3aee104cf4c1e245dd020f743fbc58c17fd75976 mmaddren Mon Apr 9 12:12:44 2012 -0700 added encode.py to store global constants and other encode stuff, and made all other libraries interface correctly with it diff --git python/programs/mkGeoPkg/mkGeoPkg python/programs/mkGeoPkg/mkGeoPkg index 22cef27..fdac241 100755 --- python/programs/mkGeoPkg/mkGeoPkg +++ python/programs/mkGeoPkg/mkGeoPkg @@ -1,707 +1,677 @@ #!/hive/groups/encode/dcc/bin/python -import sys, os, shutil, stat, argparse, datetime -from ucscgenomics import track, ra, soft, cv -""" +import sys, os, shutil, stat, argparse, datetime, hashlib +from ucscgenomics import track, ra, soft, cv, mdb, geo, encode + +''' mkGeoPkg - create a soft file and upload script for a given track, so that it may be sumbitted to GEO. To invoke the script, you must pass the composite and track name: mkGeoPkg hg19 wgEncodeSomeTrack This is typically not enough however; most tracks are not completely covered by their metadata, and it is necessary to supply additional information. The most commonly needed information is: !Series_summary - this is taken from the track's html page description. In most cases it can be copied, one paragraph per line. !Series_overall_design - this is taken from the Methods section on the track's page. As with summary, 1 paragraph per line. !Series_contributor - this is taken from the contributors list on the track's page. It has a special format: "Last,First" where each person is listed on a separate line. !Sample_instrument_model - this is a bit more difficult, as it technically supposed to be a per-sample field. Occasionally this appears in the metaDb for newer tracks, if so, it's automatically added in. Otherwise it must be either specified on a whole-series basis, or added to the metadata. In many cases, we don't actually know all of them. This is okay. GEO will allow us to submit whatever information we do have, and they can take care of the rest. The instrumentModels dictionary below gives a list of the allowable entered values (the keys). The values map to the "human readable" version used by GEO. You can supply all of the above information in an additional file and specify it using the r (replace) option: mkGeoPkg -r somefile hg19 wgEncodeSomeTrack The replace file must be organized with each of the above key value pairs as in a soft file: !Series_summary = some summary stuff ... !Series_summary = another paragraph of summary ... !Series_overall_design = ... !Series_contributor = Researcher,Some !Series_contributor = Researcher,Another !Sample_instrument_model = Illumina_GA2 There is a template for this, named replaceTemplate in the directory. You may need to only submit a part of the track, in this case you can specify experiment ID numbers to include: One problem you may run into while running the script is that the DataType is not valid. This means that the huge dictionary called datatypes below isn't filled in for that entry. If you can get ahold of the information, modify the script and push the changes back out. You may also get an error when trying to submit MicroArray data. This is to be expected: MicroArray is currently not functional at all. We have no way as of current to map our data to the format expected by GEO, so we've punted on this issue for the time being. Once you've successfully run the script, you'll have generated a soft file and a script that will handle the uploading process. All of this will be put into a directory named 'database_wgEncodeSomeTrack_year-month-day'. To begin the upload, simply cd into the directoy and run upload.sh. This will start the aspera copy program, copying files, a files list, and the soft file itself. For each submission, you need to email GEO. Our current contact is: Steve Wilhite, wilhite@ncbi.nlm.nih.gov You must specify which track you're submitting. GEO will only allow us 1TB of space dedicated to ENCODE, so you must break down submissions larger than 1TB and only submit as many submissions as they have room to process at any given time. In a few days, GEO will get back to you with a list of accession numbers which need to be put back into our metadata (see encodeAddGeoAccessions). - -""" - -class DataType(object): - - def __init__(self, molecule, strategy, source, selection, soft): - self.molecule = molecule - self.strategy = strategy - self.source = source - self.selection = selection - self.soft = soft - -datatypes = { - 'Cage': DataType('OVERRIDE RNA', 'OTHER', 'transcriptomic', 'CAGE', soft.HighThroughputSoftFile), - 'ChipSeq': DataType('genomic DNA', 'ChIP-Seq', 'genomic', 'ChIP', soft.HighThroughputSoftFile), - 'DnaPet': DataType('genomic DNA', 'OTHER', 'genomic', 'size fractionation', soft.HighThroughputSoftFile), - 'DnaseDgf': DataType('genomic DNA', 'DNase-Hypersensitivity', 'genomic', 'DNase', soft.HighThroughputSoftFile), - 'DnaseSeq': DataType('genomic DNA', 'DNase-Hypersensitivity', 'genomic', 'DNase', soft.HighThroughputSoftFile), - 'FaireSeq': DataType('genomic DNA', 'OTHER', 'genomic', 'other', soft.HighThroughputSoftFile), - 'MethylSeq': DataType('genomic DNA', 'MRE-Seq', 'genomic', 'Restriction Digest', soft.HighThroughputSoftFile), - 'MethylRrbs': DataType('genomic DNA', 'Bisulfite-Seq', 'genomic', 'Reduced Representation', soft.HighThroughputSoftFile), - 'Orchid': DataType('genomic DNA', 'OTHER', 'genomic', 'other', soft.HighThroughputSoftFile), - 'Proteogenomics': DataType('protein', 'mass spectrometry-based proteogenomic mapping', 'protein', 'chromatographically fractionated peptides', soft.HighThroughputSoftFile), - 'RnaPet': DataType('OVERRIDE RNA', 'OTHER', 'transcriptomic', 'other', soft.HighThroughputSoftFile), - 'RnaSeq': DataType('OVERRIDE RNA', 'RNA-Seq', 'transcriptomic', 'cDNA', soft.HighThroughputSoftFile), - - #these need to be curated - '5C': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'AffyExonArray': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', soft.MicroArraySoftFile), - 'Bip': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'Cluster': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'Cnv': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'Combined': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'Genotype': DataType('genomic DNA', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'Gencode': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'ChiaPet': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'Mapability': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'MethylArray': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'NRE': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'Nucleosome': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'RnaChip': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'RipGeneSt': DataType('OVERRIDE RNA', 'REPLACE', 'transcriptomic', 'RNA binding protein antibody', soft.HighThroughputSoftFile), #this isn't correct - 'RipTiling': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'RipChip': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'RipSeq': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'Switchgear': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'TfbsValid': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None) -} - -#compare this to the source in datatype, give GP ids depending on the type -gpIds = { - 'human genomic': '63443', - 'human transcriptomic': '30709', - 'human protein': '63447', - - 'mouse genomic': '63471', - 'mouse transcriptomic': '66167', - 'mouse protein': '63475' -} +''' cvDetails = { 'cell': [ 'organism', 'description', 'karyotype', 'lineage', 'sex' ], 'antibody': [ 'antibodyDescription', 'targetDescription', 'vendorName', 'vendorId' ] } #if the term appears in the mdb and must overriding the value in the cv cvOverride = [ 'sex' ] #talk to Venkat lol cvPretend = { 'antibody Input': 'control' } #if its not in cvDetails, which things should we check by default cvDefaults = [ 'description' ] mdbWhitelist = [ 'age', 'bioRep', 'control', 'controlId', 'fragSize', 'labExpId', 'labVersion', 'mapAlgorithm', 'obtainedBy', 'phase', 'readType', 'region', 'replicate', 'restrictionEnzyme', 'run', 'softwareVersion', 'spikeInPool', 'strain' ] -# if the molecule is RNA, we need to map our data into !Sample_molecule, which only takes certain fields -# first we check rnaExtractMapping. If its not there, we use the localization. This is because (at current) -# polyA is the most important trait, otherwise its going to be nonPolyA which GEO doesn't accept that. -rnaExtractMapping = { - 'shortPolyA': 'polyA RNA', - 'longPolyA': 'polyA RNA', - 'polyA': 'polyA RNA' -} - -localizationMapping = { - 'cytosol': 'cytoplasmic RNA', - 'polysome': 'cytoplasmic RNA', - 'membraneFraction': 'cytoplasmic RNA', - 'mitochondria': 'cytoplasmic RNA', - 'nucleus': 'nuclear RNA', - 'nucleolus': 'nuclear RNA', - 'nucleoplasm': 'nuclear RNA', - 'nuclearMatrix': 'nuclear RNA', - 'chromatin': 'nuclear RNA', - 'cell': 'total RNA' -} - -# map our instrument names to GEO's names -instrumentModels = { - 'Illumina_GA2x': 'Illumina Genome Analyzer II', - 'Illumina_GA2': 'Illumina Genome Analyzer II', - 'Illumina_HiSeq_2000': 'Illumina HiSeq 2000', - 'Illumina_GA1': 'Illumina Genome Analyzer', - 'Illumina_GA1_or_GA2': 'Illumina Genome Analyzer, Illumina Genome Analyzer II', - 'SOLiD_Unknown': 'SOLiD', - 'Unknown': 'Illumina Genome Analyzer' -} - - def isRawFile(file): return (file.extension == 'fastq' or file.extension == 'fasta') def isSupplimentaryFile(file): return not isRawFile(file) def sampleTitle(stanza, expVars, warn=False): concat = stanza[expVars[0]].replace('-m', '') for expVar in expVars[1:len(expVars)]: if expVar in stanza and stanza[expVar] != 'None': concat += '_' + stanza[expVar] elif warn: print 'warning: %s is None or not in %s' % (expVar, stanza.name) return concat def linkName(file, track): return '%s_%s' % (track.database, file.name) -def createMappings(mdb): +def createMappings(metadb): expIds = dict() geoMapping = dict() expVars = None series = None datatype = None - for stanza in mdb.itervalues(): + for stanza in metadb.itervalues(): if 'objType' in stanza and stanza['objType'] == 'composite': series = stanza expVars = stanza['expVars'].split(',') continue if 'expId' not in stanza: print stanza.name + ': no expId' continue - if 'geoSampleAccession' not in stanza or 1: + if 'objStatus' in stanza: + print stanza.name + ': skipping because ' + stanza['objStatus'] + continue + + if 'geoSampleAccession' not in stanza: # if this hasn't been submitted to GEO yet, we'll add it to the submission list if stanza['expId'] not in expIds: expIds[stanza['expId']] = list() expIds[stanza['expId']].append(stanza) else: # otherwise we keep track of the geo number for partially submitted samples if stanza['expId'] not in geoMapping: geoMapping[stanza['expId']] = stanza['geoSampleAccession'] elif geoMapping[stanza['expId']] != 'Inconsistent' and geoMapping[stanza['expId']] != stanza['geoSampleAccession']: geoMapping[stanza['expId']] = 'Inconsistent' print stanza.name + ': inconsistent geo mapping' if datatype == None and 'dataType' in stanza: datatype = stanza['dataType'] elif datatype != None and 'dataType' in stanza and datatype != stanza['dataType']: raise KeyError(stanza.name + ': inconsistent data type') try: dt = datatype - datatype = datatypes[dt] + datatype = encode.dataTypes[dt] datatype.name = dt except KeyError: raise KeyError(datatype) return expIds, expVars, geoMapping, series, datatype -def createSeries(softfile, compositeTrack, expIds, expVars, geoMapping, series, datatype, replace, audit): +def createSeries(softfile, compositeTrack, expIds, expVars, geoMapping, series, datatype, replace, audit, argseries): if 'geoSeriesAccession' in series: print 'Existing series ' + series['composite'] + ' using geoSeriesAccession ' + series['geoSeriesAccession'] return print 'Writing series ' + series['composite'] seriesStanza = soft.SeriesStanza() seriesStanza['^SERIES'] = series['composite'] seriesStanza['!Series_title'] = compositeTrack.trackDb[compositeTrack.name]['longLabel'] #STILL INCORRECT if '!Series_summary' in replace: seriesStanza['!Series_summary'] = replace['!Series_summary'] else: print 'warning: no series summary found. Please include in replace file.' seriesStanza['!Series_summary'] = '[REPLACE]' if audit: print seriesStanza.name + ': no summary' if '!Series_overall_design' in replace: seriesStanza['!Series_overall_design'] = replace['!Series_overall_design'] else: print 'no series overall design found. Please include in replace file.' seriesStanza['!Series_overall_design'] = '[REPLACE]' if audit: print seriesStanza.name + ': no overall design' seriesStanza['!Series_web_link'] = [ compositeTrack.url, 'http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html' ] if '!Series_contributor' in replace: seriesStanza['!Series_contributor'] = replace['!Series_contributor'] else: seriesStanza['!Series_contributor'] = '[REPLACE]' if audit: print seriesStanza.name + ': no contributor' - seriesStanza['!Series_gp_id'] = gpIds[compositeTrack.organism + ' ' + datatype.source] + seriesStanza['!Series_gp_id'] = mdb.gpIds[compositeTrack.organism + ' ' + datatype.source] # could use !Series_variable_* and !Series_repeats_* + if not argseries: seriesStanza['!Series_sample_id'] = list() for idNum in expIds.iterkeys(): if idNum in geoMapping and geoMapping[idNum] != 'Inconsistent': seriesStanza['!Series_sample_id'].append(geoMapping[idNum]) else: seriesStanza['!Series_sample_id'].append(sampleTitle(expIds[idNum][0], expVars)) softfile[series['composite']] = seriesStanza -def createHighThroughputSoftFile(compositeTrack, cv, expIds, expVars, geoMapping, series, datatype, replace, audit): +def createHighThroughputSoftFile(compositeTrack, cv, expIds, expVars, geoMapping, series, datatype, replace, audit, tarpath, argseries): print 'Creating HighThroughput soft file' softfile = soft.HighThroughputSoftFile() fileList = list() - createSeries(softfile, compositeTrack, expIds, expVars, geoMapping, series, datatype, replace, audit) + createSeries(softfile, compositeTrack, expIds, expVars, geoMapping, series, datatype, replace, audit, argseries) + + if argseries: + return softfile, fileList for idNum in expIds.iterkeys(): expId = expIds[idNum] firstStanza = expId[0] print 'Writing sample ' + firstStanza['metaObject'] + ' (' + idNum + ')' sample = soft.HighThroughputSampleStanza() sample['^SAMPLE'] = sampleTitle(firstStanza, expVars, 1) sample['!Sample_type'] = 'SRA' sample['!Sample_title'] = sample['^SAMPLE'] if 'geoSeriesAccession' in series: sample['!Sample_series_id'] = series['geoSeriesAccession'] count = 1 #figure out if the instrument model is consistent across the entire sample instrumentModel = None for stanza in expId: if 'seqPlatform' in stanza: if instrumentModel == None: - instrumentModel = stanza['seqPlatform'] + instrumentModel = geo.instrumentModels[stanza['seqPlatform']] else: - if instrumentModel != stanza['seqPlatform']: + if instrumentModel != geo.instrumentModels[stanza['seqPlatform']]: instrumentModel = None if audit: print 'expId' + str(expId) + ': inconsistent instrument model' break for stanza in expId: for fname in stanza['fileName'].split(','): + file = compositeTrack.files[fname] + filelist = list() if isRawFile(file): - sample['!Sample_raw_file_' + str(count)] = linkName(file, compositeTrack) - sample['!Sample_raw_file_type_' + str(count)] = file.extension - if file.md5sum != None: - sample['!Sample_raw_file_checksum_' + str(count)] = file.md5sum + if file.name.endswith('.tgz') or file.name.endswith('.tar.gz'): + + if tarpath == None: + raise IOError('this track contains tarred fastqs. Please specify a path through the -z option') + dirname = tarpath + file.name.split('.')[0] + '/' + if os.path.exists(dirname): + raise IOError(dirname + ' already exists') + else: + os.mkdir(dirname) + + os.system('tar -xf %s -C %s' % (file.path + file.name, dirname)) + + for root, dirnames, filenames in os.walk(dirname): + for filename in filenames: + if filename.endswith('.fastq') or filename.endswith('.txt'): + os.system('gzip %s' % (root + '/' + filename)) + + for root, dirnames, filenames in os.walk(dirname): + for filename in filenames: + print root + '/' + filename + filelist.append(track.TrackFile(root + '/' + filename)) + + else: + filelist.append(file) + + for f in filelist: + + sample['!Sample_raw_file_' + str(count)] = linkName(f, compositeTrack) + if f.extension == 'txt': + sample['!Sample_raw_file_type_' + str(count)] = 'fastq' + else: + sample['!Sample_raw_file_type_' + str(count)] = f.extension + + sample['!Sample_raw_file_checksum_' + str(count)] = f.md5sum if instrumentModel == None and 'seqPlatform' in stanza: - sample['!Sample_raw_file_instrument_model_' + str(count)] = stanza['seqPlatform'] + sample['!Sample_raw_file_instrument_model_' + str(count)] = geo.instrumentModels[stanza['seqPlatform']] - fileList.append(file) + fileList.append(f) count = count + 1 count = 1 for stanza in expId: for fname in stanza['fileName'].split(','): file = compositeTrack.files[fname] if isSupplimentaryFile(file): sample['!Sample_supplementary_file_' + str(count)] = linkName(file, compositeTrack) if file.md5sum != None: sample['!Sample_supplementary_file_checksum_' + str(count)] = file.md5sum sample['!Sample_supplementary_file_build_' + str(count)] = compositeTrack.database if instrumentModel == None and 'seqPlatform' in stanza: - sample['!Sample_supplementary_file_instrument_model_' + str(count)] = stanza['seqPlatform'] + sample['!Sample_supplementary_file_instrument_model_' + str(count)] = geo.instrumentModels[stanza['seqPlatform']] fileList.append(file) count = count + 1 sample['!Sample_source_name'] = firstStanza['cell'] sample['!Sample_organism'] = compositeTrack.organism sample['!Sample_characteristics'] = list() allVars = expVars + mdbWhitelist for var in allVars: if var in firstStanza: foobar = var sample['!Sample_characteristics'].append(var + ': ' + firstStanza[var]) for pretend in cvPretend.iterkeys(): if var + ' ' + firstStanza[var] == pretend: foobar = cvPretend[pretend] if foobar in cvDetails: for cvVar in cvDetails[foobar]: if cvVar in cvOverride and cvVar in firstStanza: sample['!Sample_characteristics'].append(var + ' ' + cvVar + ': ' + firstStanza[cvVar]) elif cvVar in cv[firstStanza[var]]: sample['!Sample_characteristics'].append(var + ' ' + cvVar + ': ' + cv[firstStanza[var]][cvVar]) else: for cvVar in cvDefaults: if firstStanza[var] in cv and cvVar in cv[firstStanza[var]]: sample['!Sample_characteristics'].append(var + ' ' + cvVar + ': ' + cv[firstStanza[var]][cvVar]) sample['!Sample_biomaterial_provider'] = cv[firstStanza['cell']]['vendorName'] if 'treatment' in firstStanza: sample['!Sample_treatment_protocol'] = firstStanza['treatment'] if 'protocol' in cv[firstStanza['cell']]: for protocol in cv[firstStanza['cell']]['protocol'].split(' '): key, val = protocol.split(':') if key == 'ENCODE' or key == cv[firstStanza['lab']]['labPi']: sample['!Sample_growth_protocol'] = val - if datatype.molecule == 'OVERRIDE RNA': - if firstStanza['rnaExtract'] in rnaExtractMapping: - sample['!Sample_molecule'] = rnaExtractMapping[firstStanza['rnaExtract']] - elif firstStanza['localization'] in localizationMapping: - sample['!Sample_molecule'] = localizationMapping[firstStanza['localization']] + if datatype.molecule == 'RNA': + if firstStanza['rnaExtract'] in geo.rnaExtractMapping: + sample['!Sample_molecule'] = geo.rnaExtractMapping[firstStanza['rnaExtract']] + elif firstStanza['localization'] in geo.localizationMapping: + sample['!Sample_molecule'] = geo.localizationMapping[firstStanza['localization']] else: sample['!Sample_molecule'] = datatype.molecule if '!Sample_instrument_model' in replace and replace['!Sample_instrument_model'][0] == 'Unknown': - sample['!Sample_extract_protocol'] = 'Instrument model unknown. ("%s" specified by default). For more information, see %s' % (instrumentModels[replace['!Sample_instrument_model'][0]], compositeTrack.url) + sample['!Sample_extract_protocol'] = 'Instrument model unknown. ("%s" specified by default). For more information, see %s' % (geo.instrumentModels[replace['!Sample_instrument_model'][0]], compositeTrack.url) else: sample['!Sample_extract_protocol'] = compositeTrack.url sample['!Sample_library_strategy'] = datatype.strategy sample['!Sample_library_source'] = datatype.source sample['!Sample_library_selection'] = datatype.selection # if the instrumentModel is consistent, just use that # otherwise take the first seqPlatform value from metadata # if that still fails, check the replacement file # finally just make it say [REPLACE] if instrumentModel != None: sample['!Sample_instrument_model'] = instrumentModel else: for stanza in expId: if 'seqPlatform' in stanza: - sample['!Sample_instrument_model'] = instrumentModels[stanza['seqPlatform']] + sample['!Sample_instrument_model'] = geo.instrumentModels[stanza['seqPlatform']] break if '!Sample_instrument_model' not in sample: if '!Sample_instrument_model' in replace: - sample['!Sample_instrument_model'] = instrumentModels[replace['!Sample_instrument_model'][0]] + sample['!Sample_instrument_model'] = geo.instrumentModels[replace['!Sample_instrument_model'][0]] if '!Sample_instrument_model' not in sample: sample['!Sample_instrument_model'] = '[REPLACE]' if audit: print stanza.name + ': no instrument' sample['!Sample_data_processing'] = compositeTrack.url if idNum in geoMapping and geoMapping[idNum] != 'Inconsistent': sample['!Sample_geo_accession'] = geoMapping[idNum] softfile[firstStanza['metaObject']] = sample return softfile, fileList -def createMicroArraySoftFile(database, composite, organism, compositeUrl, mdb, cv, track, md5sums, expIds, expVars, geoMapping, series, datatype): +def createMicroArraySoftFile(compositeTrack, cv, expIds, expVars, geoMapping, series, datatype, replace, audit): - raise KeyError('microarray') + #raise KeyError('microarray') print 'Creating MicroArray soft file' - softfile = SoftFile() + softfile = soft.MicroArraySoftFile() fileList = list() - createSeries(softfile, composite, compositeUrl, track, expIds, geoMapping, series) + createSeries(softfile, compositeTrack, expIds, expVars, geoMapping, series, datatype, replace, audit) for idNum in expIds.iterkeys(): expId = expIds[idNum] firstStanza = expId[0] print 'Writing sample ' + firstStanza['metaObject'] + ' (' + idNum + ')' - sample = MicroArraySampleStanza() + sample = soft.MicroArraySampleStanza() - sample['^SAMPLE'] = sampleTitle(firstStanza, expVars) + sample['^SAMPLE'] = sampleTitle(firstStanza, expVars, 1) if 'geoSeriesAccession' in series: sample['!Sample_series_id'] = series['geoSeriesAccession'] - sample['!Sample_title'] = concat + #sample['!Sample_title'] = concat + + count = 1 count = 1 for stanza in expId: - if isSupplimentaryFile(stanza['fileName']): - sample['!Sample_supplementary_file_' + str(count)] = stanza['fileName'] + for fname in stanza['fileName'].split(','): + file = compositeTrack.files[fname] - if 'checksum' in stanza: - sample['!Sample_supplementary_file_checksum_' + str(count)] = stanza['checksum'] - elif md5sums != None and stanza['fileName'] in md5sums: - sample['!Sample_supplementary_file_checksum_' + str(count)] = md5sums[stanza['fileName']] + if isSupplimentaryFile(file): + sample['!Sample_supplementary_file_' + str(count)] = linkName(file, compositeTrack) - fileList.append(stanza['fileName']) + if file.md5sum != None: + sample['!Sample_supplementary_file_checksum_' + str(count)] = file.md5sum + + sample['!Sample_supplementary_file_build_' + str(count)] = compositeTrack.database + + fileList.append(file) count = count + 1 # sample['!Sample_table'] = KeyOptional # CEL file - sample['!Sample_source_name_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered - sample['!Sample_organism_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered - sample['!Sample_characteristics_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered + # sample['!Sample_source_name_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered + # sample['!Sample_organism_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered + # sample['!Sample_characteristics_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered # sample['!Sample_biomaterial_provider_ch'] = KeyZeroPlusNumbered # sample['!Sample_treatment_protocol_ch'] = KeyZeroPlusNumbered # sample['!Sample_growth_protocol_ch'] = KeyZeroPlusNumbered - sample['!Sample_molecule_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered - sample['!Sample_extract_protocol_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered - sample['!Sample_label_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered - sample['!Sample_label_protocol_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered - sample['!Sample_hyb_protocol'] = '[REPLACE]' #KeyOnePlus - sample['!Sample_scan_protocol'] = '[REPLACE]' #KeyOnePlus - sample['!Sample_data_processing'] = '[REPLACE]' #KeyOnePlus - sample['!Sample_description'] = '[REPLACE]' #KeyZeroPlus - sample['!Sample_platform_id'] = '[REPLACE]' + # sample['!Sample_molecule_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered + # sample['!Sample_extract_protocol_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered + # sample['!Sample_label_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered + # sample['!Sample_label_protocol_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered + # sample['!Sample_hyb_protocol'] = '[REPLACE]' #KeyOnePlus + # sample['!Sample_scan_protocol'] = '[REPLACE]' #KeyOnePlus + # sample['!Sample_data_processing'] = '[REPLACE]' #KeyOnePlus + # sample['!Sample_description'] = '[REPLACE]' #KeyZeroPlus + # sample['!Sample_platform_id'] = '[REPLACE]' # sample['!Sample_geo_accession'] = KeyOptional # sample['!Sample_anchor'] = KeyRequired SAGE ONLY # sample['!Sample_type'] = KeyRequired SAGE ONLY # sample['!Sample_tag_count'] = KeyRequired SAGE ONLY # sample['!Sample_tag_length'] = KeyRequired SAGE ONLY - sample['!Sample_table_begin'] = '' - sample['!Sample_table_end'] = '' + # sample['!Sample_table_begin'] = '' + # sample['!Sample_table_end'] = '' - softfile[firstStanza['accession']] = sample + if 'geoSampleAccession' in firstStanza: + sample['!Sample_geo_accession'] = firstStanza['geoSampleAccession'] + + softfile[firstStanza['metaObject']] = sample return softfile, fileList def createSpecialSoftFile(database, composite, organism, compositeUrl, mdb, cv, track, md5sums, expIds, expVars, geoMapping, series, datatype): softfile = SoftFile() fileList = list() createSeries(softfile, composite, compositeUrl, track, expIds, geoMapping, series) for idNum in expIds.iterkeys(): expId = expIds[idNum] firstStanza = expId[0] print 'Writing sample ' + firstStanza['metaObject'] + ' (' + idNum + ')' sample = HighThroughputSampleStanza() hasbigwig = 0 for stanza in expId: if getFileType(stanza['fileName']) == 'bigWig': hasbigwig = 1 if hasbigwig == 0: continue sample['^SAMPLE'] = firstStanza['geoSampleAccession'] if 'geoSeriesAccession' in series: sample['!Sample_series_id'] = series['geoSeriesAccession'] sample['!Sample_geo_accession'] = firstStanza['geoSampleAccession'] count = 1 for stanza in expId: if getFileType(stanza['fileName']) == 'bigWig': sample['!Sample_supplementary_file_' + str(count)] = stanza['fileName'] if 'checksum' in stanza: sample['!Sample_supplementary_file_checksum_' + str(count)] = stanza['checksum'] elif md5sums != None and stanza['fileName'] in md5sums: sample['!Sample_supplementary_file_checksum_' + str(count)] = md5sums[stanza['fileName']] # sample['!Sample_supplementary_file_build_' + str(count)] = database fileList.append(stanza['fileName']) count = count + 1 softfile[firstStanza['geoSampleAccession']] = sample return softfile, fileList def main(): parser = argparse.ArgumentParser(description = 'Prepares a submission to GEO. Creates a soft file and shell script with the correct call to aspera.') parser.add_argument('-t', '--trackPath', help='Overrides the default track path ~/kent/src/hg/makeDb/trackDb/') parser.add_argument('-r', '--replace', help='Give the name of a file that has contents to be used to replace unspecified tags in metadata (description, contributers, etc) and instrument model') parser.add_argument('-a', '--audit', action='store_true', default=False, help='Instead of building the files, will just give you a list of errors') + parser.add_argument('-z', '--zip', help='Specifies a directory path to unzip tarred fastqs to, only applicable for tracks with tarred fastqs') + parser.add_argument('-s', '--series', action='store_true', default=False, help='Only generates the series stanza, instead of generating the entire soft file') parser.add_argument('database', help='The database, typically hg19 or mm9') parser.add_argument('composite', help='The composite name, wgEncodeCshlLongRnaSeq for instance') parser.add_argument('expIds', nargs='*', help='Any number of expIds separated by spaces, you can also specify a range by using a hyphen, "140 150 160-170" for instance, or leave blank to specify the entire file') if len(sys.argv) == 1: parser.print_usage() return args = parser.parse_args(sys.argv[1:]) compositeTrack = track.CompositeTrack(args.database, args.composite, args.trackPath) cvPath = compositeTrack.trackPath + 'cv/alpha/cv.ra' controlledVocab = cv.CvFile(cvPath) + if args.zip != None and not args.zip.endswith('/'): + args.zip += '/' + replace = dict() if args.replace != None: for line in open(args.replace): if line == '': continue key, val = map(str.strip, line.split('=', 1)) if key not in replace: replace[key] = list() replace[key].append(val) - + tempids = list() ids = list() for id in args.expIds: if '-' in id: start, end = id.split('-', 1) - ids.extend(range(int(start), int(end) + 1)) + tempids.extend(range(int(start), int(end) + 1)) else: + tempids.append(int(id)) + for id in tempids: + if str(id) in compositeTrack.alphaMetaDb.experiments.keys(): ids.append(int(id)) expIds, expVars, geoMapping, series, datatype = createMappings(compositeTrack.alphaMetaDb) submission = dict() if len(ids) == 0: submission = expIds else: for expId in ids: + if str(expId) in expIds.keys(): submission[str(expId)] = expIds[str(expId)] - expIdStr = ' ' for id in args.expIds: expIdStr = expIdStr + id + ',' expIdStr = expIdStr[:len(expIdStr) - 1] - print 'Generating soft using expIds ' + expIdStr + print 'Generating soft using expIds ' + ','.join(submission.keys()) - if datatype.soft == soft.HighThroughputSoftFile: - softfile, fileList = createHighThroughputSoftFile(compositeTrack, controlledVocab, submission, expVars, geoMapping, series, datatype, replace, args.audit) - elif datatype.soft == soft.MicroArraySoftFile: - softfile, fileList = createMicroArraySoftFile(compositeTrack, controlledVocab, submission, expVars, geoMapping, series, datatype) + if datatype.type == 'HighThroughput': + softfile, fileList = createHighThroughputSoftFile(compositeTrack, controlledVocab, submission, expVars, geoMapping, series, datatype, replace, args.audit, args.zip, args.series) + elif datatype.type == 'MicroArray': + softfile, fileList = createMicroArraySoftFile(compositeTrack, controlledVocab, submission, expVars, geoMapping, series, datatype, replace, args.audit, args.zip, args.series) else: raise KeyError('unsupported type ' + datatype.name) - if not args.audit: + if not args.audit and not args.series: print 'Creating directory' d = datetime.datetime.today() datestring = '%4d-%02d-%02d' % (d.year, d.month, d.day) dirname = '%s_%s_%s/' % (compositeTrack.database, compositeTrack.name, datestring) linkdirname = '%s_%s/' % (compositeTrack.database, compositeTrack.name) os.mkdir(dirname) os.mkdir(dirname + linkdirname) print 'Writing file' outfileName = '%s%s_%s.soft' % (dirname + linkdirname, compositeTrack.database, compositeTrack.name) outfile = open(outfileName, 'w') outfile.write(str(softfile)) fileslistname = '%sfiles.txt' % (dirname + linkdirname) fileslist = open(fileslistname, 'w') scriptname = '%supload.sh' % dirname outscript = open(scriptname, 'w') outscript.write('#!/bin/sh\n\n') outscript.write('/cluster/home/mmaddren/.aspera/connect/bin/ascp -i ~/encode_geo_key/encode_geo_key.ppk --symbolic-links=follow -QTdr -l300m %s asp-geo@upload.ncbi.nlm.nih.gov:ENCODE\n' % linkdirname) outscript.close() + elif args.series: + outfileName = '%s_%s.soft' % (compositeTrack.database, compositeTrack.name) + outfile = open(outfileName, 'w') + outfile.write(str(softfile)) + outfile.close() for file in fileList: if not os.path.exists(file.path): print IOError(file.path + ' does not exist') elif not args.audit: linkname = linkName(file, compositeTrack) linkpath = linkdirname + linkname os.symlink(file.fullname, dirname + linkpath) #outscript.write(linkpath + ' \\\n') fileslist.write(linkname + '\n') - if not args.audit: + if not args.audit and not args.series: #outscript.write() fileslist.close() os.system('chmod +x ' + scriptname) print 'Finished!' if __name__ == '__main__': main() \ No newline at end of file