', 'H3K79me2':'170,170,0', 'H3T11ph':'0,185,134', 'H4K20me1':'0,150,150', 'H4K5ac':'150,0,150', 'H4K8ac':'94,97,11', 'H4K12ac':'123,0,102', 'H4K91ac':'0,120,120', 'Mre':'0,100,00', 'MRE':'0,100,00', 'mre':'0,100,00', 'MRE-Seq':'0,100,00', 'MRE':'0,100,00', 'medip':'153,0,0', 'MeDIP':'153,0,0', 'MeDIP-Seq':'153,0,0', 'mbd':'128,0,0', 'ChromatinAccessibility':'0,77,0', 'DNase hypersensitivity':'0,77,0', 'DNase':'0,77,0', 'BisulfiteSeq':'200,0,0', 'Bisulfite-Seq':'200,0,0', 'Bismark':'255,51,102', 'BS':'200,0,0', 'SBS':'200,0,0', 'methylCRF':'172,0,230', 'methylcrf':'172,0,230', 'Cov':'200,0,0', 'CAGE':'40,113,155', 'mRNASeq':'40,113,155', 'RNASeq':'40,113,155', 'mRNA':'40,113,155', 'RNA':'40,113,155', 'mRNA-Seq':'40,113,155', 'smRNASeq':'0,43,173', 'smRNA':'0,43,173', 'smRNA-Seq':'0,43,173', 'ssRNA-Seq':'0,43,173', 'ssRNA-seq':'0,43,173', 'DGF':'0,0,255', 'Digital_Genomic_Footprinting':'11,59,23', 'Digital Genomic Footprinting':'11,59,23', 'RRBS':'180,49,4', 'STAT1':'102,0,153', 'IgG':'77,121,255', '4074-1':'255,83,26', '4074-2':'255,83,26', '4074-3':'255,83,26', '4074-0':'209,157,0', 'V5-1':'198,26,255', 'V5-3':'198,26,255', 'V5-4':'198,26,255', 'infm':'204,51,255', } tkColor2 = { 'SBS':'122,0,0', 'RRBS':'240,64,5', 'mCRF':'172,0,230', } def trackGraColor(x, tot, fold): # x = assay alis = [] try: col = tkColor[x] except KeyError: print >> sys.stderr, "ERROR: {0} not existed in assay list".format(x) sys.exit(1) blis = col.split(',') alis = blis clis = [int(i) for i in blis] if 0 in clis: aind = clis.index(0) step = 255/tot alis[aind] = str(step*fold) elif 255 in clis: aind = clis.index(255) step = 255/tot alis[aind] = str(255-step*fold) else: amax = max(clis) aind = clis.index(amax) step = amax/tot alis[aind] = str(amax-step*fold) return ','.join(alis) class trackDb: '''trackDb parser''' def __init__(self,f): self.f = f def parse(self): with open(self.f, 'rU') as ff: lines = [] for line in ff: if line.startswith('#'): continue aline = line.strip() if aline: if aline.startswith('track'): if lines: yield track(lines) lines = [] lines.append(aline) if lines: # the last track yield track(lines) lines = [] class track(object): '''a track record''' def __init__(self, lines): self.lines = lines self.info = {} self.parent = '' #self.children = [] self.isSuper = False self.isComposite = False self.isContainer = False self.isCompsub = False self.isCompchild = False self.isNormal = True for i in self.lines: if i.startswith('#'): continue t = i.split() a = t[0] b = ' '.join(t[1:]) if a not in self.info: self.info[a] = b else: raise dupKeyError(a, self.info['track']) if 'compositeTrack' in self.info: self.isComposite = True self.isNormal = False if 'parent' in self.info or 'superTrack' in self.info: self.isCompchild = True #self.isComposite = False if 'superTrack' in self.info and 'container' not in self.info: self.isSuper = True self.isNormal = False if 'container' in self.info: self.isContainer = True self.isNormal = False if 'view' in self.info: self.isCompsub = True self.isNormal = False #self.track = self.info['track'].replace('-', '_') self.track = self.info['track'] self.shortLabel = self.info['shortLabel'] if 'longLabel' in self.info: self.longLabel = self.info['longLabel'] #self.metadata = self.info['metadata'] if 'visibility' in self.info: self.visibility = self.info['visibility'] if 'parent' in self.info: self.parent = self.info['parent'] if 'superTrack' in self.info and not self.isSuper: self.parent = self.info['superTrack'] if 'subTrack' in self.info: self.parent = self.info['subTrack'] self.view = self.sampleType = self.cellType = self.assayType = self.donorID = '' if self.isNormal: if 'subGroups' in self.info: d = {} subGroups = self.info['subGroups'] for i in subGroups.split(): j = i.split('=') d[j[0]] = j[1] if 'view' in d: self.view = d['view'] if 'sampleType' in d: self.sampleType = d['sampleType'] if 'cellType' in d: self.cellType = d['cellType'] if 'assayType' in d: self.assayType = d['assayType'] if 'donorID' in d: self.donorID = d['donorID'] if 'dataType' in d: self.dataType = d['dataType'] else: t = self.shortLabel.split() self.assayType = t[1] self.sampleType = t[0] if self.shortLabel == 'UCSD H9 H3K18ac SK375': self.assayType = 'H3K18ac' self.sampleType = 'H9' if self.shortLabel == 'H22510 FB MRE 10': self.assayType = 'MRE' self.sampleType = 'FB' if self.shortLabel == 'H22510 FB MeDIP 10': self.assayType = 'MeDIP' self.sampleType = 'FB' if self.sampleType == '': t = self.shortLabel.split() self.sampleType = t[0] if self.assayType == '': t = self.shortLabel.split() self.assayType = t[1] if self.assayType == 'BS': self.assayType = 'Bisulfite-Seq' if self.assayType == 'MeDIP': self.assayType = 'MeDIP-Seq' if self.assayType == 'MRE': self.assayType = 'MRE-Seq' if self.assayType == 'mRNA': self.assayType = 'mRNA-Seq' if self.assayType == 'smRNA': self.assayType = 'smRNA-Seq' if self.assayType == 'DNase': self.assayType = 'ChromatinAccessibility' #if self.isContainer: # self.assayType = self.track.replace('edacc6','').replace('ContainerRoadmap','') if self.isCompsub: self.view = self.info['view'] if self.isComposite: if 'subGroup1' in self.info: self.viewList = self.subGroupParse(self.info['subGroup1']) if 'subGroup2' in self.info: self.sampleList = self.subGroupParse(self.info['subGroup2']) if 'subGroup3' in self.info: self.assayList = self.subGroupParse(self.info['subGroup3']) if 'subGroup4' in self.info: self.donorList = self.subGroupParse(self.info['subGroup4']) if 'bigDataUrl' in self.info: self.bigDataUrl = self.info['bigDataUrl'] def __str__(self): outline = [] #outline.append('\n') space = '' if self.isContainer or self.isCompsub: space = ' ' if self.isNormal: space = ' ' for i in self.lines: outline.append(space + i + '\n') outline.append('\n') return ''.join(outline) def __repr__(self): return self.__str__() def subGroupParse(self, line): d = {} for i in line.split(): if '=' in i: j = i.split('=') if j[1] not in d: d[j[1]] = j[0] #if j[0] not in d: # d[j[0]] = j[1] #else: # raise dupKeyError(j[1], line) return d def changeShow(self): x = 'off' if self.sampleType == 'H1' or self.isCompchild or self.isContainer or self.isCompsub: x = 'on' if self.isNormal: for i,j in enumerate(self.lines): if j.startswith('parent'): self.lines[i] = "{} {}".format(j, x) if j.startswith('visibility'): del self.lines[i] else: self.changevisibility('dense') if self.isNormal or self.isContainer: for i,j in enumerate(self.lines): if j.startswith('type'): t = j.split() if t[1] == 'bigWig': if self.assayType == 'Bisulfite-Seq' or 'Bisulfite' in self.longLabel or 'RRBS' in self.longLabel: self.lines[i] = 'type bigWig 0 1' self.lines.append('viewLimits 0.0:1.0') else: self.lines[i] = 'type bigWig 0 30' self.lines.append('viewLimits 0.0:30.0') def fixParent(self): '''change subTrack,superTrack to parent''' if self.isNormal or self.isCompsub: for i,j in enumerate(self.lines): if j.startswith('subTrack'): self.lines[i] = j.replace('subTrack','parent') if self.isContainer or self.isComposite: for i,j in enumerate(self.lines): if j.startswith('superTrack'): self.lines[i] = j.replace('superTrack','parent') if self.isCompchild or self.isComposite: for i,j in enumerate(self.lines): if j.startswith('dragAndDrop'): self.lines[i] = 'dragAndDrop on' #self.lines.append('allButtonPair on') # caused problem that no grid selection for samples for composite tracks def changeParent(self, x): for i,j in enumerate(self.lines): if j.startswith('subTrack'): #self.lines[i] = "subTrack {0}".format(x) self.lines[i] = "parent {0}".format(x) elif j.startswith('parent'): self.lines[i] = "parent {0}".format(x) def changevisibility(self, x): nothave = True for i,j in enumerate(self.lines): if j.startswith('visibility'): self.lines[i] = "visibility {0}".format(x) nothave = False if nothave: self.lines.append("visibility {0}".format(x)) def changelongLabel(self, x): for i,j in enumerate(self.lines): if j.startswith('longLabel'): self.lines[i] = "longLabel {0}".format(x) def changeshortLabel(self, x): for i,j in enumerate(self.lines): if j.startswith('shortLabel'): self.lines[i] = "shortLabel {0}".format(x) def changeColor(self, x): for i,j in enumerate(self.lines): if j.startswith('color'): self.lines[i] = "color {0}".format(x) def changePriority(self, x): if 'priority' in self.info: for i,j in enumerate(self.lines): if j.startswith('priority'): self.lines[i] = "priority {0}".format(x) else: self.lines.insert(-1, "priority {0}".format(x)) def changeBigDataUrl(self, x): if 'bigDataUrl' in self.info: for i,j in enumerate(self.lines): if j.startswith('bigDataUrl'): self.lines[i] = "bigDataUrl {0}".format(x) else: self.lines.insert(1, "bigDataUrl {0}".format(x)) def changesubGroups(self, d1, d2, d3): for i,j in enumerate(self.lines): if j.startswith('subGroups'): self.lines[i] = "subGroups view={0} sampleType={1} assayType={2} donorID={3}".format(self.view, d1[self.sampleType], d2[self.assayType], d3[self.donorID]) def changesampleType(self, x): for i,j in enumerate(self.lines): if j.startswith('subGroups'): self.lines[i] = "subGroups view={0} sampleType={1} assayType={2} donorID={3}".format(self.view, x, self.assayType, self.donorID) def removesubGroupsSample(self): for i,j in enumerate(self.lines): if j.startswith('subGroups'): self.lines[i] = "subGroups view={0} assayType={1} donorID={2}".format('COV', self.assayType, self.donorID) def removesubGroupsAssay(self): for i,j in enumerate(self.lines): if j.startswith('subGroups'): self.lines[i] = "subGroups view={0} sampleType={1} donorID={2}".format('COV', self.sampleType, self.donorID) def addSample(self, x): x = x.strip() if x: if self.sampleList: self.sampleList[x] = x for i,j in enumerate(self.lines): if j.startswith('subGroup2'): self.lines[i] += " {0}={0}".format(x) def addAssay(self, x): x = x.strip() if x: if self.assayList: self.assayList[x] = x for i,j in enumerate(self.lines): if j.startswith('subGroup3'): self.lines[i] += " {0}={0}".format(x) def addDonor(self, x): x = x.strip() if x: if self.donorList: self.donorList[x] = x for i,j in enumerate(self.lines): if j.startswith('subGroup4'): self.lines[i] += " {0}={0}".format(x) def nameAletter(self, x): self.lines[0] = "track {0}{1}".format(x, self.track) #self.track = "{0}{1}".format(x, self.track) def replaceAletter(self, x): self.lines[0] = "track {0}{1}".format(x, self.track[1:]) #self.track = "{0}{1}".format(x, self.track[1:]) def changeTrackName(self, x): self.lines[0] = "track {0}".format(x) self.track = x def copyTrackinDB(self, db, aLetter): con = MySQLdb.connect('localhost','hguser','hguser',db) cur = con.cursor() #ntk = "{0}{1}".format(aLetter, self.track[1:]) ntk = "{0}{1}".format(aLetter, self.track) try: cur.execute("drop table if exists {0}".format(ntk)) #cur.execute("create table {0}{1} like {1}".format(aLetter, self.track)) cur.execute("create table {0} (fileName varchar(255) not null)".format(ntk)) cur.execute("insert {0} select * from {1}".format(ntk, self.track)) except: print >> sys.stderr, "copy track {0} to {1} error".format(self.track, ntk) sys.exit(1) cur.close() con.close() def deleteTrackinDB(self, db): con = MySQLdb.connect('localhost','hguser','hguser',db) cur = con.cursor() try: cur.execute("drop table if exists {0}".format(self.track)) except: print >> sys.stderr, "Error: delete track {0} error".format(self.track) #sys.exit(1) print >> sys.stderr, "delete track {0} success".format(self.track) cur.close() con.close() def getbbiTrackPath(self, db, tk): con = MySQLdb.connect('localhost','hguser','hguser',db) cur = con.cursor() row = 'None' try: cur.execute("select * from {}".format(tk)) row = cur.fetchone()[0] except: print >> sys.stderr, "{} not existed".format(tk) #sys.exit(1) cur.close() con.close() return row def lenAssay(tklis): alis = [] for tk in tklis: alis.append(tk.assayType) alis = list(set(alis)) return len(alis) def lenSample(tklis): alis = [] for tk in tklis: alis.append(tk.sampleType) alis = list(set(alis)) return len(alis) def main(): tks = trackDb(sys.argv[1]).parse() for tk in tks: tk.fixParent() tk.changeShow() print tk if __name__=="__main__": main()