''' @copyright: Copyright 2012 ETH Zuerich, CISD @license: Licensed under the Apache License, Version 2.0 (the 'License'); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an 'AS IS' BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. @author: Manuel Kohler @description: Creates the SampleSheet.csv out of values from openBIS for Demultiplexing used in the Illumina pipeline (configureBclToFastq.pl) @attention: Runs under Jython @note: Takes into account to replace special characters with an underscore so that the Illumina script does not fail HiSeq Header Description ======================== Column Header Description FCID Flow cell ID Lane Positive integer, indicating the lane number (1-8) SampleID ID of the sample SampleRef The reference used for alignment for the sample Index Index sequences. Multiple index reads are separated by a hyphen (for example, ACCAGTAA-GGACATGA). Description Description of the sample Control Y indicates this lane is a control lane, N means sample Recipe Recipe used during sequencing Operator Name or ID of the operator SampleProject The project the sample belongs to ''' from __future__ import with_statement import os import logging import re import sys import string import smtplib from ConfigParser import SafeConfigParser from optparse import OptionParser from datetime import * from email.MIMEMultipart import MIMEMultipart from email.MIMEBase import MIMEBase from email.MIMEText import MIMEText from email.Utils import COMMASPACE, formatdate from email import Encoders from ch.systemsx.cisd.openbis.dss.client.api.v1 import OpenbisServiceFacadeFactory from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria lineending = {'win32':'\r\n', 'linux':'\n', 'mac':'\r'} COMMA = ',' def login(logger, configMap): logger.info('Logging into ' + configMap['openbisServer']) service = OpenbisServiceFacadeFactory.tryCreate(configMap['openbisUserName'], configMap['openbisPassword'], configMap['openbisServer'], configMap['connectionTimeout']) return service def logout (service, logger): service.logout() logger.info('Logged out') def setUpLogger(logPath, logLevel=logging.INFO): logFileName = 'createSampleSheet' d = datetime.now() logFileName = logFileName + '_' + d.strftime('%Y-%m-%d_%H_%M_%S') + '.log' logging.basicConfig(filename=logPath + logFileName, format='%(asctime)s [%(levelname)s] %(message)s', level=logLevel) logger = logging.getLogger(logFileName) return logger def parseOptions(logger): logger.info('Parsing command line parameters') parser = OptionParser(version='%prog 1.0') parser.add_option('-f', '--flowcell', dest='flowcell', help='The flowcell which is used to create the SampleSheet.csv', metavar='') parser.add_option('-m', '--mailist', dest='maillist', default=False, action='store_true', help='Generated Sample Sheet will be addtionally sent as email to the defined list of recipients', metavar='') parser.add_option('-l', '--lineending', dest='lineending', type='choice', action='store', choices=['win32', 'linux', 'mac'], default='win32', help='Specify end of line separator: win32, linux, mac. Default: win32' , metavar='') parser.add_option('-o', '--outdir', dest='outdir', default='./', help='Specify the ouput directory. Default: ./' , metavar='') parser.add_option('-s', '--singlelane', dest='singlelane', default=False, action='store_true', help='Creates a single Sample Sheet for each lane. Default: False') parser.add_option('-d', '--debug', dest='debug', default=False, action='store_true', help='Verbose debug logging. Default: False') parser.add_option('-v', '--verbose', dest='verbose', default=False, action='store_true', help='Write Sample Sheet to stout. Default: False') (options, args) = parser.parse_args() if options.outdir[-1] <> '/': options.outdir = options.outdir + '/' if options.flowcell is None: parser.print_help() exit(-1) return options def parseConfigurationFile(propertyFile='etc/createSampleSheet.properties'): ''' Parses the given config files and returns the values ''' config = SafeConfigParser() config.read(propertyFile) config.sections() return config def readConfig(logger): GENERAL = 'GENERAL' OPENBIS = 'OPENBIS' ILLUMINA = 'ILLUMINA' logger.info('Reading config file') configMap = {} configParameters = parseConfigurationFile() configMap['facilityName'] = configParameters.get(GENERAL, 'facilityName') configMap['facilityNameShort'] = configParameters.get(GENERAL, 'facilityNameShort') configMap['facilityInstitution'] = configParameters.get(GENERAL, 'facilityInstitution') configMap['mailList'] = configParameters.get(GENERAL, 'mailList') configMap['mailFrom'] = configParameters.get(GENERAL, 'mailFrom') configMap['smptHost'] = configParameters.get(GENERAL, 'smptHost') configMap['SampleSheetFileName'] = configParameters.get(GENERAL, 'SampleSheetFileName') configMap['separator'] = configParameters.get(GENERAL, 'separator') configMap['indexSeparator'] = configParameters.get(GENERAL, 'indexSeparator') configMap['openbisUserName'] = configParameters.get(OPENBIS, 'openbisUserName') configMap['openbisPassword'] = configParameters.get(OPENBIS, 'openbisPassword', raw=True) configMap['openbisServer'] = configParameters.get(OPENBIS, 'openbisServer') configMap['connectionTimeout'] = configParameters.getint(OPENBIS, 'connectionTimeout') configMap['illuminaFlowCellTypeName'] = configParameters.get(OPENBIS, 'illuminaFlowCellTypeName') configMap['index1Name'] = configParameters.get(OPENBIS, 'index1Name') configMap['index2Name'] = configParameters.get(OPENBIS, 'index2Name') configMap['index1Length'] = configParameters.get(OPENBIS, 'index1Length') configMap['index2Length'] = configParameters.get(OPENBIS, 'index2Length') configMap['endType'] = configParameters.get(OPENBIS, 'endType') configMap['cycles'] = configParameters.get(OPENBIS, 'cycles') configMap['controlLane'] = configParameters.get(OPENBIS, 'controlLane') configMap['ncbi'] = configParameters.get(OPENBIS, 'ncbi') configMap['externalSampleName'] = configParameters.get(OPENBIS, 'externalSampleName') configMap['laneCount'] = configParameters.get(OPENBIS, 'laneCount') configMap['kit'] = configParameters.get(OPENBIS, 'kit') configMap['hiSeqNames'] = configParameters.get(ILLUMINA, 'hiSeqNames') configMap['miSeqNames'] = configParameters.get(ILLUMINA, 'miSeqNames') configMap['hiSeqHeader'] = configParameters.get(ILLUMINA, 'hiSeqHeader') configMap['miSeqHeaderSection'] = configParameters.get(ILLUMINA, 'miSeqHeaderSection') configMap['miSeqReadsSection'] = configParameters.get(ILLUMINA, 'miSeqReadsSection') configMap['miSeqSettingsSection'] = configParameters.get(ILLUMINA, 'miSeqSettingsSection') configMap['miSeqDataSectionSingleRead'] = configParameters.get(ILLUMINA, 'miSeqDataSectionSingleRead') configMap['miSeqDataSectionDualRead'] = configParameters.get(ILLUMINA, 'miSeqDataSectionDualRead') configMap['miSeqWorkflow'] = configParameters.get(ILLUMINA, 'miSeqWorkflow') configMap['miSeqApplication'] = configParameters.get(ILLUMINA, 'miSeqApplication') configMap['miSeqChemistry'] = configParameters.get(ILLUMINA, 'miSeqChemistry') configMap['nextSeqDataSectionSingleRead'] = configParameters.get(ILLUMINA, 'nextSeqDataSectionSingleRead') configMap['nextSeqDataSectionDualRead'] = configParameters.get(ILLUMINA, 'nextSeqDataSectionDualRead') configMap['truSeqAdapter1'] = configParameters.get(ILLUMINA, 'truSeqAdapter1') configMap['truSeqAdapter2'] = configParameters.get(ILLUMINA, 'truSeqAdapter2') configMap['nexteraAdapter'] = configParameters.get(ILLUMINA, 'nexteraAdapter') configMap['iemFileVersion'] = configParameters.get(ILLUMINA, 'iemFileVersion') configMap['configureBclToFastqPath'] = configParameters.get(ILLUMINA, 'configureBclToFastqPath') configMap['failedReads'] = configParameters.get(ILLUMINA, 'failedReads') configMap['clusterCount'] = configParameters.get(ILLUMINA, 'clusterCount') configMap['clusterCountNumber'] = configParameters.get(ILLUMINA, 'clusterCountNumber') configMap['outputDir'] = configParameters.get(ILLUMINA, 'outputDir') configMap['sampleSheetName'] = configParameters.get(ILLUMINA, 'sampleSheetName') configMap['baseMask'] = configParameters.get(ILLUMINA, 'baseMask') return configMap def getDate(): d = datetime.now() return d.strftime('%A, %d of %B %Y') def sanitizeString(myString): return re.sub('[^A-Za-z0-9]+', '_', myString) def getVocabulary(vocabularyCode, service): ''' Returns the vocabulary terms and vocabulary labels of a vocabulary in a dictionary specified by the parameter vocabularyCode ''' terms = [] vocabularies = service.listVocabularies() vocabularyDict = {} for vocabulary in vocabularies: if (vocabulary.getCode() == vocabularyCode): terms = vocabulary.getTerms() if terms: for term in terms: vocabularyDict[term.getCode()] = term.getLabel() else: print ('No vocabulary found for ' + vocabularyCode) return vocabularyDict def sendMail(emails, files, flowCellName, configMap, logger): ''' Send out an email to the specified recipients ''' COMMASPACE = ', ' listofEmails = emails.split() msg = MIMEMultipart() msg['From'] = configMap['mailFrom'] msg['To'] = COMMASPACE.join(listofEmails) msg['Date'] = formatdate(localtime=True) msg['Subject'] = 'Generated Sample Sheet for flowcell ' + flowCellName msg.attach(MIMEText('Sample Sheet for ' + flowCellName + ' attached.')) for f in files: part = MIMEBase('application', 'octet-stream') part.set_payload(open(f, 'rb').read()) Encoders.encode_base64(part) part.add_header('Content-Disposition', 'attachment; filename="%s"' % os.path.basename(f)) msg.attach(part) smtp = smtplib.SMTP(configMap['smptHost']) smtp.sendmail(configMap['mailFrom'], listofEmails, msg.as_string()) smtp.close() logger.info('Sent email to ' + COMMASPACE.join(listofEmails)) def getFlowCell (illuminaFlowCellTypeName, flowCellName, service, logger): ''' Getting the the matching FlowCell ''' sc = SearchCriteria(); sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, illuminaFlowCellTypeName)); sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, flowCellName)); foundSample = service.searchForSamples(sc) try: assert foundSample.size() == 1 except AssertionError: print (str(foundSample.size()) + ' flow cells found which match.') exit(1) logger.info('Found ' + foundSample[0].getCode() + ' in openBIS') # Search for contained samples sampleSc = SearchCriteria() sampleSc.addSubCriteria(SearchSubCriteria.createSampleContainerCriteria(sc)) foundContainedSamples = service.searchForSamples(sampleSc) return foundSample[0], foundContainedSamples def getParents(sampleName, service): ''' Returns a list of parents of a sample ''' sc = SearchCriteria(); sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleName)); foundSample = service.searchForSamples(sc) try: assert foundSample.size() == 1 except AssertionError: print (str(foundSample.size()) + ' flow lanes found which match.') # set the criteria for getting the parents when providing the child name sampleSc = SearchCriteria() sampleSc.addSubCriteria(SearchSubCriteria.createSampleChildCriteria(sc)) foundParentSamples = service.searchForSamples(sampleSc) return foundParentSamples def getContainedSampleProperties(containedSamples, service): # TODO: update description and function name ''' Takes a list of contained samples, retrieves the parents and their properties and returns it as a dictionary. The key is the sample name, the value is a list of the properties Additionally a dictionary with the lane (key) and the number of samples (value) is returned ''' parentDict = {} samplesPerLaneDict = {} for lane in containedSamples: parents = getParents (lane.getCode(), service) try: assert parents.size() >= 1 except AssertionError: print (str(parents.size()) + ' parents found for lane ' + lane.getCode()) samplesPerLaneDict[lane.getCode()[-1]] = len(parents) for parent in parents: parentCode = parent.getCode() parentProperties = parent.getProperties() propertyDict = {} for property in parentProperties: propertyDict[property] = parentProperties.get(property) propertyDict['LANE'] = lane.getCode() myKey = sanitizeString(parentCode + '_' + lane.getCode()) parentDict[myKey] = propertyDict return parentDict, samplesPerLaneDict def convertSampleToDict(foundFlowCell): ''' converts to a python dict ''' flowCellDict = {} fcProperties = foundFlowCell.getProperties() for property in fcProperties: flowCellDict[property] = fcProperties.get(property) flowCellDict['Project'] = foundFlowCell.getExperimentIdentifierOrNull().split('/')[-1] flowCellDict['Name'] = foundFlowCell.getIdentifier().split('/')[-1] return flowCellDict def pickleDemultiplexCommandList(logger, demultiplexCommandList, fileName): import pickle try: with open(fileName, 'w') as pickleDemux: pickle.dump(demultiplexCommandList, pickleDemux) logger.info('Writing file ' + fileName) except IOError, err: logger.error('File error: ' + str(err)) print ('File error: ' + str(err)) def writeMiSeqSampleSheet(sampleSheetDict, headerList, flowCellName, myoptions, logger, fileName): ''' Writes the given dictionary to a csv file. The order does not matter. As the header is not fixed we first need to write the headerList in the file. This is specific to MiSeq ''' newline = lineending[myoptions.lineending] try: with open(fileName, 'wb') as sampleSheetFile: for listElement in headerList: if myoptions.verbose: print listElement sampleSheetFile.write(listElement + newline) for sample in sampleSheetDict: if myoptions.verbose: print sampleSheetDict[sample][0] sampleSheetFile.write(sampleSheetDict[sample][0] + newline) logger.info('Writing file ' + fileName) except IOError: logger.error('File error: ' + str(err)) print ('File error: ' + str(err)) return fileName def get_reverse_complement(sequence): lookup_table = {'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G'} reverse_complement = '' for nucleotide in reversed(sequence): reverse_complement += lookup_table[nucleotide] return reverse_complement def createSampleSheet(parentDict, flowCellDict, configMap, index1Vocabulary, index2Vocabulary, flowCellName, logger, myoptions): ''' ''' kitsDict = {"CHIP_SEQ_SAMPLE_PREP" : ["",""], "TRUSEQ_RNA_SAMPLEPREPKIT_V2_ILLUMINA" : ["A","TruSeq LT"], "NEXTERA_XT_DNA_SAMPLE_PREPARATION_KIT_ILLUMINA" : ["S", "Nextera XT"], "TRUSEQ_CHIP_SAMPLE_PREP_KIT" : ["A","TruSeq LT"], "MRNA_SEQ_SAMPLE_PREP" : ["",""], "TRUSEQRNA_SAMPLE_PREP_KIT" : ["A","TruSeq LT"], "NEBNEXT_DNA_SAMPLE_PREP_MASTER_MIX_SET1" : ["A","TruSeq LT"], "NEBNEXT_CHIP-SEQ_LIBRARY_PREP_REAGENT_SET" : ["A","TruSeq LT"], "RIBOZERO_SCRIPTSEQ_MRNA-SEQ_KIT" : ["",""], "NEXTERA_DNA_SAMPLE_PREPARATION_KIT_ILLUMINA" : ["N", "Nextera"], "GENOMICDNA_SAMPLE_PREP" : ["",""], "AGILENT_SURESELECTXT_AUTOMATEDLIBRARYPREP" : ["",""], "TRUSEQ_DNA_SAMPLE_PREP_KIT" : ["A","TruSeq LT"], "NEXTERA_DNA_SAMPLE_PREP_KITS" : ["N", "Nextera"], "AGILENT_SURESELECT_ENRICHMENTSYSTEM" : ["",""], "TRUSEQ_DNA_SAMPLE_PREP_KIT_V2" : ["A","TruSeq LT"], "AGILENT_SURESELECT_HUMAN_ALL_EXON_V5_UTRS" : ["",""], "POLYA_SCRIPTSEQ_MRNA-SEQ_KIT" : ["",""], "AGILENT_SURESELECTXT2_MOUSE_ALL_EXON" : ["",""], "PAIRED_END_DNA_SAMPLE_PREP" : ["",""], "NEXTERA_DNA_SAMPLE_PREP_KIT_BUFFER_HMW" : ["N", "Nextera"] } sampleSheetDict = {} headerList = [] # here we take the fisrat sample to determine the Sample Prep Kit try: assay = kitsDict [parentDict.itervalues().next()[configMap['kit']]][1] except: print "No Kit set for sample. Will not set the assay value in the sample sheet" assay = "" pass separator = configMap['separator'] miSeqHeaderSection = configMap['miSeqHeaderSection'].split(separator) miSeqHeaderSection.reverse() headerList = [miSeqHeaderSection.pop().strip()] headerList.append(miSeqHeaderSection.pop().strip() + separator + configMap['iemFileVersion']) headerList.append(miSeqHeaderSection.pop().strip() + separator + configMap['facilityInstitution']) headerList.append(miSeqHeaderSection.pop().strip() + separator + configMap['facilityName']) headerList.append(miSeqHeaderSection.pop().strip() + separator + flowCellDict['Name']) headerList.append(miSeqHeaderSection.pop().strip() + separator + datetime.now().strftime('%m/%d/%Y')) headerList.append(miSeqHeaderSection.pop().strip() + separator + configMap['miSeqWorkflow']) headerList.append(miSeqHeaderSection.pop().strip() + separator + configMap['miSeqApplication']) headerList.append(miSeqHeaderSection.pop().strip() + separator + assay) headerList.append(miSeqHeaderSection.pop().strip() + separator + flowCellDict[configMap['endType']] + '_' + flowCellDict[configMap['cycles']]) headerList.append(miSeqHeaderSection.pop().strip() + separator + configMap['miSeqChemistry']) headerList.append('') miSeqReadsSection = configMap['miSeqReadsSection'].split(separator) miSeqReadsSection.reverse() headerList.append(miSeqReadsSection.pop()) headerList.append(flowCellDict[configMap['cycles']]) if (flowCellDict[configMap['endType']] == 'PAIRED_END'): headerList.append(flowCellDict[configMap['cycles']]) headerList.append('') miSeqSettingsSection = configMap['miSeqSettingsSection'].split(separator) miSeqSettingsSection.reverse() headerList.append(miSeqSettingsSection.pop()) if ('nextera' in assay.lower()): headerList.append(configMap['nexteraAdapter']) if ('truseq' in assay.lower()): headerList.append(configMap['truSeqAdapter1']) headerList.append(configMap['truSeqAdapter2']) headerList.append('') if int(flowCellDict['INDEXREAD2']) > 0: miSeqDataSection = configMap['nextSeqDataSectionDualRead'].split(',') else: miSeqDataSection = configMap['nextSeqDataSectionSingleRead'].split(',') miSeqDataSection.reverse() headerList.append(miSeqDataSection.pop()) headerList.append(','.join(miSeqDataSection.pop().strip().split())) for key in parentDict.keys(): lane = parentDict[key]['LANE'][-1:] # If no index then just skip this sample if (configMap['index1Name'] not in parentDict[key]) or (parentDict[key][configMap['index1Name']] == 'NOINDEX'): continue index1 = parentDict[key][configMap['index1Name']] if configMap['index2Name'] in parentDict[key]: index2 = parentDict[key][configMap['index2Name']] indexNumber = index2Vocabulary[parentDict[key][configMap['index2Name']]].split()[2] try: kit = parentDict[key][configMap['kit']] prefix = kitsDict[kit][0] except: print "Missing Kit on " + str(key) prefix = "" len_index1 = int(flowCellDict['INDEXREAD']) len_index2 = int(flowCellDict['INDEXREAD2']) if int(flowCellDict['INDEXREAD2']) > 0: sampleSheetDict[lane + '_' + key] = [ lane + separator + key + separator + key + '_' + sanitizeString(parentDict[key][configMap['externalSampleName']]) + '_' + index1[0:len_index1] + '_' + index2[0:len_index2] + separator + separator + separator + index1Vocabulary[index1].split()[1] + separator + index1[0:len_index1] + separator + prefix + indexNumber + separator + get_reverse_complement(index2[0:len_index2]) + separator + key + separator ] else: sampleSheetDict[lane + '_' + key] = [ lane + separator + key + separator + key + '_' + sanitizeString(parentDict[key][configMap['externalSampleName']]) + '_' + index1[0:len_index1] + separator + separator + separator + index1Vocabulary[index1].split()[1] + separator + index1[0:len_index1] + separator + key + separator ] myFileName = myoptions.outdir + configMap['SampleSheetFileName'] + '_' + \ flowCellName + '.csv' sampleSheetFile = writeMiSeqSampleSheet(sampleSheetDict, headerList, flowCellName, myoptions, logger, fileName=myFileName) return sampleSheetFile ''' Main script ''' def main (): logger = setUpLogger('log/') logger.info('Started Creation of Sample Sheet...') myoptions = parseOptions(logger) if myoptions.debug: logger.setLevel(logging.DEBUG) flowCellName = myoptions.flowcell configMap = readConfig(logger) service = login(logger, configMap) foundFlowCell, containedSamples = getFlowCell(configMap['illuminaFlowCellTypeName'], flowCellName, service, logger) parentDict, samplesPerLaneDict = getContainedSampleProperties(containedSamples, service) logger.info('Found ' + str(len(parentDict)) + ' samples on the flow cell ' + flowCellName) flowCellName = foundFlowCell.getCode() if '-' in flowCellName: flowCellName = flowCellName.split('_')[3] elif len(flowCellName) > 12: flowCellName = flowCellName.split('_')[3][1:] else: pass flowCellDict = convertSampleToDict(foundFlowCell) hiseqList = configMap['hiSeqNames'].split() miseqList = configMap['miSeqNames'].split() runFolderName = flowCellDict['Name'] index1Vocabulary = getVocabulary(configMap['index1Name'], service) index2Vocabulary = getVocabulary(configMap['index2Name'], service) SampleSheetFile = createSampleSheet(parentDict, flowCellDict, configMap, index1Vocabulary, index2Vocabulary, flowCellName, logger, myoptions) if myoptions.maillist: sendMail(configMap['mailList'], [SampleSheetFile], flowCellName, configMap, logger) logout(service, logger) if __name__ == "__main__": main()