c5a92d81293edb5d95fbeb37cbe381557e61fac0 max Thu Oct 17 09:04:56 2024 -0700 extending hubtools to convert track archives to hubs, only supports BED for now, refs #34472 diff --git src/utils/hubtools/hubtools src/utils/hubtools/hubtools index a9c06a7..37e55bc 100755 --- src/utils/hubtools/hubtools +++ src/utils/hubtools/hubtools @@ -1,694 +1,1086 @@ #!/usr/bin/env python3 -import logging, sys, optparse, os, json, subprocess, shutil, string +import logging, sys, optparse, os, json, subprocess, shutil, string, glob, tempfile, re +import shlex +from pathlib import Path from collections import defaultdict, OrderedDict from os.path import join, basename, dirname, isfile, relpath, abspath, splitext, isdir #import pyyaml # not loaded here, so it's not a hard requirement, is lazy loaded in parseMetaYaml() # ==== functions ===== +asHead = """table bed +"Browser extensible data (<=12 fields) " + ( +""" + +asLines = """ + string chrom; "Chromosome (or contig, scaffold, etc.)" + uint chromStart; "Start position in chromosome" + uint chromEnd; "End position in chromosome" + string name; "Name of item" + uint score; "Score from 0-1000" + char[1] strand; "+ or -" + uint thickStart; "Start of where display should be thick (start codon)" + uint thickEnd; "End of where display should be thick (stop codon)" + uint reserved; "Used as itemRgb as of 2004-11-22" + int blockCount; "Number of blocks" + int[blockCount] blockSizes; "Comma separated list of block sizes" + int[blockCount] chromStarts; "Start positions relative to chromStart" +""".split("\n") def parseArgs(): " setup logging, parse command line arguments and options. -h shows auto-generated help page " parser = optparse.OptionParser("""usage: %prog [options] <cmd> - create and edit UCSC track hubs hubtools make <assemblyCode>: create a track hub for all bigBed/bigWig files under a directory. Creates single-file hub.txt - bigBed/bigWig files in the current directory will be top level tracks - big* files in subdirectories become composites - for every filename, the part before the first dot becomes the track base name - if a directory has more than 80% of track base names with both a bigBed and bigWig file, views are activated for this composite - - track attributes can be changed using tracks.tsv or tracks.json files, in + - track attributes can be changed using tracks.ra, tracks.tsv, tracks.json or tracks.yaml files, in each top or subdirectory - - tracks.tsv must have a first column named 'track'. + - The first column of tracks.tsv must be 'track'. + - tracks.json and tracks.yaml must be object at the top level, the attributes are <trackName> or + the special attribute "hub". hubtools up: upload files to hubSpace - needs ~/.hubt.conf with username and password. Create one with 'hubt conf' - uploads all files from the -i directory or the current dir if not specified. hubtools jbrowse <url> <db> : convert Jbrowse trackList.json files to hub.txt. - <url> is the URL to the Jbrowse2 installation, e.g. http://furlonglab.embl.de/FurlongBrowser/ - <db> is assembly identifier hubtools tab <fname>: convert a hub.txt or trackDb.txt to tab-sep format, easier to bulk-edit with sed/cut/etc. - <fname> is the input filename. "hub" and "genome" stanzas are skipped. - output goes to stdout + hubtools conv -i myTsvDir + - convert .tsv files in inDir to .bigBed files in current directory + + hubtools ct -i xxx/archive -o outDir + - Create a hub from an extracted xxx.tar.gz file "archive" directory. You can download a .tar.gz from + in the Genome Browser under My Data > My Session. The archive contains all your custom tracks. + Examples: + hubtools conv -i myTsvs/ hubtools make hg38 hubtools jbrowse http://furlonglab.embl.de/FurlongBrowser/ dm3 hubtools tab hub.txt > tracks.tsv - tracks.json can look like this: - { "hub" : {"hub": "mouse_motor_atac", "shortLabel":"scATAC-seq Developing Cranial Motor Neurons"} } + tar xvfz SC_20230723_backup.tar.gz + hubtools ct -i archive -o hub + + For the "make" step: + + tracks.json can look like this, can have more keys, one per track, or the special key "hub": + { + "hub" : { "hub": "mouse_motor_atac", "shortLabel":"scATAC-seq Developing Cranial Motor Neurons" }, + "myTrack" : { "shortLabel" : "My nice track" } + } + + tracks.tsv should look like this, but can have any number of columns: + #track<tab>shortLabel + myTrack<tab>My nice track """) parser.add_option("-i", "--inDir", dest="inDir", action="store", help="Input directory where files are stored. Default is current directory") parser.add_option("-o", "--outDir", dest="outDir", action="store", help="Input directory where hub.txt file is created. Default is same as input directory.") #parser.add_option("", "--igv", dest="igv", action="store", help="import an igv.js trackList.json file hierarchy") parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show verbose debug messages") parser.add_option("-u", "--upload", dest="upload", action="store_true", help="upload all files from outDir to hubSpace") (options, args) = parser.parse_args() if len(args)==0: parser.print_help() exit(1) if options.debug: logging.basicConfig(level=logging.DEBUG) else: logging.basicConfig(level=logging.INFO) return args, options def errAbort(msg): " print and abort) " logging.error(msg) sys.exit(1) +def makedirs(d): + if not isdir(d): + os.makedirs(d) + def parseMetaRa(fname): """parse tracks.ra or tracks.txt and return as a dict of trackName -> dict of key->val """ logging.debug("Reading %s as .ra" % fname) trackName = None stanzaData = {} ret = {} for line in open(fname): line = line.strip() if line.startswith("#"): continue if line=="": if len(stanzaData)==0: # double newline continue if trackName is None: errAbort("File %s has a stanza without a track name" % fname) if trackName in ret: errAbort("File %s contains two stanzas with the same track name '%s' " % trackName) ret[trackName] = stanzaData stanzaData = {} trackName = None continue key, val = line.split(" ", maxsplit=1) if key == "track": trackName = val continue else: stanzaData[key] = val if len(stanzaData)!=0: ret[trackName] = stanzaData logging.debug("Got %s from .ra" % str(ret)) return ret def parseMetaTsv(fname): " parse a tracks.tsv file and return as a dict of trackName -> dict of key->val " headers = None meta = {} logging.debug("Parsing track meta data from %s in tsv format" % fname) for line in open(fname): row = line.rstrip("\r\n").split("\t") if headers is None: assert(line.startswith("track\t") or line.startswith("#track")) row[0] = row[0].lstrip("#") headers = row continue assert(len(row)==len(headers)) key = row[0] rowDict = {} for header, val in zip(headers[1:], row[1:]): rowDict[header] = val #row = {k:v for k,v in zip(headers, fs)} meta[key] = rowDict return meta def parseMetaJson(fname): " parse a json file and merge it into meta and return " logging.debug("Reading %s as json" % fname) newMeta = json.load(open(fname)) return newMeta def parseMetaYaml(fname): " parse yaml file " import yaml # if this doesn't work, run 'pip install pyyaml' with open(fname) as stream: try: return yaml.safe_load(stream) except yaml.YAMLError as exc: logging.error(exc) def parseMeta(inDir): " parse a tab-sep file with headers and return an ordered dict firstField -> dictionary " fname = join(inDir, "tracks.tsv") meta = OrderedDict() if isfile(fname): tsvMeta = parseMetaTsv(fname) meta = allMetaOverride(meta, tsvMeta) fname = join(inDir, "tracks.json") if isfile(fname): jsonMeta = parseMetaJson(fname) meta = allMetaOverride(meta, jsonMeta) fname = join(inDir, "tracks.ra") if isfile(fname): raMeta = parseMetaRa(fname) meta = allMetaOverride(meta, raMeta) fname = join(inDir, "tracks.yaml") if isfile(fname): yamlMeta = parseMetaYaml(fname) meta = allMetaOverride(meta, yamlMeta) logging.debug("Got meta from %s: %s" % (inDir, str(meta))) return meta def writeHubGenome(ofh, db, inMeta): " create a hub.txt and genomes.txt file, hub.txt is just a template " meta = inMeta.get("hub", {}) ofh.write("hub autoHub\n") ofh.write("shortLabel %s\n" % meta.get("shortLabel", "Auto-generated hub")) ofh.write("longLabel %s\n" % meta.get("longLabel", "Auto-generated hub")) #ofh.write("genomesFile genomes.txt\n") if "descriptionUrl" in meta: ofh.write("descriptionUrl %s\n" % meta["descriptionUrl"]) ofh.write("email %s\n" % meta.get("email", "yourEmail@example.com")) ofh.write("useOneFile on\n\n") ofh.write("genome %s\n\n" % db) return ofh def readSubdirs(inDir, subDirs): " given a list of dirs, find those that are composite dirs (not supporting supertracks for now) " compDicts, superDicts = {}, {} for subDir in subDirs: subPath = join(inDir, subDir) subSubDirs, subDict = readFnames(subPath) if len(subDict)==0: # no files in this dir continue if len(subSubDirs)==0: compDicts[subDir] = subDict #else: #superDicts[subDir] = subDict return compDicts, superDicts def reorderDirs(compDirs, meta): " order the directories in compDirs in the order that they appear in the meta data -> will mean that composites have the right order " if len(meta)==0: logging.debug("Not reordering these subdirectories: %s" % compDirs.keys()) return compDirs # first use the names in the meta data, and put in the right order newCompDirs = OrderedDict() for dirName in meta.keys(): if dirName in compDirs: newCompDirs[dirName] = compDirs[dirName] # then add everything else at the end for dirName in compDirs: if dirName not in newCompDirs: newCompDirs[dirName] = compDirs[dirName] logging.debug("Reordered input directories based on meta data. New order is: %s" % newCompDirs.keys()) return newCompDirs def readDirs(inDir, meta): " recurse down into directories and return containerType -> parentName -> fileBase -> type -> list of absPath " ret = {} subDirs, topFiles = readFnames(inDir) ret["top"] = { None : topFiles } # top-level track files have None as the parent compDirs, superDirs = readSubdirs(inDir, subDirs) compDirs = reorderDirs(compDirs, meta) # superDirs not used yet, no time ret["comps"] = compDirs ret["supers"] = superDirs return ret def readFnames(inDir): " return dict with basename -> fileType -> filePath " fnameDict = defaultdict(dict) #tdbDir = abspath(dirname(trackDbPath)) subDirs = [] for fname in os.listdir(inDir): filePath = join(inDir, fname) if isdir(filePath): subDirs.append(fname) continue baseName, ext = splitext(basename(fname)) ext = ext.lower() # actually, use the part before the first dot, not the one before the extension, as the track name # this means that a.scaled.bigBed and a.raw.bigWig get paired correctly fileBase = basename(fname).split(".")[0] if ext==".bw" or ext==".bigwig": fileType = "bigWig" elif ext==".bb" or ext==".bigbed": fileType = "bigBed" else: logging.debug("file %s is not bigBed nor bigWig, skipping" % fname) continue absFname = abspath(filePath) #relFname = relFname(absFname, tdbDir) fnameDict[fileBase].setdefault(fileType, []) #fnameDict[baseName][fileType].setdefault([]) fnameDict[fileBase][fileType].append(absFname) return subDirs, fnameDict def mostFilesArePaired(fnameDict): " check if 80% of the tracks have a pair bigBed+bigWig" pairCount = 0 for baseName, typeDict in fnameDict.items(): if "bigBed" in typeDict and "bigWig" in typeDict: pairCount += 1 pairShare = pairCount / len(fnameDict) return ( pairShare > 0.8 ) def writeLn(ofh, spaceCount, line): "write line to ofh, with spaceCount before it " ofh.write("".join([" "]*spaceCount)) ofh.write(line) ofh.write("\n") def writeStanza(ofh, indent, tdb): " write a stanza given a tdb key-val dict " track = tdb["track"] shortLabel = tdb.get("shortLabel", track.replace("_", " ")) visibility = tdb.get("visibility", "pack") longLabel = tdb.get("longLabel", shortLabel) + if not "type" in tdb: + errAbort("Track info has no type attribute: %s" % tdb) trackType = tdb["type"] writeLn(ofh, indent, "track %s" % track) writeLn(ofh, indent, "shortLabel %s" % shortLabel) if longLabel: writeLn(ofh, indent, "longLabel %s" % longLabel) if "parent" in tdb: writeLn(ofh, indent, "parent %s" % tdb["parent"]) writeLn(ofh, indent, "type %s" % trackType) writeLn(ofh, indent, "visibility %s" % visibility) if "bigDataUrl" in tdb: writeLn(ofh, indent, "bigDataUrl %s" % tdb["bigDataUrl"]) for key, val in tdb.items(): if key in ["track", "shortLabel", "longLabel", "type", "bigDataUrl", "visibility", "parent"]: continue writeLn(ofh, indent, "%s %s" % (key, val)) ofh.write("\n") def metaOverride(tdb, meta): " override track info for one single track, from meta into tdb " trackName = tdb["track"] if trackName not in meta and "__" in trackName: logging.debug("Using only basename of track %s" % trackName) trackName = trackName.split("__")[1] if trackName not in meta: logging.debug("No meta info for track %s" % tdb["track"]) return trackMeta = meta[trackName] for key, val in trackMeta.items(): if val!="": tdb[key] = trackMeta[key] def allMetaOverride(tdb, meta): " override track info for all tracks, from meta into tdb " if meta is None: return tdb for trackName in meta: trackMeta = meta[trackName] if trackName not in tdb: tdb[trackName] = {} trackTdb = tdb[trackName] for key, val in trackMeta.items(): trackTdb[key] = val return tdb def reorderTracks(fileDict, meta): " given an unsorted dictionary of files and ordered metadata, try to sort the files according to the metadata" if len(meta)==0: return fileDict # no meta data -> no ordering necessary trackOrder = [] # meta is an OrderedDict, so the keys are also ordered for trackName in meta.keys(): if "__" in trackName: # in composite mode, the tracknames contain the parent and the track type trackName = trackName.split("__")[1] trackOrder.append( trackName ) trackOrder = list(meta.keys()) newFiles = OrderedDict() doneTracks = set() # first add the tracks in the order of the meta data for trackBase in trackOrder: # the tsv file can have the track names either as basenames or as full tracknames if trackBase not in fileDict and "__" in trackBase: trackBase = trackBase.split("__")[1] if trackBase in fileDict: newFiles[trackBase] = fileDict[trackBase] doneTracks.add(trackBase) logging.debug("Track ordering from meta data used: %s" % newFiles.keys()) # then add all other tracks for trackBase, fileData in fileDict.items(): if trackBase not in doneTracks: newFiles[trackBase] = fileDict[trackBase] logging.debug("Not specified in meta, so adding at the end: %s" % trackBase) logging.debug("Final track order is: %s" % newFiles.keys()) assert(len(newFiles)==len(fileDict)) return newFiles def writeTdb(inDir, dirDict, dirType, tdbDir, ofh): " given a dict with basename -> type -> filenames, write track entries to ofh " # this code is getting increasingly complex because it supports composites/views and pairing of bigBed/bigWig files # either this needs better comments or maybe a separate code path for this rare use case global compCount fnameDict = dirDict[dirType] for parentName, typeDict in fnameDict.items(): if parentName is None: # top level tracks: use top tracks.tsv subDir = inDir else: # container tracks -> use tracks.tsv in the subdirectory subDir = join(inDir, parentName) parentMeta = parseMeta(subDir) indent = 0 parentHasViews = False groupMeta = {} if dirType=="comps": tdb = { "track" : parentName, "shortLabel": parentName, "visibility" : "dense", "compositeTrack" : "on", "autoScale" : "group", "type" : "bed 4" } metaOverride(tdb, parentMeta) groupMeta = parentMeta parentHasViews = mostFilesArePaired(typeDict) if parentHasViews: tdb["subGroup1"] = "view Views PK=Peaks SIG=Signals" logging.info("Container track %s has >80%% of paired files, activating views" % parentName) writeStanza(ofh, indent, tdb) indent = 4 if parentHasViews: # we have composites with paired files? -> write the track stanzas for the two views groupMeta = parseMeta(subDir) tdbViewPeaks = { "track" : parentName+"ViewPeaks", "shortLabel" : parentName+" Peaks", "parent" : parentName, "view" : "PK", "visibility" : "dense", "type" : "bigBed", "scoreFilter" : "off", "viewUi" : "on" } metaOverride(tdbViewPeaks, parentMeta) writeStanza(ofh, indent, tdbViewPeaks) tdbViewSig = { "track" : parentName+"ViewSignal", "shortLabel" : parentName+" Signal", "parent" : parentName, "view" : "SIG", "visibility" : "dense", "type" : "bigWig", "viewUi" : "on" } metaOverride(tdbViewSig, parentMeta) writeStanza(ofh, indent, tdbViewSig) else: # no composites groupMeta = parseMeta(subDir) typeDict = reorderTracks(typeDict, groupMeta) for trackBase, typeFnames in typeDict.items(): for fileType, absFnames in typeFnames.items(): assert(len(absFnames)==1) # for now, not sure what to do when we get multiple basenames of the same file type absFname = absFnames[0] fileBase = basename(absFname) relFname = relpath(absFname, tdbDir) labelSuff = "" if parentHasViews: if fileType=="bigWig": labelSuff = " Signal" elif fileType=="bigBed": labelSuff = " Peaks" else: assert(False) # views and non-bigWig/Bed are not supported yet? if parentName is not None: parentPrefix = parentName+"__" else: parentPrefix = "" trackName = parentPrefix+trackBase+"__"+fileType tdb = { "track" : trackName, "shortLabel" : trackBase+labelSuff, "longLabel" : trackBase+labelSuff, "visibility" : "dense", "type" : fileType, "bigDataUrl" : relFname, } if parentName: tdb["parent"] = parentName if parentHasViews: onOff = "on" if trackName in groupMeta and "visibility" in groupMeta[trackName]: vis = groupMeta[trackName]["visibility"] if vis=="hide": onOff = "off" del tdb["visibility"] if fileType=="bigBed": tdb["parent"] = parentName+"ViewPeaks"+" "+onOff tdb["subGroups"] = "view=PK" else: tdb["parent"] = parentName+"ViewSignal"+" "+onOff tdb["subGroups"] = "view=SIG" metaOverride(tdb, groupMeta) if trackName in groupMeta and "visibility" in groupMeta[trackName]: del tdb["visibility"] writeStanza(ofh, indent, tdb) def importJbrowse(baseUrl, db, outDir): " import an IGV trackList.json hierarchy " import requests outFn = join(outDir, "hub.txt") ofh = open(outFn, "w") writeHubGenome(ofh, db, {}) trackListUrl = baseUrl+"/data/trackList.json" logging.info("Loading %s" % trackListUrl) trackList = requests.get(trackListUrl).json() tdbs = [] for tl in trackList["tracks"]: - #print(tl) if "type" in tl and tl["type"]=="SequenceTrack": logging.info("Genome is: "+tl["label"]) continue if tl["storeClass"]=="JBrowse/Store/SeqFeature/NCList": logging.info("NCList found: ",tl) continue tdb = {} tdb["track"] = tl["label"] tdb["shortLabel"] = tl["key"] if "data_file" in tl: tdb["bigDataUrl"] = baseUrl+"/data/"+tl["data_file"] else: tdb["bigDataUrl"] = baseUrl+"/data/"+tl["urlTemplate"] if tl["storeClass"] == "JBrowse/Store/SeqFeature/BigWig": tdb["type"] = "bigWig" dispMode = tl.get("display_mode") if dispMode: if dispMode=="normal": tdb["visibility"] = "pack" elif dispMode=="compact": tdb["visibility"] = "dense" else: tdb["visibility"] = "pack" else: tdb["visibility"] = "pack" writeStanza(ofh, 0, tdb) def installModule(package): " install a package " logging.info("Could not find Python module '%s', trying to install with pip" % package) subprocess.check_call([sys.executable, "-m", "pip", "install", package]) def uploadFiles(tdbDir): "upload files to hubspace" try: from tusclient import client except ModuleNotFoundError: installModule("tuspy") serverUrl="https://hgwdev-hubspace.gi.ucsc.edu/files" my_client = client.TusClient(serverUrl, headers={}) logging.info(f"Target server is {serverUrl}") for fname in os.listdir(tdbDir): fpath = join(tdbDir, fname) if isdir(fpath): continue logging.info(f"Uploading {fpath}") meta = {"db":"hg19"} uploader = my_client.uploader(fpath, metadata=meta) uploader.upload() def iterRaStanzas(fname): " parse an ra-style (trackDb) file and yield dictionaries " data = dict() logging.debug("Parsing %s in trackDb format" % fname) with open(fname, "rt") as ifh: for l in ifh: l = l.lstrip(" ").rstrip("\r\n") if len(l)==0: yield data data = dict() else: if " " not in l: continue key, val = l.split(" ", maxsplit=1) data[key] = val if len(data)!=0: yield data def raToTab(fname): " convert .ra file to .tsv " stanzas = [] allFields = set() for stanza in iterRaStanzas(fname): if "hub" in stanza or "genome" in stanza: continue allFields.update(stanza.keys()) stanzas.append(stanza) if "track" in allFields: allFields.remove("track") if "shortLabel" in allFields: allFields.remove("shortLabel") hasLongLabel = False if "longLabel" in allFields: allFields.remove("longLabel") hasLongLabel = True sortedFields = sorted(list(allFields)) # make sure that track shortLabel and longLabel come first and always there, handy for manual edits if hasLongLabel: sortedFields.insert(0, "longLabel") sortedFields.insert(0, "shortLabel") sortedFields.insert(0, "track") ofh = sys.stdout ofh.write("#") ofh.write("\t".join(sortedFields)) ofh.write("\n") for s in stanzas: row = [] for fieldName in sortedFields: row.append(s.get(fieldName, "")) ofh.write("\t".join(row)) ofh.write("\n") -def hubt(args, options): - """ get writeLn(ofh, indent, d .bb files under dirName and create a trackDb.txt for them""" +def guessFieldDesc(fieldNames): + "given a list of field names, try to guess to which fields in bed12 they correspond " + logging.info("No field description specified, guessing fields from TSV headers: %s" % fieldNames) + fieldDesc = {} + skipFields = set() + + for fieldIdx, fieldName in enumerate(fieldNames): + caseField = fieldName.lower() + if caseField in ["chrom", "chromosome"]: + name = "chrom" + elif caseField.endswith(" id") or caseField.endswith("accession"): + name = "name" + elif caseField in ["start", "chromstart", "position"]: + name = "start" + elif caseField in ["Reference"]: + name = "refAllele" + elif caseField in ["strand"]: + name = "strand" + elif caseField in ["score"]: + name = "score" + else: + continue + fieldDesc[name] = fieldIdx + skipFields.add(fieldIdx) + logging.info("TSV <-> BED correspondance: %s" % fieldDesc) + return fieldDesc, skipFields + +def parseFieldDesc(fieldDescStr, fieldNames): + " given a string chrom=1,start=2,end=3,... return dict {chrom:1,...} " + if not fieldDescStr: + return guessFieldDesc(fieldNames) + + fieldDesc, skipFields = guessFieldDesc(fieldNames) + + if fieldDescStr: + for part in fieldDescStr.split(","): + fieldName, fieldIdx = part.split("=") + fieldIdx = int(fieldIdx) + fieldDesc[fieldName] = fieldIdx + skipFields.add(fieldIdx) + + return fieldDesc, skipFields + +def makeBedRow(row, fieldDesc, skipFields, isOneBased): + " given a row of a tsv file and a fieldDesc with BedFieldName -> field-index, return a bed12+ row with extra fields " + bedRow = [] + + # first construct the bed 12 fields + for fieldName in ["chrom", "start", "end", "name", "score", "strand", + "thickStart", "thickEnd", "itemRgb", "blockCount", "blockSizes", "chromStarts"]: + + fieldIdx = fieldDesc.get(fieldName) + if fieldIdx is not None: + if fieldName=="start": + chromStart = int(row[fieldDesc["start"]]) + if isOneBased: + chromStart = chromStart-1 + val = str(chromStart) + elif fieldName=="end": + chromEnd = int(val) + else: + val = row[fieldIdx] + else: + if fieldName=="end": + chromEnd = chromStart+1 + val = str(chromEnd) + elif fieldName=="score": + val = "0" + elif fieldName=="strand": + val = "." + elif fieldName=="thickStart": + val = str(chromStart) + elif fieldName=="thickEnd": + val = str(chromEnd) + elif fieldName=="itemRgb": + val = "0,0,0" + elif fieldName=="blockCount": + val = "1" + elif fieldName=="blockSizes": + val = str(chromEnd-chromStart) + elif fieldName=="chromStarts": + #val = str(chromStart) + val = "0" + else: + logging.error("Cannot find a field for %s" % fieldName) + sys.exit(1) + + bedRow.append(val) + + # now handle all other fields + for fieldIdx, val in enumerate(row): + if not fieldIdx in skipFields: + bedRow.append( row[fieldIdx] ) + + return bedRow + +def fetchChromSizes(db, outputFileName): + " find on local disk or download a <db>.sizes text file " + # Construct the URL based on the database name + url = f"https://hgdownload.cse.ucsc.edu/goldenPath/{db}/database/chromInfo.txt.gz" + # Send a request to download the file + response = requests.get(url, stream=True) + # Check if the request was successful + if response.status_code == 200: + # Open the output gzip file for writing + with gzip.open(outputFileName, 'wt') as outFile: + # Open the response content as a gzip file in text mode + with gzip.GzipFile(fileobj=response.raw, mode='r') as inFile: + # Read the content using csv reader to handle tab-separated values + reader = csv.reader(inFile, delimiter='\t') + writer = csv.writer(outFile, delimiter='\t', lineterminator='\n') + # Iterate through each row, and retain only the first two fields + for row in reader: + writer.writerow(row[:2]) # Write only the first two fields + else: + raise Exception(f"Failed to download file from {url}, status code: {response.status_code}") + logging.info("Downloaded %s to %s" % (db, outputFileName)) + +def getChromSizesFname(db): + " return fname of chrom sizes, download into ~/.local/ucscData/ if not found " + fname = "/hive/data/genomes/%s/chrom.sizes" % db + if isfile(fname): + return fname + + dataDir = "~/.local/hubtools" + fname = join(dataDir, "%s.sizes" % db) + fname = os.path.expanduser(fname) + if not isfile(fname): + makedirs(dataDir) + fetchChromSizes(db, fname) + return fname + +def convTsv(db, tsvFname, outBedFname, outAsFname, outBbFname): + " convert tsv files in inDir to outDir, assume that they all have one column for chrom, start and end. Try to guess these or fail. " + #tsvFname, outBedFname, outAsFname = args + + # join and output merged bed + bigCols = set() # col names of columns with > 255 chars + + #bedFh = open(bedFname, "w") + unsortedBedFh = tempfile.NamedTemporaryFile(suffix=".bed", dir=dirname(outBedFname), mode="wt") + fieldNames = None + #isOneBased = options.oneBased + isOneBased = True + bedFieldsDesc = None # in the future, the user may want to input a string like name=0,start=1, but switch this off for now + + for line in open(tsvFname): + row = line.rstrip("\r\n").split("\t") + if fieldNames is None: + fieldNames = row + fieldDesc, notExtraFields = parseFieldDesc(bedFieldsDesc, fieldNames) + continue + + # note fields with data > 255 chars. + for colName, colData in zip(fieldNames, row): + if len(colData)>255: + bigCols.add(colName) + + bedRow = makeBedRow(row, fieldDesc, notExtraFields, isOneBased) + + chrom = bedRow[0] + if chrom.isdigit() or chrom in ["X", "Y"]: + bedRow[0] = "chr"+bedRow[0] + + unsortedBedFh.write( ("\t".join(bedRow))) + unsortedBedFh.write("\n") + unsortedBedFh.flush() + + cmd = "sort -k1,1 -k2,2n %s > %s" % (unsortedBedFh.name, outBedFname) + assert(os.system(cmd)==0) + unsortedBedFh.close() # removes the temp file + + # generate autosql + # BED fields + #bedColCount = int(options.type.replace("bed", "").replace("+" , "")) + bedColCount = 12 + asFh = open(outAsFname, "w") + asFh.write(asHead) + asFh.write("\n".join(asLines[:bedColCount+1])) + asFh.write("\n") + + # extra fields + #fieldNames = fieldNames[bedColCount:] + for fieldIdx, field in enumerate(fieldNames): + if fieldIdx in notExtraFields: + continue + name = field.replace(" ","") + name = field.replace("%","perc_") + name = re.sub("[^a-zA-Z0-9]", "", name) + name = name[0].lower()+name[1:] + fType = "string" + if field in bigCols: + fType = "lstring" + asFh.write(' %s %s; "%s" \n' % (fType, name, field)) + asFh.write(")\n") + asFh.close() + + chromSizesFname = getChromSizesFname(db) + + cmd = ["bedToBigBed", outBedFname, chromSizesFname, outBbFname, "-tab", "-type=bed%d+" % bedColCount, "-as=%s" % outAsFname] + subprocess.check_call(cmd) + +def convTsvDir(inDir, db, outDir): + " find tsv files under inDir and convert them all to .bb " + ext = "tsv" + pat = join(inDir, '**/*.'+ext) + logging.debug("Finding files under %s (%s), writing output to %s" % (inDir, pat, outDir)) + + for fname in glob.glob(pat, recursive=True): + logging.debug("Found %s" % fname) + absFname = abspath(fname) + relFname = relpath(absFname, inDir) + outPath = Path(join(outDir, relFname)) + + if not outPath.parents[0].is_dir(): + logging.debug("mkdir -p %s" % outPath.parents[0]) + makedirs(outPath.parents[0]) + + bedFname = outPath.with_suffix(".bed") + asFname = outPath.with_suffix(".as") + bbFname = outPath.with_suffix(".bb") + + convTsv(db, fname, bedFname, asFname, bbFname) + +def parseTrackLine(s): + " Use shlex to split the string respecting quotes, written by chatGPT " + lexer = shlex.shlex(s, posix=True) + lexer.whitespace_split = True + lexer.wordchars += '=' # Allow '=' as part of words + + tokens = list(lexer) + + # Convert the tokens into a dictionary + it = iter(tokens) + result = {} + for token in it: + if '=' in token: + key, value = token.split('=', 1) + result[key] = value.strip('"') # Remove surrounding quotes if present + else: + result[token] = next(it).strip('"') # Handle cases like name="...". + + return result + +def readTrackLines(fnames): + " read the first line and convert to a dict of all fnames. " + logging.debug("Reading track lines from %s" % fnames) + ret = {} + for fn in fnames: + line1 = open(fn).readline().rstrip("\n") + notTrack = line1.replace("track ", "", 1) + tdb = parseTrackLine(notTrack) + ret[fn] = tdb + return ret + +def stripFirstLine(inputFilename, outputFilename): + " written by chatGpt: copies all lines to output, except the first line " + with open(inputFilename, 'r') as infile, open(outputFilename, 'w') as outfile: + # Skip the first line + next(infile) + # Write the rest of the lines to the output file + for line in infile: + outfile.write(line) + +def bedToBigBed(inFname, db, outFname): + " convert bed to bigbed file, handles chrom.sizes download " + chromSizesFname = getChromSizesFname(db) + cmd = ["bedToBigBed", inFname, chromSizesFname, outFname] + logging.debug("Running %s" % cmd) + logging.info(f'Converting {inFname} to {outFname}. (chromSizes: {chromSizesFname}') + subprocess.check_call(cmd) + +def convCtDb(db, inDir, outDir): + " convert one db part of a track archive to an output directory " + findGlob = join(inDir, "*.ct") + inFnames = glob.glob(findGlob) + if len(inFnames)==0: + logging.info("No *.ct files found in %s" % findGlob) + return + + tdbData = readTrackLines(inFnames) + + makedirs(outDir) + hubTxtFname = join(outDir, "hub.txt") + ofh = open(hubTxtFname, "wt") + + meta = parseMeta(inDir) + writeHubGenome(ofh, db, meta) + + tdbIdx = 0 + for fname, tdb in tdbData.items(): + tdbIdx += 1 + # custom track names can include spaces, spec characters, etc. Strip all those + # append a number to make sure that the result is unique + track = tdb["name"] + track = re.sub('[^A-Za-z0-9]+', '', track)+"_"+str(tdbIdx) + tdb["track"] = track + + tdb["shortLabel"] = tdb["name"] + del tdb["name"] + tdb["longLabel"] = tdb["description"] + del tdb["description"] + + if "bigDataUrl" not in tdb: + bedFname = join(outDir, tdb["track"]+".bed") + bbFname = join(outDir, tdb["track"]+".bb") + stripFirstLine(fname, bedFname) + bedToBigBed(bedFname, db, bbFname) + os.remove(bedFname) + tdb["bigDataUrl"] = tdb["track"]+".bb" + tdb["type"] = "bigBed" + + writeStanza(ofh, 0, tdb) + + logging.info("Wrote %s" % hubTxtFname) + ofh.close() + +def convCtDir(inDir, outDir): + " convert a directory created from the .tar.gz file downloaded via our track archive feature " + dbContent = os.listdir(inDir) + dbDirs = [] + for db in dbContent: + subDir = join(inDir, db) + if isdir(subDir): + dbDirs.append((db, subDir)) + + if len(dbDirs)==0: + errAbort("No directories found under %s. Extract the tarfile and point this program at the 'archive' directory." % inDir) + + for db, inSubDir in dbDirs: + logging.debug("Processing %s, db=%s" % (inSubDir, db)) + outSubDir = join(outDir, db) + convCtDb(db, inSubDir, outSubDir) + +def hubtools(args, options): + """ find files under dirName and create a trackDb.txt for them""" cmd = args[0] inDir = "." if options.inDir: inDir = options.inDir + outDir = "." + if options.outDir: + outDir = options.outDir + if cmd=="up": uploadFiles(inDir) return tdbDir = inDir if options.outDir: tdbDir = options.outDir if cmd=="jbrowse": importJbrowse(args[1], args[2], tdbDir) elif cmd == "tab": raToTab(args[1]) elif cmd == "make": db = args[1] meta = parseMeta(inDir) dirFiles = readDirs(inDir, meta) hubFname = join(tdbDir, "hub.txt") logging.info("Writing %s" % hubFname) ofh = open(hubFname, "w") meta = parseMeta(inDir) writeHubGenome(ofh, db, meta) writeTdb(inDir, dirFiles, "top", tdbDir, ofh) writeTdb(inDir, dirFiles, "comps", tdbDir, ofh) ofh.close() + + elif cmd=="conv": + db = args[1] + + convTsvDir(inDir, db, outDir) + + elif cmd=="ct": + convCtDir(inDir, outDir) + else: logging.error("Unknown command: '%s'" % args[1]) # ----------- main -------------- def main(): args, options = parseArgs() - hubt(args, options) + hubtools(args, options) - #if options.test: - #logging.debug("test is set") - #f = open(options.file, "r") main()