'''
@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 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
from java.util import EnumSet
lineending = {'win32':'\r\n', 'linux':'\n', 'mac':'\r'}
COMMA = ','
def login(configMap, logger):
logger.info('Logging into ' + configMap['openbisServer'])
try:
service = OpenbisServiceFacadeFactory.tryCreate(configMap['openbisUserName'],
configMap['openbisPassword'],
configMap['openbisServer'],
configMap['connectionTimeout'])
except:
raise ('Could not connect to ' + configMap['openbisServer'] + '. Please check if the server ' +
'address is OK, the firewall is not blocking the communication or openBIS is down.')
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('-l', '--lineending',
dest='lineending',
type='choice',
action='store',
choices=['win32', 'linux', 'mac'],
default='linux',
help='Specify end of line separator: win32, linux, mac. Default: linux' ,
metavar='<lineending>')
parser.add_option('-o', '--outdir',
dest='outdir',
default='./',
help='Specify the ouput directory. Default: ./' ,
metavar='<outdir>')
parser.add_option('-d', '--debug',
dest='debug',
default=False,
action='store_true',
help='Verbose debug logging. 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(logger, propertyFile='etc/createSampleSheet_nov.properties'):
'''
Parses the given config files and returns the values
'''
logger.info('Reading config file ' + propertyFile)
config = SafeConfigParser()
config.read(propertyFile)
config.sections()
return config
def readConfig(logger):
GENERAL = 'GENERAL'
OPENBIS = 'OPENBIS'
ILLUMINA = 'ILLUMINA'
configMap = {}
logger.info('Reading config file')
configParameters = parseConfigurationFile(logger)
configMap['facilityName'] = configParameters.get(GENERAL, 'facilityName')
configMap['facilityNameShort'] = configParameters.get(GENERAL, 'facilityNameShort')
configMap['facilityInstitution'] = configParameters.get(GENERAL, 'facilityInstitution')
configMap['sampleSheetFileName'] = configParameters.get(GENERAL, 'sampleSheetFileName')
configMap['lanePrefix'] = configParameters.get(GENERAL, 'lanePrefix')
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['species'] = configParameters.get(OPENBIS, 'species')
configMap['sampleName'] = configParameters.get(OPENBIS, 'sampleName')
configMap['operator'] = configParameters.get(OPENBIS, 'operator')
configMap['endType'] = configParameters.get(OPENBIS, 'endType')
configMap['readLength'] = configParameters.get(OPENBIS, 'readLength')
configMap['lengthIndex1'] = configParameters.get(OPENBIS, 'lengthIndex1')
configMap['lengthIndex2'] = configParameters.get(OPENBIS, 'lengthIndex2')
configMap['gaNumber'] = configParameters.get(OPENBIS, 'gaNumber')
configMap['hiSeqNames'] = configParameters.get(ILLUMINA, 'hiSeqNames')
configMap['hiSeqHeader'] = configParameters.get(ILLUMINA, 'hiSeqHeader')
return configMap
def sanitizeString(myString):
return re.sub('[^A-Za-z0-9]+', '_', myString)
def getVocabulary(vocabularyCode):
''' 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 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)
# 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(logger, containedSamples, service):
'''
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
'''
laneParentDict = {}
for lane in containedSamples:
parents = getParents (lane.getCode(), service)
for parent in parents:
parentCode = parent.getCode()
parentProperties = parent.getProperties()
propertyDict = {}
for property in parentProperties:
propertyDict[property] = parentProperties.get(property)
propertyDict['LANE'] = lane.getCode()
propertyDict['SAMPLE_TYPE'] = parent.getSampleTypeCode()
myKey = sanitizeString(parentCode + '_' + lane.getCode())
laneParentDict[myKey] = propertyDict
logger.info('Found ' + str(len(laneParentDict)) + ' samples on the flow cell.')
return laneParentDict
def convertSampleToDict(foundFlowCell, configMap):
'''
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['Name'] = foundFlowCell.getIdentifier().split('/')[-1]
flowCellDict['CODE'] = foundFlowCell.getCode()
return flowCellDict
def getIndex(indx1, indx2, index1ReadLength, indexRead2Length, properties, configMap):
if indx1 in properties and index1ReadLength > 0:
index = properties[indx1][0:index1ReadLength]
else:
index = ''
if indx2 in properties and indexRead2Length > 0:
index = index + configMap['indexSeparator'] + properties[indx2][0:index1ReadLength]
return index
def getSampleProperties(parentsKey, service, logger):
for sample in parentsKey:
sampleProperties = sample.getProperties()
logger.debug(sample.getSampleTypeCode() + ' ' + sample.getCode())
parentSamples = getParents(sample.getCode(), service)
for parentSample in parentSamples:
logger.debug(parentSample.getSampleTypeCode() + ' ' + parentSample.getCode())
parentSampleProperties = parentSample.getProperties()
return parentSample, parentSampleProperties
def createSampleSheetDict(configMap, control, sampleSheetDict, flowCellName, flowCellOperator,
end_type, cycles, lane, gaNumber, index, sample, sampleProperties):
sampleSheetDict[lane + '_' + sample.getCode()] = [
flowCellName + COMMA + configMap['lanePrefix'] + lane + COMMA + sample.getCode() + COMMA +
sampleProperties[configMap['species']] + COMMA + index + COMMA +
sanitizeString(sampleProperties[configMap['sampleName']]) + COMMA + control + COMMA +
end_type + '_' + cycles + COMMA + flowCellOperator + COMMA + gaNumber]
def createHiseqSampleSheet(laneParentDict, flowCellDict, configMap, service, logger, myoptions):
'''
Builds up a dictionary with all entries in the Sample Sheet
'''
control = 'N'
# the illlumina pipeline uses always one base less than the sequencer is sequencing
demultiplexIndexLengthPenalty = 0
sampleSheetDict = {}
# Making sure this is on the top of the Sample Sheet
sampleSheetDict[u'!'] = ([configMap['hiSeqHeader']])
indx1 = configMap['index1Name']
indx2 = configMap['index2Name']
flowCellName = flowCellDict['CODE']
flowCellOperator = flowCellDict[configMap['operator']]
end_type = flowCellDict[configMap['endType']]
cycles = flowCellDict[configMap['readLength']]
index1ReadLength = int(flowCellDict[configMap['lengthIndex1']]) + demultiplexIndexLengthPenalty
indexRead2Length = int(flowCellDict[configMap['lengthIndex2']]) + demultiplexIndexLengthPenalty
for key in laneParentDict.keys():
lane = laneParentDict[key]['LANE'][-1:]
properties = laneParentDict[key]
sampleName = laneParentDict[key]['LIBRARYID']
# already Library with index
if indx1 in properties:
gaNumber = laneParentDict[key][configMap['gaNumber']]
index = getIndex(indx1, indx2, index1ReadLength, indexRead2Length, properties, configMap)
sample, sampleProperties = getSampleProperties(getParents(sampleName, service), service, logger)
createSampleSheetDict(configMap, control, sampleSheetDict, flowCellName, flowCellOperator,
end_type, cycles, lane, gaNumber, index, sample, sampleProperties)
else:
for library in getParents(sampleName, service):
libraryProperties = library.getProperties()
gaNumber = libraryProperties[configMap['gaNumber']]
if not gaNumber:
logger.warning('No GA number found for ' + library.getCode())
index = getIndex(indx1, indx2, index1ReadLength, indexRead2Length, libraryProperties, configMap)
if not index:
logger.warning('No index found for ' + library.getCode())
sample, sampleProperties = getSampleProperties(getParents(library.getCode(), service), service, logger)
createSampleSheetDict(configMap, control, sampleSheetDict, flowCellName, flowCellOperator,
end_type, cycles, lane, gaNumber, index, sample, sampleProperties)
logger.debug(sampleSheetDict)
sortedSampleSheetList = sampleSheetDict.keys()
sortedSampleSheetList.sort()
writeSampleSheet(flowCellName, sampleSheetDict, sortedSampleSheetList, myoptions, logger, fileName=myoptions.outdir +
configMap['sampleSheetFileName'])
def writeSampleSheet(flowCellName, sampleSheetDict, sortedSampleSheetList, myoptions, logger, fileName):
'''
Write the given dictionary to a csv file
'''
newline = lineending[myoptions.lineending]
myFile = fileName + '_' + flowCellName + '.csv'
try:
with open(myFile, 'w') as sampleSheetFile:
for listElement in sortedSampleSheetList:
sampleSheetFile.write(sampleSheetDict[listElement][0] + newline)
logger.info('Writing file ' + myFile)
print ('Written ' + myFile)
except IOError:
logger.error('File error: ' + str(err))
print ('File error: ' + str(err))
def main():
'''
Main script
'''
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(configMap, logger)
foundFlowCell, containedSamples = getFlowCell(configMap['illuminaFlowCellTypeName'], flowCellName, service, logger)
flowCellName = foundFlowCell.getCode()
flowCellDict = convertSampleToDict(foundFlowCell, configMap)
laneParentDict = getContainedSampleProperties(logger, containedSamples, service)
createHiseqSampleSheet(laneParentDict, flowCellDict, configMap, service, logger, myoptions)
logout(service, logger)
print('DONE')
if __name__ == "__main__":
main()