'''
@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='<flowcell>')
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='<maillist>')
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='<lineending>')
parser.add_option('-o', '--outdir',
dest='outdir',
default='./',
help='Specify the ouput directory. Default: ./' ,
metavar='<outdir>')
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['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 <type 'ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample'> 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 createMiSeqSampleSheet(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['miSeqDataSectionDualRead'].split(',')
else:
miSeqDataSection = configMap['miSeqDataSectionSingleRead'].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] = [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] = [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 = createMiSeqSampleSheet(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()