d9ce74c9310f90a8d631e048499434cc6b954f6d max Wed Mar 1 06:07:32 2023 -0800 finally fixing various old uniprot bugs that stopped the update in January and October: now stops if an error occurs, working around a symlink permissions problem, making the release message easier to read, ML ticket, refs #30701 diff --git src/hg/utils/otto/uniprot/doUniprot src/hg/utils/otto/uniprot/doUniprot index 4f3351f..ba88eef 100755 --- src/hg/utils/otto/uniprot/doUniprot +++ src/hg/utils/otto/uniprot/doUniprot @@ -1,2243 +1,2467 @@ #!/usr/bin/env python3 import urllib.request, urllib.error, urllib.parse, time, os, atexit import datetime, optparse, sys, logging, subprocess, glob, shutil import sys, gzip, logging,re, json from urllib.parse import urlparse from os.path import * from os import system, makedirs, mkdir, remove, listdir from shutil import move from subprocess import PIPE from collections import defaultdict, namedtuple, Counter, OrderedDict # main driver script for uniprot updates # This script has evolved over a long time. Parts of it do not have an optimal structure. # One reason is that the script used to parse only mutations. Even normal annotations # are still put into a structure that resembles mutations. # the script first uses makeUniProtPsl.sh to create a mapping from UniProt Sequence to genome as a PSL file. # makeUniProtPsl uses mapUniprot_doBlast to BLAST the UniProt sequence to a transcript sequence, then pslMaps # this alignment to the genome using a transcript -> genome alignment. For this, makeUniProtPsl.sh needs a # transcript track, findBestGeneTable() tries to guess a good one. # Globals --- # in 2020, the FTP feature to get the date doesn't work anymore. We use https now #upUrl = "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz" upUrl = "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz" # proteins have to match the transcript as at least at this percent ID # of these matches, only the top ones within 1% are used, see makeUniProtPsl.sh MINALI=0.93 # manual mapping from uniProt taxon IDs to UCSC databases, the default mapping is taken from dbDb # these are added in addition, I obtained them in 2018 using some Apache log mining # the list could probably be shorter now manualTaxIdDbs = { 9606 : ["hg19", "hg38"], # human - keep hg19 mapping for a long time. UniProt is important for medical genetics. 10090 : ["mm10"], # mouse 10116 : ["rn6"], # rat 8364 : ["xenTro9"], # xenopus 6239 : ["ce11", "ce10"], # c elegans 7227 : ["dm6"], # fruitfly 7955 : ["danRer7", "danRer10"], # zebrafish - 4932 : ["sacCer3"], # yeast + 559292 : ["sacCer3"], # yeast 9940 : ["oviAri3"], # sheep 9823 : ["susScr3"], # pig 2697049: ["wuhCor1"]} # see also covidCheck.sh notAutoDbs = [ # do not run on wuhCor1 - wuhCor1 has a special daily otto job in /hive/data/genomes/wuhCor1/bed/uniprot # because UniProt releases SARS-CoV-2 much more often "wuhCor1", +# no monkeypox yet +"mpxvRivers", +# do not run on hs1, has no good gene model and BLAT protein takes forever +"hs1", # sea urchin doesn't have any normal gene model track, not even Augustus "strPur2" ] # the script will stop if the difference between the last uniprot version and the current version is > than <maxDiffVersions> # but this check is only done for some important assemblies. For fringe assemblies, the numbers can easily # change 10x, as trembl predictions are the majority of annotations maxDiffVersions = 5.0 checkDbs = ["hg19", "hg38", "mm10", "rn6", "danRer10", "danRer7", "ce11"] # when we rename the parasol cluster, no need to change this file # probably overkill in retrospect but seemed like a good idea back then clusterFname = "/cluster/bin/scripts/cluster.txt" TREMBLCOLOR="0,150,250" # light blue SWISSPCOLOR="12,12,120" # dark blue asDir = dirname(__file__) # some feature types should not go into the bed name field. # for these features, we use the 'comment' as the bed name # e.g. "region of interest" is not very interesting, the actual # description is usually much more interesting. useComment = set(["domain", "chain","region of interest","topological domain","short sequence motif"]) # mostly for the "other annotations" subtrack, to show the different types featTypeColors = { "modified residue" : "200,200,0", "glycosylation site" : "0,100,100", "disulfide bond" : "100,100,100", "topological domain" : "100,0,0", "zinc finger region" : "100,100,0" } # some very common disease codes are not in the diseases.txt file disShortNames = { "hepatocellular carcinoma" : "HepatocC", "a hepatocellular carcinoma" : "HepatocC", "a hepatocellular carcinoma sample" : "HepatocC", "hepatocellular carcinomas" : "HepatocC", "ovarian cancer" : "OvC", "colon cancer" : "ColC", "colorectal cancer" : "ColrectC", "hepatoblastoma" : "HepatoBl", "a sporadic cancer": "sporadic", "sporadic cancers": "sporadic", "non-small cell lung cancer cell lines": "NSCLC-CL", "a colon cancer cell line":"ColC-CL" } # directory for the NCBI flatfiles NCBIDIR = "ncbi" # global variable needed for atexit callback function flagFname = None +def errAbort(msg): + " stop " + logging.error(msg) + assert(False) # generate stacktrace + def getTaxIdDbs(onlyDbs): """ return a dict with taxonId -> list of most recent dbs (e.g. for human, it's hg19 and hg38) if onlyDbs is a set, keep only these dbs. If onlyDbs is None, remove all nonAutoDbs. """ query = "select taxId, name from dbDb where active=1 order by orderKey;" rows = runQuery("hgcentral", query, usePublic=True) taxIdToDbs = defaultdict(list) # take only the first database for every taxonId for taxId, dbCode in rows: if onlyDbs: if dbCode not in onlyDbs: continue else: if dbCode in notAutoDbs: continue taxId = int(taxId) if taxId not in taxIdToDbs: taxIdToDbs[taxId].append(dbCode) for taxId, manNames in manualTaxIdDbs.items(): if manNames is None: del taxIdToDbs[taxId] else: for dbCode in manNames: if onlyDbs: if dbCode not in onlyDbs: continue else: if dbCode in notAutoDbs: continue if dbCode not in taxIdToDbs[taxId]: taxIdToDbs[taxId].append(dbCode) + # Check that every UCSC db has only a single taxon ID, otherwise all hell will break lose, as this script will run twice + # and the second run will overwrite all results from the previous run. We do not support "merging" annotations from two uniprot organisms. + # During testing this only happened for yeast strains, but it may come up again, so make sure it never happens again. + allDbs = set() + for taxId, dbs in taxIdToDbs.items(): + for db in dbs: + if not db in allDbs: + allDbs.add(db) + else: + assert(False) # This should not happen: a UCSC assembly is assigned to two taxon IDs + return taxIdToDbs def parseArgs(): parser = optparse.OptionParser("""usage: %prog [options] [run] - run uniprot update: download UniProt, parse the annotations to .tab files, build liftOver .psls and lift the annotations to bigBed files, one set per genome db Assumptions: - - proteins that are in UniProt but have no annotations are not shown. see SKIPPROT in code. + - proteins that are in UniProt but have no annotations are not shown in the alignments. - on hg38/hg19, the mapping uses ncbiRefSeq/refGene. see findBestGeneTable() """) parser.add_option("-d", "--debug", dest="debug", action="store_true", \ help="show debug messages") parser.add_option("-l", "--skipDownload", dest="skipDownload", action="store_true", \ help="Skip the download step (debugging)") parser.add_option("", "--skipTrembl", dest="skipTrembl", action="store_true", \ help="Skip processing Trembl") parser.add_option("-p", "--skipParse", dest="skipParse", action="store_true", \ help="Skip the download and parsing step (debugging)") parser.add_option("", "--dbs", dest="onlyDbs", action="store", \ help="only run on certain databases, comma-sep list of UCSC database names, e.g. 'hg19,mm10' (debugging). Implies -l and -p.") parser.add_option("", "--onlyMap", dest="onlyMap", action="store_true", \ help="only create the pslMap files (debugging)") parser.add_option("-u", "--uniprotDir", dest="uniprotDir", action="store", \ help="UniProt download data directory, default %default", default="/hive/data/outside/uniProt/current/") parser.add_option("-t", "--tabDir", dest="tabDir", action="store", \ help="directory for Uniprot tab-sep and fasta files, default %default", default="tab") parser.add_option("-f", "--faDir", dest="faDir", action="store", \ help="directory for full fasta files, default %default", default="fasta") parser.add_option("-m", "--mapDir", dest="mapDir", action="store", \ help="directory for pslMap (~liftOver) psl files, default %default", default="protToGenome") parser.add_option("-b", "--bigBedDir", dest="bigBedDir", action="store", \ help="directory for bigBed files, one subdirectory per db will be created", default="bigBed") parser.add_option("", "--force", dest="force", action="store_true", \ help="skip the check of differences against the previous version") parser.add_option("", "--onlyLinks", dest="onlyLinks", action="store_true", \ help="only create the /gbdb/ symlinks") parser.add_option("", "--skipLinks", dest="skipLinks", action="store_true", \ help="do not create the /gbdb/ symlinks") parser.add_option("", "--archiveDir", dest="archiveDir", action="store", \ default="/usr/local/apache/htdocs-hgdownload/goldenPath/archive/", help="Location of archive directory, default %default") parser.add_option("", "--mapQa", dest="mapQa", action="store_true", \ help="output some QA stats for the maps") parser.add_option("", "--db", dest="db", action="store_true", \ help="output the trackDb make command and uniprot <-> UCSC db assignments for debugging trackDb problems and showing which UCSC databases will be processed by the otto job and why") parser.add_option("", "--onlyFlip", dest="onlyFlip", action="store_true", \ help="After a run was aborted because of too many changes, now flip the files and ignore the size of the changes. Do not check for size increases anymore.") (options, args) = parser.parse_args() if options.db: taxIdDbs = getTaxIdDbs(None) print("-- Current TaxId<->database assignment:") for key, val in taxIdDbs.items(): print (key, val) allDbs = [] for taxId, dbs in taxIdDbs.items(): allDbs.extend(dbs) print(("To make the uniProt trackDbs for all DBs, run this in kent/src/hg/makeDb/trackDb: make alpha DBS='%s'" % " ".join(allDbs))) print("Total number of UCSC assemblies that this pipeline would run on: %d" % len(allDbs)) taxIdStr = ",".join([str(x) for (x,y) in taxIdDbs.items()]) # just the taxIds themselves print(("to just convert the XML files (debugging?), run this: uniprotToTab %s %s %s" % (options.uniprotDir, taxIdStr, options.tabDir))) sys.exit(1) if len(args)==0 and not options.mapQa: print("To actually run the pipeline, you need to specify the argument 'run'.") parser.print_help() print("To actually run the pipeline, you need to specify the argument 'run'.") sys.exit(0) if options.debug: consLevel = logging.DEBUG else: consLevel = logging.INFO # '' is the root logger logger = logging.getLogger('') logger.setLevel(logging.DEBUG) #By default, logs all messages # log to console ch = logging.StreamHandler() #StreamHandler logs to console ch.setLevel(consLevel) ch_format = logging.Formatter('%(asctime)s - %(message)s') ch.setFormatter(ch_format) # also always log everything to file fname = abspath("doUniprot.log") fh = logging.FileHandler(fname, "w+") # w+ means to overwrite the old file, "a" = append fh.setLevel(logging.DEBUG) #fh.setLevel(logging.INFO) fh_format = logging.Formatter('%(asctime)s - %(lineno)d - %(levelname)-8s - %(message)s') fh.setFormatter(fh_format) logger.addHandler(fh) logger.addHandler(ch) logging.info("Logging messages to %s" % fname) return args, options # ------------- def iterTsvRows(inFile,encoding="utf8", fieldSep="\t", isGzip=False): """ parses tab-sep file with headers as field names yields collection.namedtuples strips "#"-prefix from header line """ fh = inFile line1 = fh.readline() line1 = line1.strip("\n").strip("#") headers = line1.split(fieldSep) headers = [re.sub("[^a-zA-Z0-9_]","_", h) for h in headers] Record = namedtuple('tsvRec', headers) for line in fh: line = line.rstrip("\n") fields = line.split(fieldSep) if encoding!=None: fields = [f for f in fields] try: rec = Record(*fields) except Exception as msg: logging.error("Exception occured while parsing line, %s" % msg) logging.error("Filename %s" % fh.name) logging.error("Line was: %s" % line) logging.error("Does number of fields match headers?") logging.error("Headers are: %s" % headers) raise Exception("wrong field count in line %s" % line) # convert fields to correct data type yield rec threeToOne = \ {'Cys': 'C', 'Asp': 'D', 'Ser': 'S', 'Gln': 'Q', 'Lys': 'K', 'Ile': 'I', 'Pro': 'P', 'Thr': 'T', 'Phe': 'F', 'Asn': 'N', 'Gly': 'G', 'His': 'H', 'Leu': 'L', 'Arg': 'R', 'Trp': 'W', 'Ala': 'A', 'Val':'V', 'Glu': 'E', 'Tyr': 'Y', 'Met': 'M', 'Glx' : 'Z', 'Asx' : 'B', 'Pyl' : 'O', "Xaa" : "X", 'Sec': 'U' # very very rare amino acid (=stop codon) } oneToThree = dict([[v,k] for k,v in list(threeToOne.items())]) def aaToLong(seq): " convert amino acid to three letter code " res = [] for aa in seq: longAa = oneToThree.get(aa, aa) if longAa==aa: logging.error("unknown iupac "+ aa) res.append(longAa) return "-".join(res) def shortenDisCode(code): " some disease names are not shortened yet by UniProt. Do this now. " if code=="": return [] newCodes = [] if " and " in code: splitCodes = code.split(" and ") newCodes.append(disShortNames.get(splitCodes[0], splitCodes[0])) newCodes.append(disShortNames.get(splitCodes[1], splitCodes[1])) else: newCodes.append(disShortNames.get(code, code)) return newCodes def addExtraAnnotFields(bed, acc, isMut, annoType, firstAnnot, dbName): # status field bed.append( getStatusFromDb(dbName) ) bed.append(annoType) if isMut: bed.append(firstAnnot.disease) if isMut: # create description of mutation if int(firstAnnot.end)-int(firstAnnot.begin)==1: posStr = "position %s" % firstAnnot.begin else: posStr = "position %s-%s" % (firstAnnot.begin, firstAnnot.end) if firstAnnot.origAa=="": bed.append("%s, removal of amino acids" % (posStr)) else: bed.append("%s, %s changed to %s" % \ (posStr, aaToLong(firstAnnot.origAa), aaToLong(firstAnnot.mutAa))) else: # just position of feature if int(firstAnnot.end)-int(firstAnnot.begin)==1: posStr = "amino acid %s" % str(int(firstAnnot.begin)) # show a 1-based coordinate else: posStr = "amino acids %s-%s" % (firstAnnot.begin, str(int(firstAnnot.end)-1)) posStr += " on protein %s" % firstAnnot.acc bed.append(posStr) if not isMut: bed.append(firstAnnot.longName) bed.append(firstAnnot.syns.replace("|", "; ")) bed.append(firstAnnot.subCellLoc) # construct the comment field, which is also used for the mouse over commentField = firstAnnot.comment # add the disease to the mouse over if firstAnnot.disease!="": commentField = firstAnnot.disease + "; " + commentField if firstAnnot.featType == "sequence conflict": commentField = "%s, %s changed to %s, %s" % \ (posStr, aaToLong(firstAnnot.origAa), aaToLong(firstAnnot.mutAa), commentField) bed.append(commentField) # fields that are only used for mutations if isMut: varId = firstAnnot.varId if varId!="": varId = "%s#%s|%s" % (acc, varId, varId) # Andrew Nightingale requested that we link to UniProt bed.append(varId) bed.append(firstAnnot.dbSnpId) bed.append(htmlLink('uniProt', [acc])) pmids = firstAnnot.pmid.split(",") bed.append(htmlLink('pubmed', pmids)) # there was no filtering option yet for bigBed at the time of writing # so this allowed to filter by SwissProt/Trembl based on the score # These days, you can filter using the special bigBed statements if dbName=="trembl": bed[4] = "0" bed[8] = TREMBLCOLOR else: bed[4] = "1000" return bed def htmlLink(urlType, accs): # at the moment, not creating any html links, but this may be needed one day later, when # the links are not as well-formed as they are at the moment #strList = [] #for acc in accs: #strList.append('<a href="%s%s">%s</a>' % (urls[urlType], acc, acc)) #return ", ".join(strList) return ",".join(accs) def makeBedFields(dbName, firstAnnot, bed, isMut, color, recAnnot): """ convert a list of annotation objects and a bed with their positions to a single BED line with extra fields. This produces bigGenePred-input for the full proteins. While the input is already in basic BED format, this function fixes up the various BED fields (color, etc) and adds many extra fields. """ # try to create a more human-readable version of the disease codes acc = firstAnnot.acc # set the bed name field to a disease, to the mutation or something else if isMut and firstAnnot.origAa=="": disCodes = shortenDisCode(firstAnnot.disCode) disName = ",".join(disCodes) if len(disName)>30: disName = disName[:30]+"..." bed[3] = "%s-%sdel" % (firstAnnot.begin, firstAnnot.end) if len(disCodes)>0 and not "strain" in disName: bed[3] += " in %s" % disName else: bed[3] = "%s%s%s" % (firstAnnot.origAa, firstAnnot.begin, firstAnnot.mutAa) + if len(bed[3]) > 20: + bed[3] = "%daa to %daa" % (len(firstAnnot.origAa), len(firstAnnot.mutAa)) color = None if firstAnnot.featType=="sequence variant": annoType = "Naturally occurring sequence variant" color = "100,0,0" elif firstAnnot.featType=="mutagenesis site": annoType = "Experimental mutation of amino acids" color = "0,0,100" else: bed[3] = firstAnnot.shortFeatType if firstAnnot.featType in useComment: comment = firstAnnot.comment # trembl doesn't have comments for chains so make one up if comment=="": comment = "%s:%s-%s" % (acc, str(firstAnnot.begin), str(firstAnnot.end)) bed[3] = comment if firstAnnot.featType=="signal peptide": bed[3] = "Signal peptide" if firstAnnot.featType=="lipid moiety-binding region": bed[3] = "Lipidation" if firstAnnot.featType=="transmembrane region": bed[3] = "Transmembrane" if firstAnnot.comment=="Nuclear localization signal": bed[3] = "Nuclear loc" if firstAnnot.comment=="Involved in receptor recognition and/or post-binding events": bed[3] = "Recept recog" if firstAnnot.comment=="Fibronectin type-III": bed[3] = "FibronectIII" # more general rules if firstAnnot.comment.startswith("Zinc finger protein "): bed[3] = firstAnnot.comment.replace("Zinc finger protein ", "ZF-") if firstAnnot.comment.startswith("Necessary for the"): bed[3] = firstAnnot.comment.replace("Necessary for the ", "") if firstAnnot.comment.startswith("Interaction with "): bed[3] = firstAnnot.comment.replace("Interaction with ", "Int:") if firstAnnot.comment.startswith("Involved in the"): bed[3] = firstAnnot.comment.replace("Involved in the ", "") if firstAnnot.comment.startswith("Required for "): bed[3] = firstAnnot.comment.replace("Required for ", "") if firstAnnot.comment.startswith("Cleavage; by host "): bed[3] = "Cleave:"+firstAnnot.comment.split()[-1] if firstAnnot.comment=="Receptor-binding motif; binding to human ACE2": bed[3] = "binds ACE2" # chain annotations if firstAnnot.longName!="": bed[3] = firstAnnot.longName if firstAnnot.shortName!="": bed[3] = firstAnnot.shortName if bed[3] == "Intrinsically disordered": bed[3] = "Disordered" if len(bed[3])>17: bed[3] = bed[3][:14]+"..." annoType = firstAnnot.featType if color is None: bed[8] = featTypeColors.get(annoType, SWISSPCOLOR) else: bed[8] = color if annoType=="strand": annoType="beta strand" # bigGenePred format makes no sense for mutations but a lot for the other annotations # add the bigGenePred fields: name2, cdsStartStat, cdsEndStat, exonFrames, type, geneName, geneName2, geneType if not isMut: bed.append("") # name2 bed.append("cmpl") # cdsStartStat bed.append("cmpl") # cdsEndStat blockCount = int(bed[9]) bed.append(",".join(blockCount*["0"])) #exonFrames bed.append(dbName) # type bed.append("") # geneName bed.append("") # geneName2 bed.append("") # geneType bed = addExtraAnnotFields(bed, acc, isMut, annoType, firstAnnot, dbName) return bed def nuclToProtSizes(inFname): # keep protein lengths for later, we'll add one feature for every protein sequence seqSizes = {} for line in open(inFname): seq, size = line.rstrip("\n").split() seqSizes[seq] = int(int(size)/3) logging.debug("Parsed %s, found %d sequence sizes" % (inFname, len(seqSizes))) return seqSizes def makeSeqSizes(uniprotFa, outFname): " create a file with the lengths of the uniprot seqs " if not isfile(uniprotFa): raise Exception("Not found: %s" % uniprotFa) logging.debug("writing nucleotide lengths of %s to %s" % (uniprotFa, outFname)) cmd = "faSize %s -detailed | gawk '{$2=$2*3; print}'> %s" % (uniprotFa, outFname) #cmd = "faSize %s -detailed > %s" % (uniprotFa, outFname) run(cmd) def getMainIsoAcc(annot): acc = annot.mainIsoAcc return acc def getAllIsoAccs(annot): allIds = annot.isoIds.split("|") allIds.append(annot.mainIsoAcc) # for some reason trembl9606 B5WYT0 doesn't have any isoIds return allIds def writeProtAnnot(annotFnames, protBedName, seqSizes): " write bed file in prot coordinates, one bed per uniprot annotation " allFnames = ", ".join(annotFnames) logging.debug("converting UniProt tab %s to bed %s" % (allFnames, protBedName)) ofh = open(protBedName, "w") # index data by pos and write coords to BED doneAnnots = set() Record = None for annotFname in annotFnames: logging.debug("Reading %s" % annotFname) for annot in iterTsvRows(open(annotFname)): acc = getMainIsoAcc(annot) if acc not in seqSizes: logging.warning("skipping %s, not in seqSizes" % annot.mainIsoAcc) continue annotName = annotToString(annot) annotPos = 3*(int(annot.begin)-1) annotPosEnd = 3*(int(annot.end)-1) if annotName not in doneAnnots: isoAcc = getMainIsoAcc(annot) newLine = "\t".join([isoAcc, str(int(annotPos)), str(int(annotPosEnd)), annotName]) ofh.write(newLine+"\n") doneAnnots.add(annotName) ofh.close() def annotToString(annot): " create a unique key for an annotation " annotName = "|".join(annot).replace(" ", "_") assert("\t" not in annotName) return annotName def parseAnnots(fnames, seqSizes): """ return uniprot annots indexed by unique string key """ logging.debug("Parsing %s" % ",".join(fnames)) annotData = defaultdict(list) Record = None for fname in fnames: for annot in iterTsvRows(open(fname)): annotName = annotToString(annot) annotData[annotName].append(annot) # keep a copy of the fields for later #if Record is None: #fields = annot._fields #if "isBlacklisted" in fields: #fields = fields[:-1] #Record = namedtuple('fullSeqRec', annot._fields) logging.debug("Found %d annotations" % len(annotData)) for key, annots in annotData.items(): if len(annots)!=1: # they do have complete dupes, maybe typos, e.g. on O44342 at position 50 logging.debug("Duplicated annotation, will be collapsed: %s" % repr( annots)) return annotData def convertToBigBed(bedFiles, genomeChromSizesFname, bigBedDir): for f in list(bedFiles.values()): f.close() myDir = dirname(__file__) bbFnames = [] for trackName, bedFile in bedFiles.items(): asFname = join(asDir, "bed12UniProtAnnotBgp.as") if trackName=="unipMut": asFname = join(asDir, "bed12UniProtMut.as") bedFname = bedFile.name if os.path.getsize(bedFname)==0: logging.debug("%s is 0 bytes -> skipping" % bedFname) continue assert(isfile(bedFname)) bbFname = join(bigBedDir, trackName+".new.bb") bbFnames.append(bbFname) cmd = "bedSort %(bedFname)s %(bedFname)s" % locals() run(cmd) cmd = "bedToBigBed -as=%(asFname)s %(bedFname)s %(genomeChromSizesFname)s %(bbFname)s -type=bed12+ -tab" % locals() run(cmd) assert(isfile(bbFname)) return bbFnames def moveBigBedToOutDir(bbFnames, outDir): " move all bigBeds over to the output directory, assures some leve of atomicity " for bbFname in bbFnames: targetFname = join(outDir, basename(bbFname)) logging.debug("moving %s to %s" % (bbFname, targetFname)) if isfile(targetFname): logging.debug("Removing old file %s" % targetFname) remove(targetFname) move(bbFname, targetFname) commentRe = re.compile(r' [(][^)]+[)]') def parseGroupAndAnnotate(genomeBedName, annotData, accToDb): """ parse bed file, pull out original UniProt fields, and group by genomePosition+category: group all beds with same coordinates and uniprot features together. this is important for two reasons: 1) the pslMap file may use multiple transcripts for each protein and as such can result in multiple mappings that all are exactly at the same place in the genome 2) trembl often annotates the same identical thing on two proteins that are otherwise almost identical we do not want to show it twice on the genome. """ logging.debug("parsing %s and removing overlaps (same uniProt feature 'category' and same chrom/start/end/blocks)" % genomeBedName) bedGroups = defaultdict(list) for line in open(genomeBedName): bed = line.rstrip("\n").split("\t") bedName = bed[3] annots = annotData[bedName] if len(annots)!=1: logging.debug("? duplicate annots: %s" % repr(annots)) annot = annots[0] # group identifier is: genome position and block structure + # feature type + comment + disease + mutation from -> to # we need the genome block structure, as a feature could be split over different exons # depending on the splicing keyFields = [bed[0], bed[1], bed[2], bed[10], bed[11]] # for mutations, we need the from -> to amino acids, otherwise two mutations at the same position # would get filtered out keyFields.append(annot.origAa) keyFields.append(annot.mutAa) keyFields.append(annot.featType) # we don't want to remove identical annotations with different comments # but UniProt maps things to other proteins and then adds (By similarity) # to avoid duplicates, remove these comments in comments comment = commentRe.sub("", annot.comment) # strips things like: ... (By similarity) (PubMed:32198291, PubMed:32272481) keyFields.append(comment) # I hope the comment does not include the accession # keyFields.append(annot.disease) keyFields.append(annot.disCode) #keyFields.append(annot.varId) # for chains this is the unique chain identifier, so cannot use it keyFields.append(annot.dbSnpId) bedKey = tuple(keyFields) dbName = accToDb.get(getMainIsoAcc(annot)) # why is this necessary ... ? if dbName is None: dbName = accToDb[annot.acc] bedGroups[bedKey].append((dbName, bed, annot)) return bedGroups def uniprotLift(seqFname, annotFnames, genomeChromSizesFname, liftFname, outDir, accToDb, accToMeta, options): " lift uniProt annotations from annotFname using liftFname and write bigBed files to outDir " cdnaSizesFname = seqFname.replace(".fa", ".cdnaSize") makeSeqSizes(seqFname, cdnaSizesFname) protSizes = nuclToProtSizes(cdnaSizesFname) annotFnameStr = ", ".join(annotFnames) logging.debug("lifting %(annotFnameStr)s using %(liftFname)s and writing bigBeds to %(outDir)s" % locals()) tempDir = "uniprotLift-"+basename(liftFname).split(".")[0]+".tmp" genomeBedName = join(tempDir, "genomeCoords.bed") protBedName = join(tempDir, "protCoords.bed") logging.debug("Cleaning directory %s, used for all temp files" % tempDir) cmd = "rm -rf %s; mkdir %s" % (tempDir, tempDir) run(cmd) writeProtAnnot(annotFnames, protBedName, protSizes) # lift the raw start-end information from the protein to the genome if (options.debug and isfile(genomeBedName) and os.path.getsize(genomeBedName)!=0): logging.info("%s already exists, not remaking" % genomeBedName) else: logging.debug("lifting to genome coords") # added tawk '($16!=$17)' because in strPur2, with lots of tiny contigs, just a few amino acids got mapped # and after pslMap, nothing was left of a domain on the contig # "$@" cmd = "bedToPsl %(cdnaSizesFname)s %(protBedName)s stdout | pslMap stdin %(liftFname)s stdout | awk -v 'FS=\\t' -v 'OFS=\\t' '($16!=$17)' | pslToBed stdin stdout | LC_COLLATE=C sort -k1,1 -k2,2n | bedFixBlockOverlaps /dev/stdin > %(genomeBedName)s" % locals() run(cmd) annotData = parseAnnots(annotFnames, protSizes) logging.debug("Adding extra fields to lifted coords") tracks = [ "unipMut", # variants "unipStruct", # structural features "unipSplice", # splice variants "unipRepeat", # repeated regions "unipConflict", # sequence conflicts #"unipBlacklist", #blacklisted high-throughput-only features "unipLocSignal", "unipLocExtra", "unipLocTransMemb", "unipLocCytopl", # localization-related "unipDomain", "unipModif", "unipChain", "unipDisulfBond", # domains, etc "unipInterest", # regions of interest "unipOther", # all other features ] bedFiles = {} for t in tracks: bedFiles[t] = open(join(tempDir, t+".bed"), "w") bedGroups = parseGroupAndAnnotate(genomeBedName, annotData, accToDb) count = 0 # total number of annotations for bedName, beds in bedGroups.items(): beds.sort() # because "swissprot" comes before trembl alphabetically, all swissprot annotations are now first in this list # features are grouped by bedName, bedName includes chrom,start,end,type and various other fields # the aim is to not show something twice. UniProt projects features from one protein to others # and so often we risk ending up with duplicated annotation, when we project to the genome. # The grouping of features by (start, end, bedName, ...) removes the duplicates. # It is also dangerous, as we may drop some annotations accidentally. # The current system looks OK but may drop too much # if UniProt ever changes the way it uses the fields. dbName, bed, annot = beds[0] # of a group of identical annotations, we only show the first BED feature #if len(beds)>1: #logging.debug("Of the group '%s', only kept this feature: %s" % (bedName, repr(beds[0]))) #logging.debug("Dropped these features because they have the same key: %s" % (repr(beds[1:]))) # pull out the original full Uniprot fields of this BED group bedName = bed[3] acc = annot.acc recAnnot = accToMeta.get(acc, None) isMut = False color = None if annot.featType in ["mutagenesis site", "sequence variant"]: isMut = True ofh = bedFiles["unipMut"] elif annot.featType in ["splice variant"]: ofh = bedFiles["unipSplice"] elif annot.featType in ["strand","helix", "coiled-coil region", "turn"]: ofh = bedFiles["unipStruct"] # suggested by Regeneron: create four subtracks, for the subcell. localization indicators elif annot.featType in ["transmembrane region"]: ofh = bedFiles["unipLocTransMemb"] color = "0,150,0" # dark green, sent by Alejo Mujica in email from Oct 4 '17 elif annot.comment in ["Extracellular"]: ofh = bedFiles["unipLocExtra"] color = "0,110,180" # light-blue, alejo elif annot.comment in ["Cytoplasmic"]: ofh = bedFiles["unipLocCytopl"] color = "255,150,0" # light orange, alejo elif annot.featType in ["signal peptide"]: ofh = bedFiles["unipLocSignal"] color = "255,0,150" # light-red, alejo elif annot.featType in ["chain"]: ofh = bedFiles["unipChain"] elif annot.featType in ["repeat"]: ofh = bedFiles["unipRepeat"] elif annot.featType == "sequence conflict": ofh = bedFiles["unipConflict"] elif annot.featType in ["disulfide bond"]: ofh = bedFiles["unipDisulfBond"] elif annot.featType in ["domain", "zinc finger region", "topological domain"]: ofh = bedFiles["unipDomain"] elif annot.featType in ["glycosylation site", "modified residue", "lipid moiety-binding region"]: ofh = bedFiles["unipModif"] elif annot.featType in ["region of interest"]: ofh = bedFiles["unipInterest"] # everything else else: ofh = bedFiles["unipOther"] bedFields = makeBedFields(dbName, annot, bed, isMut, color, recAnnot) if bedFields is None: continue # trembl features are always light-blue, no matter what, this overrides all other colors set before here if dbName=="trembl": bedFields[8] = TREMBLCOLOR bedLine = "\t".join(bedFields)+"\n" ofh.write(bedLine) count += 1 logging.info("%d features written to bedfiles in %s" % (count, tempDir)) bigBedDir = join(tempDir, "bigBed") if not isdir(bigBedDir): logging.debug("Making dir %s" % bigBedDir) mkdir(bigBedDir) bbFnames = convertToBigBed(bedFiles, genomeChromSizesFname, bigBedDir) moveBigBedToOutDir(bbFnames, outDir) cmd = "rm -rf %s" % tempDir run(cmd) def isNewer(url, localFname): " return true if url is more recent than localFname " # little helper class to download only the http HEAD class HeadRequest(urllib.request.Request): def get_method(self): return "HEAD" # get the mtime of the file on the server if url.startswith("http"): + count = 0 + while True: + try: response = urllib.request.urlopen(HeadRequest(url)) + break + except urllib.error.URLError: + logging.error("URLError on %s, waiting for one hour, retrying" % url) + time.sleep(3600) + count +=1 + if count > 5: + errAbort("Cannot open %s" % url) + timeStr = response.headers.get("Last-Modified") serverTime = datetime.datetime.fromtimestamp(time.mktime(time.strptime(timeStr, "%a, %d %b %Y %H:%M:%S GMT"))) elif url.startswith("ftp://"): # https://stackoverflow.com/questions/25724497/getting-servers-date-using-ftp u = urlparse(url) from ftputil import FTPHost # not found? run 'pip install ftputil' with FTPHost(u.netloc, "anonymous", "genome-www@soe.ucsc.edu") as host: mod_time = host.path.getmtime(u.path) logging.debug("mod time %s" % mod_time) serverTime = datetime.datetime.fromtimestamp(mod_time) # get the mtime of the flag file localTime = datetime.datetime.fromtimestamp(0) if os.path.isfile(localFname): t = os.path.getmtime(localFname) localTime = datetime.datetime.fromtimestamp(t) logging.debug("server time %s" % serverTime) logging.debug("local time %s" % localTime) if serverTime > localTime: logging.debug("URL %s is newer than %s" % (url, localFname)) return True else: logging.debug("URL %s is not newer than %s" % (url, localFname)) return False def run(cmd, ignoreErr=False): " run command, stop on error " if type(cmd)==type([]): cmd = " ".join(cmd) logging.debug(cmd) cmd = "set -o pipefail; "+cmd ret = os.system(cmd) logging.debug("Running: %s" % (cmd)) if ret!=0 and not ignoreErr: logging.error("command returned error: %s" % cmd) - sys.exit(ret) + sys.exit(1) + return ret def fastaMd5(fname): " sort gzipped fasta by id and return its md5 " logging.debug("Getting md5 of sorted seqs in %s" % fname) if fname.endswith(".gz"): catCmd = "zcat" else: catCmd = "cat" cmd = """%s %s | awk 'BEGIN{RS=">"}{print $1"\t"$2;}' | sort -k1,1 | md5sum""" % (catCmd, fname) proc = subprocess.Popen(cmd, stdout=PIPE, shell=True, encoding="latin1") md5 = proc.stdout.readline().split()[0] logging.debug("MD5 of %s is %s" % (fname, md5)) return md5 def manyTabMd5(fnames): md5s = [] for fn in fnames: md5s.append(tabMd5(fn)) return listMd5(md5s) def tabMd5(fname): " sort gzipped tab and return its md5 " logging.debug("Getting md5 of sorted tab-sep file %s" % fname) if fname.endswith(".gz"): catCmd = "zcat" else: catCmd = "cat" cmd = """%s %s | sort | md5sum""" % (catCmd, fname) proc = subprocess.Popen(cmd, stdout=PIPE, shell=True, encoding="latin1") md5 = proc.stdout.readline().split()[0] return md5 def runQueryToFile(db, query, outFname): rows = runQuery(db, query) with open(outFname, "w") as ofh: for row in rows: ofh.write("\t".join(row)) ofh.write("\n") def runQuery(db, query, usePublic=False): " run mysql query, yield tuples " logging.debug("Running query on db %s: %s" % (db, query)) cmd = ["hgsql", db, "-NB", "-e", query] if usePublic: cmd.extend(["-h", "genome-mysql.cse.ucsc.edu", "-u", "genome", "--password="]) proc = subprocess.Popen(cmd, encoding="latin1", stdout=subprocess.PIPE) try: for line in iter(proc.stdout.readline,''): yield line.rstrip().split("\t") except: while proc.poll() is None: # Process hasn't exited yet, let's wait some time.sleep(0.5) logging.error("could not run query: %s " %query ) assert(False) def hasNoMultiMappers(db, table): " return true if the gene table has at least one geneId that is mapped to two chroms " # this happens with Ensembl scaffold assemblies. It breaks our whole data model " logging.debug("Checking for multi-mapping genes") # knownGene has no bin field... who knows why... if table=="knownGene": cmd = "hgsql %s -N -e 'select * from %s' | sort -k1 | cut -f1 | uniq -c | sort -rn | head -n1" % \ (db, table) else: cmd = "hgsql %s -N -e 'select * from %s' | cut -f2- | sort -k1 | cut -f1 | uniq -c | sort -rn | head -n1" % \ (db, table) proc = subprocess.Popen(cmd, stdout=PIPE, shell=True, encoding="latin1") row1 = proc.stdout.readline().strip().split() count, gene = row1 count = int(count) if count!=1: logging.warning("%s: Gene %s appears on %d chromosomes - this assembly has multi-mappers." % (db, gene, count)) return False return True def findBestGeneTable(db): " find the best gene table for a given organism and return it " if db=="hg19": tables = ["refGene"] # because in 2021, refSeq maps NM_001129826.3 still to chrX_jh159150_fix, confirmed as a bug by Terence # CSAG is an important gene elif db=="hg38": #tables = [ "wgEncodeGencodeCompV37lift37" ] tables = ["ncbiRefSeq"] else: tables = [ "ncbiRefSeq", "ensGene", "augustusGene"] # refGene has only a few hundred transcripts on most obscure organisms -> refGene only covers the manual NM_ sequences! for table in tables: query = "DESCRIBE %s" % (table) cmd = "hgsql %s -e 'DESCRIBE %s' > /dev/null 2>&1" % (db, table) ret = os.system(cmd) if ret==0: logging.debug("Best gene table for db %s is %s" % (db, table)) if db in ["hg19", "hg38", "mm10", "mm39"]: logging.info("DB is human or mouse. Tolerating multi mappers = transcript IDs that appear multiple times in the genome.") return table if hasNoMultiMappers(db, table): logging.info("%s: Best gene table is %s. No multi mappers." % (db, table)) return table assert(db not in ["hg19", "hg38", "mm10", "danRer10", "mm39"]) # never use BLAT on our main dbs return "blat" def gz_is_empty(fname): # from https://stackoverflow.com/questions/37874936/how-to-check-empty-gzip-file-in-python ''' Test if gzip file fname is empty Return True if the uncompressed data in fname has zero length or if fname itself has zero length Raises OSError if fname has non-zero length and is not a gzip file ''' with gzip.open(fname, 'rb') as f: data = f.read(1) return len(data) == 0 #def parseFaIds(fname): #"parse fasta, return dict seqId -> sequence " #seqIds = set() #logging.debug("Opening %s" % fname) #ifh = gzip.open(fname, "rt") #for line in ifh: #if line.startswith(">"): #seqId = line.lstrip(">").rstrip("\n").split()[0] #seqIds.add(seqId) #return seqIds def parseFasta(ifh): """ returns sequences as dict (id, sequence) """ seqLines = [] seqs = {} lastId = None for line in ifh: if line.startswith("\n") or line.startswith("#"): continue elif not line.startswith(">"): seqLines.append(line.replace(" ","").strip()) continue else: if len(seqLines)!=0: # on first >, seq is empty seqs[lastId] = "".join(seqLines) lastId = line.lstrip(">").rstrip("\n").split()[0] seqLines = [] else: if lastId!=None: sys.stderr.write("warning: when reading fasta file: empty sequence, id: %s\n" % line) lastId = line.lstrip(">").rstrip("\n").split()[0] # if it's the last sequence in a file, loop will end on the last line if len(seqLines)!=0: seqs[lastId] = "".join(seqLines) return seqs def concatFiles(fnames, outFname): "concat files and write to outFname. Also create a dict with seqId -> dbName " logging.debug("infiles: %s, outfile: %s" % (fnames, outFname)) accToDb = {} ofh = open(outFname, "wt") for dbName, fname in fnames: if not isfile(fname): raise Exception("%s not found" % fname) ifh = gzip.open(fname, "rt") try: for line in ifh: ofh.write(line) if line.startswith(">"): seqId = line.lstrip(">").rstrip("\n").split()[0] accToDb[seqId] = dbName except: logging.error("Error reading %s" % fname) - sys.exit(1) + assert(False) return accToDb -def pslToProtPsl(inFname, outFname): - " convert psl to prot coordinates " - ofh = open(outFname, "w") - - for line in open(inFname): - row = line.rstrip("\n").split("\t") - matches, misMatches, repMatches, nCount, qNumInsert, qBaseInsert, tNumInsert, \ - tBaseInsert, strand, qName, qSize, qStart, qEnd, tName, tSize, tStart, \ - tEnd, blockCount, blockSizes, qStarts, tStarts = row - # python3 now returns floats: 9/3 = 3.0 so need to cast to ints everywhere - qSize = int(float(qSize)/3) - tStarts = ",".join([str(int(int(x)/3)) for x in tStarts.rstrip(",").split(",")]) - qStarts = ",".join([str(int(int(x)/3)) for x in qStarts.rstrip(",").split(",")]) - blockSizes = ",".join([str(int(int(x)/3)) for x in blockSizes.rstrip(",").split(",")]) - qStart = int(float(qStart)/3) - qEnd = int(float(qEnd)/3) - row = [matches, misMatches, repMatches, nCount, qNumInsert, qBaseInsert, tNumInsert, \ - tBaseInsert, strand, qName, qSize, qStart, qEnd, \ - tName, tSize, tStart, tEnd, \ - blockCount, blockSizes, qStarts, tStarts] - row = [str(x) for x in row] - ofh.write("\t".join(row)) - ofh.write("\n") - ofh.close() +# not used anymore, using Mark's pslProtCnv +#def pslToProtPsl(inFname, outFname): +# " convert psl to prot coordinates " +# ofh = open(outFname, "w") +# +# for line in open(inFname): +# row = line.rstrip("\n").split("\t") +# matches, misMatches, repMatches, nCount, qNumInsert, qBaseInsert, tNumInsert, \ +# tBaseInsert, strand, qName, qSize, qStart, qEnd, tName, tSize, tStart, \ +# tEnd, blockCount, blockSizes, qStarts, tStarts = row +# # python3 now returns floats: 9/3 = 3.0 so need to cast to ints everywhere +# qSize = int(float(qSize)/3) +# tStarts = ",".join([str(int(int(x)/3)) for x in tStarts.rstrip(",").split(",")]) +# qStarts = ",".join([str(int(int(x)/3)) for x in qStarts.rstrip(",").split(",")]) +# blockSizes = ",".join([str(int(int(x)/3)) for x in blockSizes.rstrip(",").split(",")]) +# qStart = int(float(qStart)/3) +# qEnd = int(float(qEnd)/3) +# row = [matches, misMatches, repMatches, nCount, qNumInsert, qBaseInsert, tNumInsert, \ +# tBaseInsert, strand, qName, qSize, qStart, qEnd, \ +# tName, tSize, tStart, tEnd, \ +# blockCount, blockSizes, qStarts, tStarts] +# row = [str(x) for x in row] +# ofh.write("\t".join(row)) +# ofh.write("\n") +# ofh.close() def getStatusFromDb(db): if db=="trembl": dbDesc = "Unreviewed (TrEMBL)" else: dbDesc = "Manually reviewed (Swiss-Prot)" return dbDesc def addExtraGeneInfoFields(row, dbName, recAnnot): " add the 20 extra fields for gene-like tracks to a BED row " # change color and score - in the old bigBed days, there were no filters, # so the score can still be used to filter for trembl/swissprot acc = row[3] if dbName=="swissprot": color = SWISSPCOLOR score = "1000" elif dbName=="trembl": color = TREMBLCOLOR score = "0" else: assert(False) row[8] = color row[4] = score row.append( recAnnot.acc ) # uniprot accessions, field 26 / 1 row.append( recAnnot.name ) # uniprot curated name, field 27 / 2 dbDesc = getStatusFromDb(dbName) - row.append( dbDesc ) # db source, field 28 / 3 row.append( recAnnot.accList.replace("|", ", ")) # uniprot alternative IDs, #29 / 4 row.append( recAnnot.isoIds.replace("|", ", ")) # isoform IDs, #30 / 5 fullNames = recAnnot.protFullNames row.append( fullNames ) # uniprot full names, #31 / 6 # merge all these fields into one list of "gene synonyms" #14 geneSynonyms #15 isoNames #16 geneOrdLocus #17 geneOrf syns = recAnnot.geneSynonyms.split("|") syns.extend(recAnnot.isoNames.split("|")) syns.extend(recAnnot.geneOrdLocus.split("|")) syns.extend(recAnnot.geneOrf.split("|")) syns = [x.strip() for x in syns if x.strip()!=""] geneNames = recAnnot.geneName.replace("; ", ", ").replace("|", "; ") # relevant later but need it now shortNames = recAnnot.protShortNames.replace("|", "; ") if shortNames=="": shortNames = geneNames # in cov-2 pre-release, one protein only has a geneName, nothing else if shortNames=="" and len(syns)>0: shortNames = syns[0] if shortNames=="": shortNames = fullNames # in cov-2 pre-release, some proteins have no short name row.append( shortNames ) # uniprot short names #32 / 7 row.append( recAnnot.protAltFullNames.replace("; ", ", ").replace("|", "; ")) # uniprot alt names #33 / 8 row.append( recAnnot.protAltShortNames.replace("; ", ", ").replace("|", "; ")) # uniprot alt names #34 / 9 row.append( geneNames ) # #35 / 10 synStr = "; ".join(syns) row.append( synStr ) # #field 36: gene synonyms / 11 funcText = recAnnot.functionText.replace("|", "<li>").replace("-<li>-", "-|-") # address: [ILMVF]-Q-|-[SGACN] row.append( "<ul><li>"+funcText+"</ul>" ) # #37 / 12 row.append( recAnnot.hgncSym.replace("|", ", ")) #/ 13 row.append( recAnnot.hgncId.replace("|", ", ").replace("HGNC:", "")) #/ 14 row.append( recAnnot.refSeq.replace("|", ", ")) #/ 15 row.append( recAnnot.refSeqProt.replace("|", ", ")) # / 16 row.append( recAnnot.entrezGene.replace("|", ", ")) # / 17 row.append( recAnnot.ensemblGene.replace("|", ", ")) # / 18 row.append( recAnnot.ensemblProt.replace("|", ", ")) # / 19 row.append( recAnnot.ensemblTrans.replace("|", ", ")) # /20 return row def parseMapInfo(mapInfoFname): " returns a dict with (chrom,start,end,queryName) -> list of transcript IDs used for mapping " ##srcQName srcQStart srcQEnd srcQSize srcTName srcTStart srcTEnd srcStrand srcAligned mappingQName mappingQStart mappingQEnd mappingTName mappingTStart mappingTEnd mappingStrand mappingId mappedQName mappedQStart mappedQEnd mappedTName mappedTStart mappedTEnd mappedStrand mappedAligned qStartTrunc qEndTrunc #H2XQW1 0 66 66 ENSCINT00000034941.1 57 255 ++ 66 ENSCINT00000034941.1 0 799 chr12 2745838 2746956 + 3464 H2XQW1 0 198 chr12 2745895 2746412 + 198 0 -132 if not isfile(mapInfoFname): return None logging.debug("Parsing %s" % mapInfoFname) mapInfo = defaultdict(set) headers = None for line in open(mapInfoFname): row = line.lstrip("#").rstrip("\n").split("\t") if headers is None: headers = row srcQNameI = headers.index("srcQName") mappingQNameI = headers.index("mappingQName") mappedTNameI = headers.index("mappedTName") mappedTStartI = headers.index("mappedTStart") mappedTEndI = headers.index("mappedTEnd") continue acc = row[srcQNameI] transId = row[mappingQNameI] chrom = row[mappedTNameI] start = row[mappedTStartI] end = row[mappedTEndI] mapInfo[ (acc, chrom, start, end) ].add (transId) return mapInfo -def pslToBigPsl(mapFname, protSeqs, accToDb, accToMeta, accToMapSource, chromSizesFname, bigPslSwissFname, bigPslTremblFname): +def pslToBigPsl(mapFname, protSeqs, accToDb, accToMeta, accToMapSource, accToTrans, chromSizesFname, bigPslSwissFname, bigPslTremblFname, infoFname): " rewrite the mapping psl to a bigPsl with extra fields, change colors and score, add seqs and CDS info " logging.debug("Converting %s to bigPsl" % mapFname) bpInputFname = mapFname.replace(".psl", ".pslInput") - # convert to bigPslInput + # convert to bigPslInput = BED format cmd = "pslToBigPsl %(mapFname)s stdout | sort -k1,1 -k2,2n | bedFixBlockOverlaps /dev/stdin > %(bpInputFname)s" % locals() run(cmd) mapInfoFname = mapFname+".mapInfo" mapInfo = parseMapInfo(mapInfoFname) # rewrite the bigPslInput file: # - change colors and score # - add extra fields, sequence and CDS info, transcripts used from mapInfo # - split into swissprot and trembl files bpInputSwissFname = mapFname.replace(".psl", ".swissprot.pslInput") bpInputTremblFname = mapFname.replace(".psl", ".trembl.pslInput") ofhSwiss = open(bpInputSwissFname, "w") ofhTrembl = None if bigPslTremblFname: ofhTrembl = open(bpInputTremblFname, "w") + protToLocs = defaultdict(list) for line in open(bpInputFname): # chr1 11994 12144 B4E2Z4 1000 + 11994 12144 0 1 150, 0, 186 336 + 336 186, 249250621 150 0 0 0 0 row = line.rstrip("\n").split("\t") + row[-1] = "2" # seqType field: 0=empty, 1=nucleotide, 2=amino_acid + acc = row[3] recAnnot = accToMeta.get(acc, None) if recAnnot is None: logging.error("Accession: %s - no record info?" % acc) assert(False) - dbName = accToDb[acc] - # add the transcripts that were used for mapping this protein to the genome chrom, start, end = row[0], row[1], row[2] if mapInfo: transListStr = ", ".join(sorted(list(mapInfo[(acc, chrom, start, end)]))) - mapSource = accToMapSource[acc] + mapSource = accToMapSource.get(acc) + if mapSource is None: + mapSource = accToMapSource["default"] + + protToLocs[acc].append( ("%s:%s-%s" % (chrom, str(start), str(end)), mapSource, transListStr.replace(" ", "")) ) + if mapSource == "best": - mapInfo = "best match(es) when aligning protein against all transcripts" + mapDesc = "Best match(es) when aligning protein against all transcripts" + elif mapSource == "direct": + mapDesc = "Best BLAT match when aligning protein against entire genome" elif mapSource == "uniprot": - mapInfo = "alignment of protein to transcript(s) annotated by UniProt" + mapDesc = "Alignment of protein to transcript(s) annotated by UniProt" elif mapSource == "entrez": - mapInfo = "best match(es) when aligning protein against RefSeq transcripts of NCBI gene annotated by UniProt" + mapDesc = "Best match(es) when aligning protein against RefSeq transcripts of NCBI gene annotated by UniProt" else: - assert(False) # invalid mapSource ? - mapInfoStr = transListStr+" (%s)" % mapInfo + assert(False) # bug + + mapInfoStr = "%s: %s" % (mapDesc, transListStr) else: - mapInfoStr = "(mapped with direct BLAT)" + mapInfoStr = "no transcript: direct BLAT to genome" row.append(mapInfoStr) - row = addExtraGeneInfoFields(row, dbName, recAnnot) + protDb = accToDb[acc] + + # there are two types of sequences in UniProt: the "main" ones, that + # are annotated, and the others ("isoforms"), which are not annotated. I now color + # the alternative isoforms like trembl sequences + isMain = (acc==recAnnot.mainIsoAcc) + isMainStr = "alternative isoform" + if isMain: + isMainStr = "primary sequence" + if protDb=="swissprot": + if isMain: + color = "2,12,120" + else: + color= "0,150,250" # no need to distinguish, we have two different tracks for trembl and swissprot now + else: + color = "0,150,250" # trembl doesn't have isoforms, at least I've never seen one + row[8] = color + + # treat swissprot isoforms as if they were trembl sequences. This makes some sense from a user perspective. + # as the isoforms are almost as useless as the trembl annotations. :-) It makes the filtering UI simpler. + featDbName = protDb + if not isMain and protDb=="swissprot": + featDbName = "trembl" + row = addExtraGeneInfoFields(row, featDbName, recAnnot) + + # allow user to filter on main/not-main attribute + row.append(isMainStr) # add the sequence (for the alignment, oSequence) seq = protSeqs[acc] row[17] = seq # add the CDS field oCDS - row[18] = "1.."+str(3*len(seq)) + #row[18] = "1.."+str(3*len(seq)) + row[18] = "" # email from Braney: Put nothing in the CDS field - if dbName=="swissprot": + if protDb=="swissprot": ofh = ofhSwiss - elif dbName=="trembl": + elif protDb=="trembl": ofh = ofhTrembl else: assert(False) ofh.write("\t".join(row)) ofh.write("\n") ofhSwiss.close() if ofhTrembl: ofhTrembl.close() asFname = join(asDir, "bigPslUniprot.as") cmd = "bedToBigBed -extraIndex=acc,name -type=bed12+ -as=%s -tab %s %s %s" % \ (asFname, bpInputSwissFname, chromSizesFname, bigPslSwissFname) run(cmd) if ofhTrembl: cmd = "bedToBigBed -extraIndex=acc -type=bed12+ -as=%s -tab %s %s %s" % \ (asFname, bpInputTremblFname, chromSizesFname, bigPslTremblFname) run(cmd) + # output basic mapping information for debugging later + mapInfoFh = open(infoFname, "w") + mapInfoFh.write("#acc\tdb\tsyms\tentrez\tmapMethod\ttargetTrans\talignedTrans\tchromLocs\n") + for acc, db in accToDb.items(): + # write debugging information to the mapInfo file + allLocs = [] + allTrans = [] + if acc in protToLocs: + for locInfo in protToLocs[acc]: + locs, mapSource, transList = locInfo + allLocs.append(locs) + allTrans.append(transList) + locStr = ",".join(allLocs) + transStr = "|".join(allTrans) + else: + locStr = "NA" + transStr = "NA" + mapSource = "NA" + + syms = accToMeta[acc].hgncSym.replace("|", ",") + genes = accToMeta[acc].entrezGene.replace("|", ",") + if accToTrans: + filterTransList = ",".join(accToTrans[acc]) + else: + filterTransList = "NA" + row = (acc, db, syms, genes, mapSource, filterTransList, transStr, locStr) + mapInfoFh.write("\t".join(row)) + mapInfoFh.write("\n") + + mapInfoFh.close() + logging.info("Wrote %s" % mapFname) + + def parseRecordMeta(tabDir, taxId, doTrembl): """ parse the uniprot record-level annotations, like xrefs etc. return dict acc -> namedtuple links from ALL isoforms accessions of a record. """ fnames = [ (join(tabDir,"swissprot.%d.tab" % taxId)) ] if doTrembl: fnames.append( (join(tabDir,"trembl.%d.tab" % taxId)) ) ret = {} for fname in fnames: for row in iterTsvRows(open(fname)): for acc in getAllIsoAccs(row): ret[acc] = row return ret def blatProteinsKeepBest(fullFaFname, db, mapFname, stats): " blat the proteins directly, only good for small genomes where we don't have any gene models " myDir = dirname(__file__) - #nuclFname = mapFname+".nucl" cmd = "blat -q=prot -t=dnax /gbdb/{db}/{db}.2bit {inf} stdout -noHead | sort -k10 | pslReps stdin stdout /dev/null " \ "-minAli=0.95 -nohead | pslProtCnv > {out}".format(db=db, inf=fullFaFname, out=mapFname, myDir=myDir) stats["minAli"]=0.95 - # originally used "| {myDir}/pslProtCnv " but got rid of the markd-script dependency now + #nuclFname = mapFname+".nucl" + # originally used "| {myDir}/pslProtCnv " but tried to get rid of the markd-script dependency #pslToProtPsl(nuclFname, mapFname) - # figured that pslToProtPsl() is not the same as pslProtCnv... argll... + # then later figured that pslToProtPsl() is not the same as pslProtCnv and went back the MarkD way #os.remove(nuclFname) run(cmd) def getTransIds(db, geneTable, transcriptFa): """ return all possible transcript IDs given a gene table. The reason that we need is that Uniprot often refers to transcripts that don't exist and we are using a select file to map only to those. In these cases, we want to make sure that our select file contains only transcript that we actually have, so we can log how many transcript can possibly mapped (and which ones). This is important for debugging. """ # no idea how to get the version suffix out of our mysql tables - thanks Obama! if geneTable=="refGene": logging.debug("Gene table is refGene, reading IDs from %s" % transcriptFa) allTrans = set(parseFasta(open(transcriptFa)).keys()) return allTrans logging.info("Getting transcript IDs for db=%s, table=%s, field=name" % (db, geneTable)) sql = "SELECT DISTINCT name from "+geneTable cmd = ["hgsql", db, "-NBe", sql] proc = subprocess.Popen(cmd, encoding="latin1", stdout=PIPE) allTrans = set() for line in proc.stdout: idStr = line.rstrip() allTrans.add(idStr) logging.info("Got %d distinct transcript IDs from MySQL table" % len(allTrans)) return allTrans -def writeTransToSelect(upSeqId, transIds, shortToLong, notFound, outTransIds, commonTrans, ofh, verDiffCount, pairCount): - " given a list of transcript IDs, write them to select file, if their base is found in shortToLong. Return count written " +def writeTransToSelect(upSeqIds, transIds, shortToLong, notFound, outTransIds, commonTrans, \ + ofh, verDiffCount, pairCount): + """ given a list of transcript IDs, write them to select file, if their base (before dot) + is found in shortToLong. Return count written """ foundTransCount = 0 for transId in transIds: # remove the version for the comparison, but keep the version in the pslSelect file shortId = transId.split(".")[0] if shortId not in shortToLong: # if we do not have this transcript, we don't write anything into the pair select file # This means that pslSelect falls back to the defaults, passes through everything and then # pslCdnaFilter picks the best ones notFound.append(transId) continue commonTrans.add(transId) if transId!=shortToLong[shortId]: verDiffCount+=1 pairCount += 1 outTransIds.add(transId) # here we're fixing up the select file: we replace the acc.version that UniProt has # with the acc.version that we have in our transcript file. This saves a few hundred # transcripts, sometimes thousands, from getting removed + for upSeqId in upSeqIds: ofh.write("%s\t%s\n" % (upSeqId, shortToLong[shortId])) foundTransCount+=1 return foundTransCount, verDiffCount, pairCount def buildSelectFile(tabFnames, mapDir, taxId, db, geneTable, transcriptFa, geneToRefSeqs, uniprotMd5, transMd5, stats): - """ make a two-column file uniprotId <-> transcript ID for filtering the PSL file. Helps force the alignment to the correct - transcript. see makeUniProtPsl.sh """ + """ make a two-column file uniprotId <-> transcript ID for filtering the + PSL file. The tool for this is called pslSelect. This helps force the alignment + to the correct transcript. It turned out to be absolutely necessary. see makeUniProtPsl.sh """ # get the UniProt field that holds the list of annotated transcript IDs if "encode" in geneTable or "ensGene" in geneTable: transField = "ensemblTrans" elif "refGene" in geneTable or "ncbiRefSeq" in geneTable: transField = "refSeq" else: logging.info("No supported gene track found. The protein/transcript alignments will not be filtered using pslSelect.") stats["noGeneTrack"] = True - return None, stats + # anoGam1 for example, has only augustus genes as a track + return None, stats, {} allTransIds = getTransIds(db, geneTable, transcriptFa) # create a mapping from no-version (short) to with-version accession (long), so we can fix them up later # to the accessions that we actually have in our fasta file shortToLong = {} for acc in allTransIds: shortToLong[acc.split(".")[0]] = acc logging.debug("Example transcript IDs: %s" % list(allTransIds)[:10]) uniprotMd5 = uniprotMd5[:10] transMd5 = transMd5[:10] selectFname = join(mapDir, "%(geneTable)s_%(uniprotMd5)s_%(transMd5)s.upToTrans.tab" % locals()) logging.info("Building pair file %s" % selectFname) ofh = open(selectFname, "w") notFound = [] - # the following loop is FULL of statistics. It took me a long time to get my head around + # the following loop is FULL of stat tracking. It took me a long time to get my head around # all the possible ways that the mapping can go astray and I wanted to keep them all - # This makes the code hard to read + # This makes the code harder to read but simplifies debugging a lot when ML questions come in. + + # these are used to collect data for the statistics upRecCount = 0 outUpIds = set() inTransIds = set() outTransIds = set() commonTrans = set() notFoundAtAll = set() pairCount = 0 verDiffCount = 0 verDiffCount2 = 0 - protMapSource = {} sourceCounts = defaultdict(int) + # these are data that are important for other functions and are returned + protMapSource = {} # sequence accession -> "uniprot", "entrez" or "best" + mainSeqIds = set() # all the sequence accessions that are the "main" isoform, selected and annotated by UniProt. The others are not annotated. + for fname in tabFnames: fieldIdx = None entrezIdx = None + isoIdx = None for line in open(fname): row = line.rstrip("\n").split('\t') if fieldIdx is None: # header line fieldIdx = row.index(transField) entrezIdx = row.index("entrezGene") + isoIdx = row.index("isoIds") continue upRecCount += 1 - upSeqId = row[2] # not row[1], row[2] is the name of the sequence + upAcc = row[1] # uniProt record ID (NOT sequence ID, the sequences are often -1, -2, -3, etc) + + # make a list of all possible _sequence_ accessions for this record in Uniprot, so main + isoforms + mainSeqId = row[2] # not row[1], row[2] is the name of the main sequence ID + mainSeqIds.add(mainSeqId) + #logging.debug("UniProt ID: %s" % upSeqId) + allSeqIds = [mainSeqId] + isoSeqStr = row[isoIdx] + if (isoSeqStr!=""): + isoSeqIds = isoSeqStr.split("|") + allSeqIds.extend(isoSeqIds) transIdStr = row[fieldIdx] entrezGenes = row[entrezIdx] if transIdStr=="": - #logging.debug("Empty transcript ID") - continue + #logging.debug("%s: Empty transcript ID" % mainSeqId) + transIds = [] + else: transIds = transIdStr.split("|") #logging.debug("Transcript IDs: %s" % transIds) - outUpIds.add(upSeqId) + outUpIds.update(allSeqIds) inTransIds.update(transIds) - # stage 1: first try to use the RefSeq IDs as they were annotated by UniProt - foundTransCount, verDiffCount, pairCount = writeTransToSelect(upSeqId, transIds, shortToLong, notFound, outTransIds, commonTrans, ofh, verDiffCount2, pairCount) + # stage 1: first try to use the transcript (RefSeq) IDs as they were annotated by UniProt + foundTransCount, verDiffCount, pairCount = writeTransToSelect(allSeqIds, transIds, \ + shortToLong, notFound, outTransIds, commonTrans, ofh, verDiffCount2, pairCount) mapSource = None if foundTransCount != 0: mapSource = "uniprot" else: + # optional stage2: try to go through entrez gene - not as precise, but better than nothing if entrezGenes!="" and geneToRefSeqs: - # stage2: try to go through entrez gene - not as precise, but better than nothing # there can be several entrez genes for one uniprot ID entrezGenes = entrezGenes.split('|') transIds = set() for geneId in entrezGenes: if geneId in geneToRefSeqs: # and of course many refseq for one geneId refseqs = geneToRefSeqs[geneId] transIds.update(refseqs) foundTransCount, verDiffCount2, pairCount = \ - writeTransToSelect(upSeqId, transIds, shortToLong, notFound, outTransIds, commonTrans, ofh, verDiffCount2, pairCount) - if foundTransCount==0: - mapSource = "best" - else: + writeTransToSelect(allSeqIds, transIds, shortToLong, notFound, \ + outTransIds, commonTrans, ofh, verDiffCount2, pairCount) + + if foundTransCount!=0: mapSource = "entrez" else: + # if stage 2 also didn't work, simply use the best matching transcript + mapSource = "best" + else: mapSource = "best" - protMapSource[upSeqId] = mapSource + # now that we know how we map these proteins to the genome, keep this for later and keep the stats + for seqId in allSeqIds: + protMapSource[seqId] = mapSource sourceCounts[mapSource] += 1 if mapSource=="best": - notFoundAtAll.add(upSeqId) + notFoundAtAll.add(upAcc) sourceCounts = list(dict(sourceCounts).items()) stats["notFoundAtAll"] = len(notFoundAtAll) stats["notFoundAtAll_Examples"] = list(notFoundAtAll)[:10] stats["verDiffCount"] = verDiffCount stats["verDiffCount2"] = verDiffCount2 stats["sourceCounts"] = sourceCounts # for debugging if len(notFoundAtAll)!=0: notFoundFname = join(mapDir, "lastRun_noAnnotatedTranscriptIDs.txt") notFoundFh = open(notFoundFname, "w") #notFoundFh.write(str(notFoundAtAll)+"\n") for acc in notFoundAtAll: notFoundFh.write(acc+"\n") notFoundFh.close() logging.info("Wrote UniProt IDs where no transcript could be found to %s" % notFoundFname) if pairCount==0: logging.warn("No single uniprot/transcript pair is left in select file. Not doing pair file filtering at all.") stats["outPairCount"]=0 - return None, stats + return None, stats, protMapSource # make a little table with NM_ -> count, XM_ -> count, etc prefixCounts = defaultdict(int) for nfId in notFound: prefixCounts[nfId[:3]]+=1 ofh.close() logging.info("Processed %d UniProt records, trying to match with the transcript IDs from '%s'" % (upRecCount, geneTable)) logging.info("Found %d transcript IDs in UniProt" % len(inTransIds)) logging.info("Found %d transcript IDs in the genePred table %s" % (len(allTransIds), geneTable)) logging.info("%d transcript IDs found in both UniProt and transcript table" % len(commonTrans)) if len(notFound)!=0: logging.info("%d transcript IDs found in UniProt records were not found in '%s'. These mappings were removed. Example: %s" % (len(notFound), geneTable, notFound[0])) logging.info("The IDs from UniProt not found in the genePred fall into these classes: %s" % dict(prefixCounts)) logging.info("%d proteins could not be mapped by any method, so they fall back to best-alignment" % len(notFoundAtAll)) logging.info("The UniProt proteins were mapped using these methods (type:count): %s" % sourceCounts) logging.info("The transcript version suffix was corrected for %d transcripts at stage 1, and %d transcript at stage 2" % (verDiffCount, verDiffCount2)) logging.info("The pslSelect file contains %d pairs: %d uniprot IDs are associated to %d transcript IDs" % (pairCount, len(outUpIds), len(outTransIds))) + stats["uniprotRecCount"] = len(mainSeqIds) stats["protSeqCount"] = upRecCount stats["uniprotTransCount"] = len(inTransIds) stats["browserTransCount"] = len(allTransIds) stats["commonTransCount"] = len(commonTrans) stats["notFoundTransCount"] = len(notFound) if len(notFound)!=0: stats["notFound_examples"] = list(notFound[:10]) stats["notFoundClasses"] = dict(prefixCounts) stats["outPairCount"] = pairCount stats["outPairUniprot"] = len(outUpIds) stats["outPairTrans"] = len(outTransIds) return selectFname, stats, protMapSource def makeTranscriptFiles(db, geneTable, taxId, dbDir): """ given a db and a gene table, create two files, one for the transcript fasta sequences and one for the transcript -> genome PSL. Return tuple of the file names ALWAYS REMOVES _ALT/_FIX/_HAP results from the PSL! """ #dbDir = join(mapDir, db+"_"+geneTable) #if not isdir(dbDir): #os.makedirs(dbDir) faName = join(dbDir, "transcripts.fa") pslName = join(dbDir, "transcripts.psl") pslFields = "matches,misMatches,repMatches,nCount,qNumInsert,qBaseInsert,tNumInsert," \ "tBaseInsert,strand,qName,qSize,qStart,qEnd,tName,tSize,tStart,tEnd,blockCount,blockSizes,qStarts,tStarts" - if geneTable in ["ncbiRefSeq", "refGene"]: if geneTable=="ncbiRefSeq": origFa = "/gbdb/%s/ncbiRefSeq/seqNcbiRefSeq.rna.fa" % db shutil.copyfile(origFa, faName) pslTable = "ncbiRefSeqPsl" + + query = "SELECT "+pslFields+" from "+pslTable+" WHERE tName NOT LIKE '%_hap%' AND tName not like '%_alt%' AND tNAME NOT LIKE '%_fix%'" + runQueryToFile(db, query, pslName) + elif geneTable=="refGene": # ChrisL told me where these files can be found #cmd = "curl https://hgdownload.cse.ucsc.edu/goldenpath/%s/bigZips/refMrna.fa.gz | zcat > %s" % (db, faName) cmd = "zcat /hive/data/outside/genbank/data/ftp/%s/bigZips/refMrna.fa.gz | tr ' ' '.' > %s" % (db, faName) run(cmd) - pslTable = "refSeqAli" + pslFields = "matches,misMatches,repMatches,nCount,qNumInsert,qBaseInsert,tNumInsert," \ + "tBaseInsert,strand,concat(qName, '.', gbSeq.version),qSize,qStart,qEnd,tName,tSize,tStart,tEnd,blockCount,blockSizes,qStarts,tStarts" - query = "SELECT "+pslFields+" from "+pslTable+" WHERE tName NOT LIKE '%_hap%' AND tName not like '%_alt%' AND tNAME NOT LIKE '%_fix%'" + query = "SELECT "+pslFields+" from refSeqAli, hgFixed.gbSeq WHERE refSeqAli.qname=gbSeq.acc and tName NOT LIKE '%_hap%' AND tName not like '%_alt%' AND tNAME NOT LIKE '%_fix%'" runQueryToFile(db, query, pslName) else: query = "SELECT name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds from %s where cdsStart < cdsEnd" % (geneTable) gpName = join(dbDir, "transcripts.gp") cdsName = join(dbDir, "transcripts.cds") runQueryToFile(db, query, gpName) cmd = ["genePredToFakePsl", db, gpName, pslName, cdsName] run(cmd) cmd = ["getRnaPred", db, gpName, "all", faName] run(cmd) logging.info("Created %s and %s for %s/%s" % (faName, pslName, db, geneTable)) return faName, pslName def writeMapDesc(stats, db, geneTable, mapDescFname): " write a little json file that points to the map file used and some basic stats about it " logging.debug("making json file with version and other lift info") if geneTable == "ncbiRefSeq": version = open("/gbdb/"+db+"/ncbiRefSeq/ncbiRefSeqVersion.txt").read().strip() elif geneTable in ['refGene', 'augustusGene', 'knownGene']: version = datetime.datetime.today().strftime('%Y-%m-%d') elif geneTable=="blat": version = "direct" elif geneTable in ["ensGene"]: version = list(runQuery("hgFixed", "select version from trackVersion where db='%s' and name='ensGene' order by ix desc limit 1;" % db))[0][0] else: assert(False) stats["geneTable"] = geneTable stats["version"] = version stats["createdDate"] = datetime.datetime.today().strftime('%Y-%m-%d') with open(mapDescFname, "w") as mapDescFh: json.dump(stats, mapDescFh, indent=4) def listMd5(arr): " return hex md5 given list of strings " import hashlib m = hashlib.md5() for a in arr: m.update(a.encode("utf8")) return m.hexdigest() def readGeneToRefSeq(taxId): " return entrezId -> list of Refseq from tsv file " g2refseq = {} fname = join(NCBIDIR, str(taxId)+".tsv") for line in open(fname): geneId, transList = line.rstrip("\n").split('\t') transList = transList.split(',') g2refseq[geneId] = transList return g2refseq +def parseKeyVal(fname): + " given a file with key<tab>val return a dict with key -> list of values " + if fname is None: + return None + vals = defaultdict(list) + for line in open(fname): + key, val = line.rstrip("\n").split("\t") + vals[key].append(val) + return vals + def makeProteinGenomePsl(taxId, protFa, tabFnames, db, cluster, doForce, mapDir, mapDescFname): """ map proteins of a taxon stored in protFa to db via geneTable and create a PSL file for the mapping - Will try to reuse the old mapping file if possible, as it is expensive to build. - BLAST has no option to restrict the alignment, verified with an email to NCBI BLAST support team. """ + Will try to reuse the old PSL mapping file if possible, as it is expensive to build. + Need to BLAST the entire file: BLAST has no option to subset the target (unlike blast or lastz), verified + with an email to NCBI BLAST support team. A central point of this function + is buildSelectFile(). The psl select pair files have a huge influence on the result, + so it is rebuilt every time, as any change in UniProt will change it. It's also quick to create. + Its MD5 is part of the PSL mapping file. Any change to the pslSelect pair file will trigger + a realignment/rebuild of the pslMap PSL file. + """ # use MD5s of the input files to determine if the protein -> genome map has to be rebuilt global MINALI protMd5 = fastaMd5(protFa) stats = OrderedDict() stats["user"] = os.getlogin() stats["taxId"] = taxId stats["db"] = db geneTable = findBestGeneTable(db) metaMd5 = manyTabMd5(tabFnames) if geneTable!="blat": transcriptFa, transcriptPsl = makeTranscriptFiles(db, geneTable, taxId, mapDir) transMd5 = fastaMd5(transcriptFa) pslMd5 = tabMd5(transcriptPsl) else: + # this usually only happens on viral genomes or other weird cases that don't have a single gene model track + # here we blat the proteins directly onto the genome transMd5, pslMd5 = "directBlat-noTranscripts", "directBlat-noPsl" transcriptFa, transcriptPsl = None, None geneToRefSeqs = None + selectFname = None + protToTrans = None + + if geneTable in ["blat"]: + protMapSource = {"default":"direct"} + elif geneTable in ["augustusGene"]: + protMapSource = {"default":"best"} + else: if geneTable in ["refGene", "ncbiRefSeq"]: geneToRefSeqs = readGeneToRefSeq(taxId) - - selectFname, stats, protMapSource = buildSelectFile(tabFnames, mapDir, taxId, db, geneTable, transcriptFa, geneToRefSeqs, metaMd5, transMd5, stats) + selectFname, stats, protMapSource = buildSelectFile(tabFnames, mapDir, taxId, db, \ + geneTable, transcriptFa, geneToRefSeqs, metaMd5, transMd5, stats) + protToTrans = parseKeyVal(selectFname) allMd5s = [protMd5, transMd5, pslMd5] if selectFname: pairMd5 = tabMd5(selectFname) allMd5s.append(pairMd5) stats["pairMd5"] = pairMd5[:10] + stats["pairFname"] = selectFname - # if either the protein sequences, the transcripts, their alignment or the protein/transcript mapping changes - # -> create a new PSL mapping file + # if either the protein sequences, the transcripts, their alignment or the + # protein/transcript mapping changes -> create a new PSL mapping file fullMd5 = listMd5(allMd5s)[:10] mapFname = join(mapDir, "%(geneTable)s_%(fullMd5)s.psl" % locals()) if isfile(mapFname) and not doForce: logging.info("%s already exists, not rebuilding the protein -> genome mapping PSL" % mapFname) assert(os.path.getsize(mapFname)!=0) - return mapFname, geneTable, fullMd5, protMapSource, False + # careful: if you modify this, also modify the other return statement below + return mapFname, geneTable, fullMd5, protMapSource, protToTrans, False stats["protMd5"] = protMd5[:10] stats["metaMd5"] = metaMd5[:10] stats["transMd5"] = transMd5[:10] stats["fullMd5"] = fullMd5[:10] stats["mapFname"] = basename(mapFname) logging.debug("%s does not exist" % mapFname) if geneTable=="blat": logging.error("Could not find any gene table for %s, using BLAT to map proteins" % db) blatProteinsKeepBest(protFa, db, mapFname, stats) else: if db in ["ci3"]: # wow: ciona's genome is from a different organism than the refseq transcripts. MINALI = 0.85 stats["minAli"] = MINALI workDir = "clusterRun-map-%s-%s-%s.tmp" % (db, geneTable, fullMd5) scriptArgs = [protFa, transcriptFa, transcriptPsl, str(MINALI), cluster, workDir, mapFname] if selectFname is not None: scriptArgs.append(selectFname) # This is where the BLAST alignment-meat happens cmd = ["time", "./makeUniProtPsl.sh"] cmd.extend(scriptArgs) logging.info("Running %s" % cmd) run(cmd) writeMapDesc(stats, db, geneTable, mapDescFname) assert(os.path.getsize(mapFname)!=0) - return mapFname, geneTable, fullMd5, protMapSource, True + # if you modify this line, also modify the other return statement above + return mapFname, geneTable, fullMd5, protMapSource, protToTrans, True -def convMapToBigPsl(fastaFname, mapFname, bigBedDir, db, accToDb, accToMeta, accToMapSource, chromSizesFname, doTrembl): +def convMapToBigPsl(fastaFname, mapFname, bigPslDir, accToDb, accToMeta, accToMapSource, \ + accToTrans, chromSizesFname, doTrembl): " convert the .psl mapping file to bigPsl annotated with a few basic prot infos " - bigPslDir = makeSubDir(bigBedDir, db) bigPslSwissFname = join(bigPslDir, "unipAliSwissprot.new.bb" % locals()) if doTrembl: - bigPslTremblFname = join(bigBedDir, db, "unipAliTrembl.new.bb" % locals()) + bigPslTremblFname = join(bigPslDir, "unipAliTrembl.new.bb" % locals()) else: bigPslTremblFname = None protSeqs = parseFasta(open(fastaFname)) - pslToBigPsl(mapFname, protSeqs, accToDb, accToMeta, accToMapSource, chromSizesFname, bigPslSwissFname, bigPslTremblFname) + infoFname = join(bigPslDir, "protMapInfo.tsv") + pslToBigPsl(mapFname, protSeqs, accToDb, accToMeta, accToMapSource, accToTrans, chromSizesFname, bigPslSwissFname, bigPslTremblFname, infoFname) # create a raw lift file in case someone wants to run pslMap one day - liftFname = join(bigBedDir, db, "unipToGenomeLift.psl") + liftFname = join(bigPslDir, "unipToGenomeLift.psl") shutil.copyfile(mapFname, liftFname) cmd = ["gzip","-f",liftFname] run(cmd) liftFname += ".gz" logging.info("Created %s" % liftFname) - chainFname = join(bigBedDir, db, "unipToGenome.over.chain") - cmd = ["pslToChain",liftFname, chainFname] + mapSwapFname = join(bigPslDir, "unipAlign.swap.psl") + cmd = ["pslSwap", mapFname, mapSwapFname] + run(cmd) + + chainFname = join(bigPslDir, "unipToGenome.over.chain") + cmd = ["pslToChain",mapSwapFname, chainFname] run(cmd) cmd = ["gzip","-f",chainFname] run(cmd) logging.info("Created %s" % liftFname) chainFname += ".gz" + os.remove(mapSwapFname) + def makeSubDir(parent, child): " mkdir child under parent and return " newDir = join(parent, child) if not isdir(newDir): logging.info("Making dir: %s" % newDir) os.makedirs(newDir) return newDir -def updateUniprot(args, onlyDbs, taxIdDbs, options): - " This is the main function that runs a single uniprot update for a list of DBs " - uprotDir = options.uniprotDir - tmpDir = join(uprotDir, "download.tmp") - tabDir = options.tabDir - mapDir = options.mapDir - bigBedDir = options.bigBedDir - faDir = options.faDir - doTrembl = not options.skipTrembl - - relFname = join(tabDir, "version.txt") - - if not options.skipDownload and not options.skipParse and not options.onlyDbs: - # download NCBI -> refseq tables - downloadAndSplitNcbi(taxIdDbs) - - # download UniProt using LFTP +def downloadUniprot(uprotDir): + " if necessary, download UniProt using LFTP in an atomic way, update release info file " localFname = join(uprotDir, "uniprot_sprot.xml.gz") if not isNewer(upUrl, localFname): logging.info("files at %s are not newer than file in %s, nothing to do. Specify -l to skip this check." % (upUrl, localFname)) sys.exit(0) # use lftp to update uniprot and download only changed files # in late 2020, pget started to trigger errors, so removed -P 3 and --use-pget-n=4 - cmd = 'lftp ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/ -e "lcd %s && mirror . --exclude-glob *.dat.gz && exit"' % tmpDir - run(cmd) + tmpDir = join(uprotDir, "download.tmp") + if not isdir(tmpDir): + os.makedirs(tmpDir) + + # the uniprot FTP server is too slow and too unreliable. Switching to EBI's which has rsync !! + #cmd = 'lftp ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/ -e "lcd %s && mirror . --exclude-glob *.dat.gz && exit"' % tmpDir + count = 0 + while True: + cmd = "rsync -av --partial rsync://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/ %s/" % tmpDir + ret = run(cmd, ignoreErr=True) + if ret==0: + break + + logging.info("Problem with rsync, waiting for 5 hours, then retrying") + time.sleep(5*60*60) + count += 1 + if count > 5: + errAbort("Cannot run rsync cmd: %s" % cmd) # make sure that download interruptions don't mess up the files in the target dir logging.info("Moving files from %s to %s" % (tmpDir, uprotDir)) - file_names = os.listdir(tmpDir) - for file_name in file_names: - outPath = join(uprotDir, file_name) - if file_name=="docs": - shutil.rmtree(outPath) - - inPath = os.path.join(tmpDir, file_name) - if isdir(inPath): - shutil.move(inPath, outPath) + cmd = "rsync -a --remove-source-files %s/* %s" % (tmpDir, uprotDir) + run(cmd) + shutil.rmtree(tmpDir) - # only use the first four words of version string +def readRelStringUniprot(uprotDir): + # only use the first four words of version string, the four words are # 'UniProt Knowledgebase Release 2017_09 consists of:' relString = open(join(uprotDir, "reldate.txt")).read().splitlines()[0] relString = " ".join(relString.split()[:4]) + return relString + +def writeReleaseString(uprotDir, tabDir): + " read release info file from uprotDir and create a shorter version of it in tabDir " + relString = readRelStringUniprot(uprotDir) + + relFname = join(tabDir, "version.txt") relFh = open(relFname, "w") relFh.write(relString) relFh.close() logging.debug("Wrote release version string '%s' to %s" % (relString, relFname)) +def updateUniprot(args, onlyDbs, taxIdDbs, options): + " This is the main function that runs a single uniprot update for a list of DBs " + uprotDir = options.uniprotDir + tabDir = options.tabDir + mapDir = options.mapDir + bigBedDir = options.bigBedDir + faDir = options.faDir + doTrembl = not options.skipTrembl + + if not options.skipDownload and not options.skipParse and not options.onlyDbs: + # download NCBI -> refseq tables + downloadAndSplitNcbi(taxIdDbs) + downloadUniprot(uprotDir) + + downVersion = readRelStringUniprot(uprotDir) + tabVersion = open(join(tabDir, "version.txt")).read() + + doParse = True + if downVersion==tabVersion: + logging.info("Not converting to tab again, found same version is in tab directory") + doParse = False + + if options.skipParse: + logging.info("Not converting to tab, was switched off by option") + doParse = False + + if doParse: + logging.info("downloaded version is %s, parsed version is %s" % (downVersion, tabVersion)) logging.info("Converting uniprot from %s to %s, using maps in %s" % (uprotDir, tabDir, mapDir)) - if not options.skipParse and not options.onlyDbs: # parsing the UniProt XML files logging.info("Converting uniprot XML from %s to tab-sep in %s, this can take 2-3 days!! Specify -p to skip this." % (uprotDir, tabDir)) dbToTaxIds = {} if onlyDbs: for taxId, dbs in taxIdDbs.items(): for db in dbs: dbToTaxIds[db] = taxId taxIds = [dbToTaxIds[db] for db in onlyDbs] else: taxIds = [x for (x,y) in taxIdDbs.items()] # just the taxIds themselves taxIdStr = ",".join([str(x) for x in taxIds]) myDir = dirname(__file__) # directory of doUniprot # takes an hour or so cmd="%s/uniprotToTab %s %s %s" % (myDir, uprotDir, taxIdStr, tabDir) run(cmd) # takes 2-3 days on hgwdev - big data and XML don't mix... cmd="%s/uniprotToTab %s %s %s --trembl" % (myDir, uprotDir, taxIdStr, tabDir) run(cmd) + writeReleaseString(uprotDir, tabDir) + # if the uniprot update changed the sequences, update the corresponding pslMap files of that genome logging.info("checking/creating pslMap files") run("mkdir -p %s" % mapDir) # parasol cluster name assert(isfile(clusterFname)) # not running at UCSC? cluster = open(clusterFname).read().strip() # get the uniProt version for the trackVersion table that we will update later relFname = join(tabDir, "version.txt") versionString = open(relFname).read() for taxId, dbs in taxIdDbs.items(): if onlyDbs is not None and len(set(dbs).intersection(onlyDbs))==0: continue logging.info("Working on taxon ID %d" % taxId) faFnames = [ ("swissprot", join(tabDir,"swissprot.%d.fa.gz" % taxId)), ] if doTrembl: faFnames.append( ("trembl", join(tabDir,"trembl.%d.fa.gz" % taxId)) ) fullFaFname = join(faDir, str(taxId)+".fa") accToDb = concatFiles(faFnames, fullFaFname) if os.path.getsize(fullFaFname)==0: logging.warn("File %s is empty. Taxon ID %s does not have any UniProt annotations." \ " Skipping this organism." % (fullFaFname, taxId)) continue tabFnames = ["tab/swissprot.%d.tab" % taxId] if doTrembl: tabFnames.append( "tab/trembl.%d.tab" % taxId ) # find the best gene table for each database, create a mapping # protein -> genome and lift the uniprot annotations to bigBed files for db in dbs: if onlyDbs is not None and db not in onlyDbs: continue logging.debug("Annotating assembly %s" % db) chromSizesFname = "/hive/data/genomes/%s/chrom.sizes" % db accToMeta = parseRecordMeta(tabDir, taxId, doTrembl) dbMapDir = makeSubDir(mapDir, db) mapDescFname = join(dbMapDir, "liftInfo.json") - mapFname, geneTable, mapMd5, accToMapSource, isNewMap = \ + mapFname, geneTable, mapMd5, accToMapSource, accToTrans, isNewMap = \ makeProteinGenomePsl(taxId, fullFaFname, tabFnames, db, cluster, options.force, dbMapDir, mapDescFname) - if isNewMap: - convMapToBigPsl(fullFaFname, mapFname, bigBedDir, db, accToDb, accToMeta, accToMapSource, chromSizesFname, doTrembl) + dbBigBedDir = makeSubDir(bigBedDir, db) + + convMapToBigPsl(fullFaFname, mapFname, dbBigBedDir, accToDb, accToMeta, accToMapSource, accToTrans, chromSizesFname, doTrembl) shutil.copy(mapDescFname, mapDir) if options.onlyMap: continue - dbBigBedDir = makeSubDir(bigBedDir, db) - annotFnames = ["tab/swissprot.%d.annots.tab" % taxId] if doTrembl: annotFnames.append( "tab/trembl.%d.annots.tab" % taxId ) uniprotLift(fullFaFname, annotFnames, chromSizesFname, mapFname, dbBigBedDir, accToDb, accToMeta, options) shutil.copyfile(mapDescFname, join(dbBigBedDir, "liftInfo.json")) def makeSymlink(target, linkName): - if isfile(linkName): - os.remove(linkName) - if target is None or not isfile(target): - logging.error("Cannot symlink: %s does not exist" % str(target)) + assert(".new" not in linkName) # make sure that this bug never happens again + + if target is None: + logging.error("internal error, but not stopping: Symlink to a None target?") return targetPath = abspath(target) + + if not isfile(targetPath): + logging.error("Cannot symlink: %s does not exist" % str(target)) + return + + if isfile(linkName): + currTarget = os.readlink(linkName) + logging.debug("Symlink %s already exists, points to %s. But should point to %s" % (linkName, currTarget, targetPath)) + if targetPath != currTarget: + os.remove(linkName) + linkPath = abspath(linkName) cmd = "ln -sf %(targetPath)s %(linkPath)s " % locals() run(cmd) def findForMask(fileMask): fnames = glob.glob(fileMask) if len(fnames)==0: logging.error("NOT FOUND: %s" % fileMask) return None assert(len(fnames)==1) fname = fnames[0] return fname -def makeLinks(bigBedDir, faDir, onlyDbs, taxIdDbs): +def makeLinks(bigBedDir, onlyDbs, taxIdDbs): " check the /gbdb symlinks " for taxId, dbs in taxIdDbs.items(): - fullFaFname = join(faDir, str(taxId)+".fa") - md5 = None for db in dbs: if onlyDbs is not None and db not in onlyDbs: continue - if md5 is None: - md5 = fastaMd5(fullFaFname) # do only once per organism, seqs don't change dbBigBedDir = join(bigBedDir, db) # find the bigBed files bbTargetDir = makeSubDir(join("/gbdb", db), "uniprot") bbFnames = glob.glob(join(dbBigBedDir, "*.bb")) logging.debug("Found %d bigBed files in %s" % (len(bbFnames), dbBigBedDir)) # and create links to them for bbFname in bbFnames: - if "_" not in bbFname: # skip the bigPsl files with the md5 in them + # the following 'if' should not be necessary, but it has happened to me that during testing I had + # the liftOver files or .new.bb files in bigBed/, so make sure that they never get linked, because our + # qa symlink checker will immediately complain + if not "_" in basename(bbFname) and ".new" not in basename(bbFname): bbLink = join(bbTargetDir, basename(bbFname)) makeSymlink(bbFname, bbLink) + # and add the link to the bigPsls + def checkPsl(pslName, faFname): " checking the qNames in a psl input (!) file " if pslName is None: logging.debug("Not found: %s" % pslName) return seqIds = list(parseFasta(faFname).keys()) accs = set([x.split("-")[0] for x in seqIds]) qNames = Counter() pslCount = 0 for line in open(pslName): row = line.rstrip("\n").split("\t") qName = row[3] qNames[qName]+=1 pslCount += 1 accCount = len(accs) if accCount==0: logging.error("No single sequence found in %s" % faFname) return unmappedIds = seqIds - set(qNames) unmapCount = len(unmappedIds) unmappedAccs = set([x.split("-")[0] for x in seqIds]) - set([x.split("-")[0] for x in qNames]) unmappedAccCount = len(unmappedAccs) multiMapCount = 0 multiMapIds = {} for qName, qCount in qNames.items(): if qCount > 1: multiMapCount += 1 multiMapIds[qName] = qCount worstMultis = [] for qName, qCount in qNames.most_common()[:10]: if qCount > 1: worstMultis.append("%s (%d times)" % (qName, qCount)) qNameCount = len(qNames) seqCount = len(seqIds) unmappedAccPerc = 100.0 * float(unmappedAccCount) / accCount unmappedPerc = 100.0 * float(unmapCount) / seqCount multiPerc = 100.0 * float(len(multiMapIds)) / seqCount multiMapCount = len(multiMapIds) logging.info("%(faFname)s %(pslName)s: %(pslCount)d psls, %(accCount)s accessions, %(seqCount)d seqs, %(qNameCount)d mapped seqs" % locals()) logging.info("Unmapped accessions: %d (%0.02f %%) Unmapped seqs: %d (%.02f %%) Multi-mapped seqs: %d (%0.02f %%)" % (unmappedAccCount, unmappedAccPerc, unmapCount, unmappedPerc, multiMapCount, multiPerc)) logging.info("10 examples of unmapped sequences: %s" % " ".join(list(unmappedIds)[:10])) logging.info("10 examples of unmapped accessions: %s" % " ".join(list(unmappedAccs)[:10])) logging.info("10 worst multi-mappers: %s" % (", ".join(worstMultis))) def bedInfo(fname): " return number of features and coverage in bigBed file " cmd = "bigBedInfo %s" % fname proc = subprocess.Popen(cmd, encoding="latin1", stdout=PIPE, shell=True) for line in proc.stdout: # itemCount: 2,662 # basesCovered: 341,994 if line.startswith("itemCount"): itemCount = int(line.split()[1].replace(",","")) if line.startswith("basesCovered"): basesCovered = int(line.split()[1].replace(",","")) return (itemCount, basesCovered) -def flipNewVersionCheckMaxDiff(bigBedDir, onlyDbs, taxIdDbs, maxDiff=None): +def flipNewVersionCheckMaxDiff(bigBedDir, onlyDbs, taxIdDbs, doForce, maxDiff=None): """ rename all .new.bb files to .bb files, but only if they do not diff in more than factor maxDiff If any database fails the check, no files will be moved. """ for taxId, dbs in taxIdDbs.items(): for db in dbs: if onlyDbs is not None and db not in onlyDbs: continue logging.info("Flipping bigBed files for %s" % db) for newFname in glob.glob(join(bigBedDir, db, "*.new.bb")): if maxDiff is None: logging.info("Not doing maxDiff check, --force or --flipOnly specified") continue oldFname = newFname.replace(".new.bb", ".bb") if not isfile(oldFname): logging.warning("%s does not exist, cannot do max-diff check" % oldFname) else: newCount, newCov = bedInfo(newFname) oldCount, oldCov = bedInfo(oldFname) - if db in checkDbs: + if db in checkDbs and not doForce: if oldCount > 10000 and newCount / oldCount > maxDiff: logging.error("%s: old feature count %d, new feature count %d. Too big difference." % (oldFname, oldCount, newCount)) logging.error("Stopping now. Re-Run with --flipOnly to move files over.") sys.exit(1) if oldCov > 10000 and newCov / oldCov > maxDiff: logging.error("%s: old coverage %d, new coverage %d. Too big difference." % (oldFname, oldCov, newCov)) logging.error("Stopping now. Re-Run with --flipOnly to move files over.") sys.exit(1) # only when everything is OK, do the flip for taxId, dbs in taxIdDbs.items(): for db in dbs: if onlyDbs is not None and db not in onlyDbs: continue for fname in glob.glob(join(bigBedDir, db, "*.new.bb")): if isfile(fname): oldFname = fname.replace(".new.bb", ".bb") logging.debug("Renaming %s -> %s" % (fname, oldFname)) shutil.move(fname, oldFname) def mapQa(tabDir, faDir, mapDir, onlyDbs, taxIdDbs): " check the pslMap files " for taxId, dbs in taxIdDbs.items(): fullFaFname = join(faDir, str(taxId)+".fa") md5 = None for db in dbs: if onlyDbs is not None and db not in onlyDbs: continue if md5 is None: md5 = fastaMd5(fullFaFname) # do only once per organism, seqs don't change # find the psl file pslMask = join(mapDir, "%(taxId)s_%(db)s_*_%(md5)s.swissprot.pslInput" % locals()) pslName = findForMask(pslMask) faFname = join(tabDir, "swissprot.%s.fa.gz" % taxId) checkPsl(pslName, faFname) pslMask = join(mapDir, "%(taxId)s_%(db)s_*_%(md5)s.trembl.pslInput" % locals()) pslName = findForMask(pslMask) faFname = join(tabDir, "trembl.%s.fa.gz" % taxId) checkPsl(pslName, faFname) def createVersionFiles(tabDir, bigBedDir, onlyDbs, taxIdDbs): " update the release version files. This is the indicator for the auto-archiver to create a new archive " relFname = join(tabDir, "version.txt") - versionString = open(relFname, encoding="utf8").read() + versionString = open(relFname, encoding="utf8").read().strip() shortVersion = versionString.split()[-1] if (len(shortVersion)!=7): logging.warning("UniProt Version string is not seven characters long") logging.debug("Release is: %s" % shortVersion) for taxId, dbs in taxIdDbs.items(): for db in dbs: if onlyDbs is not None and db not in onlyDbs: continue dbDir = join(bigBedDir, db) if not isdir(dbDir): continue liftInfo = json.load(open(join(dbDir, "liftInfo.json"))) versionOfh = open(join(dbDir, "version.txt"), "w") - fullVersion = versionString + (", lifted through: %s %s on %s (taxId %s, %s)" % \ + fullVersion = versionString + (", mapped to genome through gene transcripts from %s %s on %s (taxId %s, %s)" % \ (liftInfo["geneTable"], liftInfo["version"], liftInfo["createdDate"], liftInfo["taxId"], liftInfo["fullMd5"])) versionOfh.write(fullVersion) versionOfh.close() linkName = join("/gbdb", db, "uniprot", "version.txt") makeSymlink(versionOfh.name, linkName) logging.debug("Wrote release string to %s, symlink from %s" % (versionOfh.name, linkName)) return versionString, shortVersion def makeTrackDb(archDir, shortVersion): " create a trackDb.txt file for the archive hub in archDir " templFname = join(dirname(__file__), "trackDb.template.txt") tdb = open(templFname).read() tdb = tdb.replace("$VER", shortVersion) + tdbLines = tdb.splitlines() + tdbLines = [l for l in tdbLines if not l.startswith("#")] + tdbFname = join(archDir, "trackDb.txt") with open(tdbFname, "w") as ofh: - ofh.write(tdb) + ofh.write("\n".join(tdbLines)) logging.info("Created %s" % tdbFname) def copyToArchive(bigBedDir, archRoot, shortVersion, onlyDbs): " make copies of the track files under the archiveDir and adapt the 'current' symlink " for db in os.listdir(bigBedDir): if onlyDbs and db not in onlyDbs: continue archDir = join(archRoot, db, "uniprot", shortVersion) if not isdir(archDir): os.makedirs(archDir) inDir = join(bigBedDir, db) count = 0 for inFname in glob.glob(join(inDir, "*")): shutil.copyfile(inFname, join(archDir, basename(inFname))) count += 1 logging.info("Archive: Copied %d files from %s to %s" % (count, inDir, archDir)) makeTrackDb(archDir, shortVersion) currLink = join(archRoot, db, "uniprot", "current") if islink(currLink): os.remove(currLink) os.symlink(archDir, currLink) logging.info("Created symlink %s -> %s" % (currLink, archDir)) def makeHubs(archRoot, onlyDbs): " concat all trackDbs into hub.txt files " archDirs = glob.glob(join(archRoot, "*", "uniprot")) for archDir in archDirs: db = archDir.split("/")[-2] if onlyDbs and db not in onlyDbs: continue hubFn = join(archDir, "hub.txt") tdbFns = glob.glob(join(archDir, "*", "trackDb.txt")) logging.debug("Concating %s" % tdbFns) with open(hubFn, "w") as ofh: ofh.write("hub uniprot%sArchHub\n" % db) ofh.write("shortLabel Archived UniProt releases (%s)\n" % db) ofh.write("longLabel Archive of previous UniProt releases for %s\n" % db) ofh.write("email genome@soe.ucsc.edu\n") ofh.write("useOneFile on\n") ofh.write("\n") ofh.write("genome %s\n" % db) ofh.write("\n") for tdbFn in tdbFns: if "current" in tdbFn: continue tdb = open(tdbFn).read() ofh.write(tdb) ofh.write("\n") logging.info("Wrote %s" % hubFn) def writeGeneTsv(geneToTrans, taxId, outDir): " write geneId -> list of transIds to ofh output file as tsv " fname = join(outDir, taxId+".tsv") logging.info("Writing RefSeq mapping of %d genes to %s" % (len(geneToTrans), fname)) ofh = open(fname, "w") for geneId, transList in geneToTrans.items(): ofh.write("%s\t%s\n" % (geneId, ",".join(list(transList)))) ofh.close() def splitGeneRefseq(fname, outDir, uniprotTaxIds): " split gene2refseq into one file per taxon " logging.info("Splitting %s into directory %s" % (fname, outDir)) lastTax = None geneToTrans = defaultdict(set) for row in iterTsvRows(gzip.open(fname, "rt")): taxId = row.tax_id if not int(taxId) in uniprotTaxIds: continue geneId = row.GeneID transId = row.RNA_nucleotide_accession_version if transId!="-": geneToTrans[geneId].add(transId) if lastTax!=taxId and lastTax is not None: writeGeneTsv(geneToTrans, lastTax, outDir) geneToTrans = defaultdict(set) lastTax = taxId writeGeneTsv(geneToTrans, lastTax, outDir) def downloadAndSplitNcbi(taxIdDbs): " download and split the NCBI genes file with a mapping NCBI gene -> RefSeq transcripts " logging.info("Downloading NCBI gene2refseq file gene2refseq.tsv") - cmd = "curl -Ss https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz | zcat > ncbi/gene2refseq.tsv" + # removed -Ss trying to get error messages to show up + cmd = "curl https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz | zcat > ncbi/gene2refseq.tsv" run(cmd) splitGeneRefseq("ncbi/gene2refseq.gz", NCBIDIR, taxIdDbs) def delFlag(): global flagFname if isfile(flagFname): os.remove(flagFname) def main(): global flagFname args, options = parseArgs() onlyDbs = None if options.onlyDbs: onlyDbs = set(options.onlyDbs.split(",")) taxIdDbs = getTaxIdDbs(onlyDbs) if options.mapQa: - #mapQa(options.tabDir, options.faDir, options.mapDir, onlyDbs, taxIdDbs) + mapQa(options.tabDir, options.faDir, options.mapDir, onlyDbs, taxIdDbs) sys.exit(0) if options.onlyFlip: - flipNewVersionCheckMaxDiff(options.bigBedDir, onlyDbs, taxIdDbs) + flipNewVersionCheckMaxDiff(options.bigBedDir, onlyDbs, taxIdDbs, options.force) # really need this here? relStr, shortVersion = createVersionFiles(options.tabDir, options.bigBedDir, onlyDbs, taxIdDbs) copyToArchive(options.bigBedDir, options.archiveDir, shortVersion, onlyDbs) makeHubs(options.archiveDir, onlyDbs) sys.exit(0) # create a lock file flagFname = join(options.uniprotDir, "doUniprot.lock") if isfile(flagFname) and not options.debug and not options.force: logging.error("%s exists. Is a doUniprot process already running ? " "If not, remove the flag file and restart this script." % flagFname) sys.exit(1) open(flagFname, "w") atexit.register(delFlag) if not options.onlyLinks: - # THIS IS THE MAIN FUNCTION + # THIS IS THE CORE PART updateUniprot(args, onlyDbs, taxIdDbs, options) - flipNewVersionCheckMaxDiff(options.bigBedDir, onlyDbs, taxIdDbs, maxDiff=maxDiffVersions) + flipNewVersionCheckMaxDiff(options.bigBedDir, onlyDbs, taxIdDbs, options.force, maxDiff=maxDiffVersions) if not options.skipLinks: - makeLinks(options.bigBedDir, options.faDir, onlyDbs, taxIdDbs) + makeLinks(options.bigBedDir, onlyDbs, taxIdDbs) relStr, shortVersion = createVersionFiles(options.tabDir, options.bigBedDir, onlyDbs, taxIdDbs) copyToArchive(options.bigBedDir, options.archiveDir, shortVersion, onlyDbs) makeHubs(options.archiveDir, onlyDbs) if isfile(flagFname): os.remove(flagFname) + logging.info("Uniprot pipeline completed.") + try: main() except Exception as e: logging.error(e, exc_info=True) + sys.exit(1)