Skip to content
Snippets Groups Projects
Commit 143ccd9e authored by kohleman's avatar kohleman
Browse files

- some refactoring/renaming 

- added test for a NexSeq and a MiSeq

SVN: 34742
parent e178506e
No related branches found
No related tags found
No related merge requests found
Expand all Hide whitespace changes
Inline Side-by-side
deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
+ 127
− 118
View file @ 143ccd9e
...@@ -77,12 +77,12 @@ class Sequencers: ...@@ -77,12 +77,12 @@ class Sequencers:
HISEQ_LIST = [Sequencers.HISEQ_2000, Sequencers.HISEQ_2500, Sequencers.HISEQ_3000, Sequencers.HISEQ_4000, Sequencers.HISEQ_X] HISEQ_LIST = [Sequencers.HISEQ_2000, Sequencers.HISEQ_2500, Sequencers.HISEQ_3000, Sequencers.HISEQ_4000, Sequencers.HISEQ_X]
def login(logger, configMap): def login(logger, config_dict):
logger.info('Logging into ' + configMap['openbisServer']) logger.info('Logging into ' + config_dict['openbisServer'])
service = OpenbisServiceFacadeFactory.tryCreate(configMap['openbisUserName'], service = OpenbisServiceFacadeFactory.tryCreate(config_dict['openbisUserName'],
configMap['openbisPassword'], config_dict['openbisPassword'],
configMap['openbisServer'], config_dict['openbisServer'],
configMap['connectionTimeout']) config_dict['connectionTimeout'])
return service return service
...@@ -143,8 +143,6 @@ def parseOptions(logger): ...@@ -143,8 +143,6 @@ def parseOptions(logger):
args = parser.parse_args() args = parser.parse_args()
print(type(args))
if args.outdir[-1] <> '/': if args.outdir[-1] <> '/':
args.outdir = args.outdir + '/' args.outdir = args.outdir + '/'
...@@ -170,59 +168,59 @@ def readConfig(logger): ...@@ -170,59 +168,59 @@ def readConfig(logger):
ILLUMINA = 'ILLUMINA' ILLUMINA = 'ILLUMINA'
logger.info('Reading config file') logger.info('Reading config file')
configMap = {} config_dict = {}
configParameters = parseConfigurationFile() configParameters = parseConfigurationFile()
configMap['facilityName'] = configParameters.get(GENERAL, 'facilityName') config_dict['facilityName'] = configParameters.get(GENERAL, 'facilityName')
configMap['facilityNameShort'] = configParameters.get(GENERAL, 'facilityNameShort') config_dict['facilityNameShort'] = configParameters.get(GENERAL, 'facilityNameShort')
configMap['facilityInstitution'] = configParameters.get(GENERAL, 'facilityInstitution') config_dict['facilityInstitution'] = configParameters.get(GENERAL, 'facilityInstitution')
configMap['mailList'] = configParameters.get(GENERAL, 'mailList') config_dict['mailList'] = configParameters.get(GENERAL, 'mailList')
configMap['mailFrom'] = configParameters.get(GENERAL, 'mailFrom') config_dict['mailFrom'] = configParameters.get(GENERAL, 'mailFrom')
configMap['smptHost'] = configParameters.get(GENERAL, 'smptHost') config_dict['smptHost'] = configParameters.get(GENERAL, 'smptHost')
configMap['SampleSheetFileName'] = configParameters.get(GENERAL, 'SampleSheetFileName') config_dict['SampleSheetFileName'] = configParameters.get(GENERAL, 'SampleSheetFileName')
configMap['separator'] = configParameters.get(GENERAL, 'separator') config_dict['separator'] = configParameters.get(GENERAL, 'separator')
configMap['indexSeparator'] = configParameters.get(GENERAL, 'indexSeparator') config_dict['indexSeparator'] = configParameters.get(GENERAL, 'indexSeparator')
configMap['openbisUserName'] = configParameters.get(OPENBIS, 'openbisUserName') config_dict['openbisUserName'] = configParameters.get(OPENBIS, 'openbisUserName')
configMap['openbisPassword'] = configParameters.get(OPENBIS, 'openbisPassword', raw=True) config_dict['openbisPassword'] = configParameters.get(OPENBIS, 'openbisPassword', raw=True)
configMap['openbisServer'] = configParameters.get(OPENBIS, 'openbisServer') config_dict['openbisServer'] = configParameters.get(OPENBIS, 'openbisServer')
configMap['connectionTimeout'] = configParameters.getint(OPENBIS, 'connectionTimeout') config_dict['connectionTimeout'] = configParameters.getint(OPENBIS, 'connectionTimeout')
configMap['illuminaFlowCellTypeName'] = configParameters.get(OPENBIS, 'illuminaFlowCellTypeName') config_dict['illuminaFlowCellTypeName'] = configParameters.get(OPENBIS, 'illuminaFlowCellTypeName')
configMap['index1Name'] = configParameters.get(OPENBIS, 'index1Name') config_dict['index1Name'] = configParameters.get(OPENBIS, 'index1Name')
configMap['index2Name'] = configParameters.get(OPENBIS, 'index2Name') config_dict['index2Name'] = configParameters.get(OPENBIS, 'index2Name')
configMap['index1Length'] = configParameters.get(OPENBIS, 'index1Length') config_dict['index1Length'] = configParameters.get(OPENBIS, 'index1Length')
configMap['index2Length'] = configParameters.get(OPENBIS, 'index2Length') config_dict['index2Length'] = configParameters.get(OPENBIS, 'index2Length')
configMap['endType'] = configParameters.get(OPENBIS, 'endType') config_dict['endType'] = configParameters.get(OPENBIS, 'endType')
configMap['cycles'] = configParameters.get(OPENBIS, 'cycles') config_dict['cycles'] = configParameters.get(OPENBIS, 'cycles')
configMap['controlLane'] = configParameters.get(OPENBIS, 'controlLane') config_dict['controlLane'] = configParameters.get(OPENBIS, 'controlLane')
configMap['ncbi'] = configParameters.get(OPENBIS, 'ncbi') config_dict['ncbi'] = configParameters.get(OPENBIS, 'ncbi')
configMap['externalSampleName'] = configParameters.get(OPENBIS, 'externalSampleName') config_dict['externalSampleName'] = configParameters.get(OPENBIS, 'externalSampleName')
configMap['laneCount'] = configParameters.get(OPENBIS, 'laneCount') config_dict['laneCount'] = configParameters.get(OPENBIS, 'laneCount')
configMap['kit'] = configParameters.get(OPENBIS, 'kit') config_dict['kit'] = configParameters.get(OPENBIS, 'kit')
configMap['headerSection'] = configParameters.get(ILLUMINA, 'headerSection') config_dict['headerSection'] = configParameters.get(ILLUMINA, 'headerSection')
configMap['readsSection'] = configParameters.get(ILLUMINA, 'readsSection') config_dict['readsSection'] = configParameters.get(ILLUMINA, 'readsSection')
configMap['settingsSection'] = configParameters.get(ILLUMINA, 'settingsSection') config_dict['settingsSection'] = configParameters.get(ILLUMINA, 'settingsSection')
configMap['dataSectionSingleRead'] = configParameters.get(ILLUMINA, 'dataSectionSingleRead') config_dict['dataSectionSingleRead'] = configParameters.get(ILLUMINA, 'dataSectionSingleRead')
configMap['dataSectionDualRead'] = configParameters.get(ILLUMINA, 'dataSectionDualRead') config_dict['dataSectionDualRead'] = configParameters.get(ILLUMINA, 'dataSectionDualRead')
configMap['workflow'] = configParameters.get(ILLUMINA, 'workflow') config_dict['workflow'] = configParameters.get(ILLUMINA, 'workflow')
configMap['application'] = configParameters.get(ILLUMINA, 'application') config_dict['application'] = configParameters.get(ILLUMINA, 'application')
configMap['chemistry'] = configParameters.get(ILLUMINA, 'chemistry') config_dict['chemistry'] = configParameters.get(ILLUMINA, 'chemistry')
configMap['truSeqAdapter1'] = configParameters.get(ILLUMINA, 'truSeqAdapter1') config_dict['truSeqAdapter1'] = configParameters.get(ILLUMINA, 'truSeqAdapter1')
configMap['truSeqAdapter2'] = configParameters.get(ILLUMINA, 'truSeqAdapter2') config_dict['truSeqAdapter2'] = configParameters.get(ILLUMINA, 'truSeqAdapter2')
configMap['nexteraAdapter'] = configParameters.get(ILLUMINA, 'nexteraAdapter') config_dict['nexteraAdapter'] = configParameters.get(ILLUMINA, 'nexteraAdapter')
configMap['iemFileVersion'] = configParameters.get(ILLUMINA, 'iemFileVersion') config_dict['iemFileVersion'] = configParameters.get(ILLUMINA, 'iemFileVersion')
configMap['configureBclToFastqPath'] = configParameters.get(ILLUMINA, 'configureBclToFastqPath') config_dict['configureBclToFastqPath'] = configParameters.get(ILLUMINA, 'configureBclToFastqPath')
configMap['failedReads'] = configParameters.get(ILLUMINA, 'failedReads') config_dict['failedReads'] = configParameters.get(ILLUMINA, 'failedReads')
configMap['clusterCount'] = configParameters.get(ILLUMINA, 'clusterCount') config_dict['clusterCount'] = configParameters.get(ILLUMINA, 'clusterCount')
configMap['clusterCountNumber'] = configParameters.get(ILLUMINA, 'clusterCountNumber') config_dict['clusterCountNumber'] = configParameters.get(ILLUMINA, 'clusterCountNumber')
configMap['outputDir'] = configParameters.get(ILLUMINA, 'outputDir') config_dict['outputDir'] = configParameters.get(ILLUMINA, 'outputDir')
configMap['sampleSheetName'] = configParameters.get(ILLUMINA, 'sampleSheetName') config_dict['sampleSheetName'] = configParameters.get(ILLUMINA, 'sampleSheetName')
configMap['baseMask'] = configParameters.get(ILLUMINA, 'baseMask') config_dict['baseMask'] = configParameters.get(ILLUMINA, 'baseMask')
return configMap return config_dict
def getDate(): def getDate():
...@@ -254,7 +252,7 @@ def get_vocabulary(vocabulary_code, service): ...@@ -254,7 +252,7 @@ def get_vocabulary(vocabulary_code, service):
return vocabulary_dict return vocabulary_dict
def send_email(emails, files, flowCellName, configMap, logger): def send_email(emails, files, flowCellName, config_dict, logger):
""" """
Send out an email to the specified recipients Send out an email to the specified recipients
""" """
...@@ -262,7 +260,7 @@ def send_email(emails, files, flowCellName, configMap, logger): ...@@ -262,7 +260,7 @@ def send_email(emails, files, flowCellName, configMap, logger):
emails_list = emails.split() emails_list = emails.split()
msg = MIMEMultipart() msg = MIMEMultipart()
msg['From'] = configMap['mailFrom'] msg['From'] = config_dict['mailFrom']
msg['To'] = COMMASPACE.join(emails_list) msg['To'] = COMMASPACE.join(emails_list)
msg['Date'] = formatdate(localtime=True) msg['Date'] = formatdate(localtime=True)
msg['Subject'] = 'Generated Sample Sheet for flowcell ' + flowCellName msg['Subject'] = 'Generated Sample Sheet for flowcell ' + flowCellName
...@@ -276,8 +274,8 @@ def send_email(emails, files, flowCellName, configMap, logger): ...@@ -276,8 +274,8 @@ def send_email(emails, files, flowCellName, configMap, logger):
part.add_header('Content-Disposition', 'attachment; filename="%s"' % os.path.basename(f)) part.add_header('Content-Disposition', 'attachment; filename="%s"' % os.path.basename(f))
msg.attach(part) msg.attach(part)
smtp = smtplib.SMTP(configMap['smptHost']) smtp = smtplib.SMTP(config_dict['smptHost'])
smtp.sendmail(configMap['mailFrom'], emails_list, msg.as_string()) smtp.sendmail(config_dict['mailFrom'], emails_list, msg.as_string())
smtp.close() smtp.close()
logger.info('Sent email to ' + COMMASPACE.join(emails_list)) logger.info('Sent email to ' + COMMASPACE.join(emails_list))
...@@ -389,7 +387,8 @@ def get_contained_sample_properties(contained_samples, service): ...@@ -389,7 +387,8 @@ def get_contained_sample_properties(contained_samples, service):
try: try:
assert parents.size() >= 1 assert parents.size() >= 1
except AssertionError: except AssertionError:
print (str(parents.size()) + ' parents found for lane ' + lane.getCode()) pass
# print (str(parents.size()) + ' parents found for lane ' + lane.getCode())
samplesPerLaneDict[lane.getCode()[-1]] = len(parents) samplesPerLaneDict[lane.getCode()[-1]] = len(parents)
...@@ -445,13 +444,18 @@ def write_sample_sheet(sampleSheetDict, headerList, myoptions, logger, fileName) ...@@ -445,13 +444,18 @@ def write_sample_sheet(sampleSheetDict, headerList, myoptions, logger, fileName)
return fileName return fileName
def write_sample_sheet_single_lane(ordered_sample_sheet_dict, flowCellDict, def write_sample_sheet_single_lane(model, ordered_sample_sheet_dict, flowCellDict, index_length_dict,
parentDict, configMap, myoptions, logger, csv_file): parentDict, config_dict, myoptions, logger, csv_file):
newline = lineending[myoptions.lineending] newline = lineending[myoptions.lineending]
header_list = create_header_section (configMap, parentDict, flowCellDict)
if (model is Sequencers.NEXTSEQ_500):
lane_number = 2
else:
lane_number = int(flowCellDict[config_dict['laneCount']]) + 1
for lane in range(1, int(flowCellDict[configMap['laneCount']]) + 1): for lane in range(1, lane_number):
header_list = create_header_section (model, config_dict, parentDict, flowCellDict, index_length_dict, lane)
per_lane_dict = [ordered_sample_sheet_dict[key] for key in ordered_sample_sheet_dict.keys() if int(key[0]) == lane] per_lane_dict = [ordered_sample_sheet_dict[key] for key in ordered_sample_sheet_dict.keys() if int(key[0]) == lane]
csv_file_path = myoptions.outdir + csv_file + "_" + str(lane) + CSV csv_file_path = myoptions.outdir + csv_file + "_" + str(lane) + CSV
try: try:
...@@ -465,7 +469,7 @@ def write_sample_sheet_single_lane(ordered_sample_sheet_dict, flowCellDict, ...@@ -465,7 +469,7 @@ def write_sample_sheet_single_lane(ordered_sample_sheet_dict, flowCellDict,
print ('File error: ' + str(err)) print ('File error: ' + str(err))
def create_header_section (configMap, parentDict, flowCellDict): def create_header_section (model, config_dict, parentDict, flowCellDict, index_length_dict, lane):
kitsDict = {"CHIP_SEQ_SAMPLE_PREP" : ["",""], kitsDict = {"CHIP_SEQ_SAMPLE_PREP" : ["",""],
"TRUSEQ_RNA_SAMPLEPREPKIT_V2_ILLUMINA" : ["A","TruSeq LT"], "TRUSEQ_RNA_SAMPLEPREPKIT_V2_ILLUMINA" : ["A","TruSeq LT"],
...@@ -490,62 +494,71 @@ def create_header_section (configMap, parentDict, flowCellDict): ...@@ -490,62 +494,71 @@ def create_header_section (configMap, parentDict, flowCellDict):
"NEXTERA_DNA_SAMPLE_PREP_KIT_BUFFER_HMW" : ["N", "Nextera"] "NEXTERA_DNA_SAMPLE_PREP_KIT_BUFFER_HMW" : ["N", "Nextera"]
} }
separator = configMap['separator'] separator = config_dict['separator']
header_list = [] header_list = []
len_index1 = index_length_dict[int(lane)][0]
len_index2 = index_length_dict[int(lane)][1]
# here we take the first sample to determine the Sample Prep Kit # here we take the first sample to determine the Sample Prep Kit
try: try:
assay = kitsDict [parentDict.itervalues().next()[configMap['kit']]][1] assay = kitsDict [parentDict.itervalues().next()[config_dict['kit']]][1]
except: except:
print "No Kit set for sample. Will not set the assay value in the sample sheet" # print "No Kit set for sample. Will not set the assay value in the sample sheet"
assay = "" assay = ""
header_section = configMap['headerSection'].split(separator) header_section = config_dict['headerSection'].split(separator)
header_section.reverse() header_section.reverse()
header_list = [header_section.pop().strip()] header_list = [header_section.pop().strip()]
header_list.append(header_section.pop().strip() + separator + configMap['iemFileVersion']) header_list.append(header_section.pop().strip() + separator + config_dict['iemFileVersion'])
header_list.append(header_section.pop().strip() + separator + configMap['facilityInstitution']) header_list.append(header_section.pop().strip() + separator + config_dict['facilityInstitution'])
header_list.append(header_section.pop().strip() + separator + configMap['facilityName']) header_list.append(header_section.pop().strip() + separator + config_dict['facilityName'])
header_list.append(header_section.pop().strip() + separator + flowCellDict['Name']) header_list.append(header_section.pop().strip() + separator + flowCellDict['Name'])
header_list.append(header_section.pop().strip() + separator + datetime.now().strftime('%m/%d/%Y')) header_list.append(header_section.pop().strip() + separator + datetime.now().strftime('%m/%d/%Y'))
header_list.append(header_section.pop().strip() + separator + configMap['workflow']) header_list.append(header_section.pop().strip() + separator + config_dict['workflow'])
header_list.append(header_section.pop().strip() + separator + configMap['application']) header_list.append(header_section.pop().strip() + separator + config_dict['application'])
header_list.append(header_section.pop().strip() + separator + assay) header_list.append(header_section.pop().strip() + separator + assay)
header_list.append(header_section.pop().strip() + separator + flowCellDict[configMap['endType']] + '_' + flowCellDict[configMap['cycles']]) header_list.append(header_section.pop().strip() + separator + flowCellDict[config_dict['endType']] + '_' + flowCellDict[config_dict['cycles']])
header_list.append(header_section.pop().strip() + separator + configMap['chemistry']) header_list.append(header_section.pop().strip() + separator + config_dict['chemistry'])
header_list.append('') header_list.append('')
reads_section = configMap['readsSection'].split(separator) reads_section = config_dict['readsSection'].split(separator)
reads_section.reverse() reads_section.reverse()
header_list.append(reads_section.pop()) header_list.append(reads_section.pop())
header_list.append(flowCellDict[configMap['cycles']]) header_list.append(flowCellDict[config_dict['cycles']])
if (flowCellDict[configMap['endType']] == 'PAIRED_END'): if (flowCellDict[config_dict['endType']] == 'PAIRED_END'):
header_list.append(flowCellDict[configMap['cycles']]) header_list.append(flowCellDict[config_dict['cycles']])
header_list.append('') header_list.append('')
settings_section = configMap['settingsSection'].split(separator) settings_section = config_dict['settingsSection'].split(separator)
settings_section.reverse() settings_section.reverse()
header_list.append(settings_section.pop()) header_list.append(settings_section.pop())
if ('nextera' in assay.lower()): if ('nextera' in assay.lower()):
header_list.append(configMap['nexteraAdapter']) header_list.append(config_dict['nexteraAdapter'])
if ('truseq' in assay.lower()): if ('truseq' in assay.lower()):
header_list.append(configMap['truSeqAdapter1']) header_list.append(config_dict['truSeqAdapter1'])
header_list.append(configMap['truSeqAdapter2']) header_list.append(config_dict['truSeqAdapter2'])
header_list.append('') header_list.append('')
if int(flowCellDict['INDEXREAD2']) > 0: if int(flowCellDict['INDEXREAD2']) > 0 and len_index2 > 0:
SeqDataSection = configMap['dataSectionDualRead'].split(',') SeqDataSection = config_dict['dataSectionDualRead'].split(',')
else: else:
SeqDataSection = configMap['dataSectionSingleRead'].split(',') SeqDataSection = config_dict['dataSectionSingleRead'].split(',')
SeqDataSection.reverse() SeqDataSection.reverse()
header_list.append(SeqDataSection.pop()) header_list.append(SeqDataSection.pop())
header_list.append(','.join(SeqDataSection.pop().strip().split()))
if model in Sequencers.NEXTSEQ_500:
# leaving out the 'Lane', as there are four but treat them as one
header_list.append(','.join(SeqDataSection.pop().strip().split()[1:]))
else:
header_list.append(','.join(SeqDataSection.pop().strip().split()))
return header_list return header_list
def verify_index_length (parentDict, flowCellDict, configMap, logger): def verify_index_length (parentDict, flowCellDict, config_dict, logger):
index_length_dict = {} index_length_dict = {}
verified_per_lane_dict = [] verified_per_lane_dict = []
...@@ -553,7 +566,7 @@ def verify_index_length (parentDict, flowCellDict, configMap, logger): ...@@ -553,7 +566,7 @@ def verify_index_length (parentDict, flowCellDict, configMap, logger):
flowcell_len_index1 = int(flowCellDict['INDEXREAD']) flowcell_len_index1 = int(flowCellDict['INDEXREAD'])
flowcell_len_index2 = int(flowCellDict['INDEXREAD2']) flowcell_len_index2 = int(flowCellDict['INDEXREAD2'])
print("Flowcell has index length [" + str(flowcell_len_index1) + ", " + str(flowcell_len_index2) + "]") logger.info("Flowcell has index length [" + str(flowcell_len_index1) + ", " + str(flowcell_len_index2) + "]")
for lane in range(1,int(flowCellDict['LANECOUNT'])+1): for lane in range(1,int(flowCellDict['LANECOUNT'])+1):
index1_set = set () index1_set = set ()
...@@ -566,12 +579,12 @@ def verify_index_length (parentDict, flowCellDict, configMap, logger): ...@@ -566,12 +579,12 @@ def verify_index_length (parentDict, flowCellDict, configMap, logger):
for sample in per_lane_list: for sample in per_lane_list:
# If no index then just skip this sample # If no index then just skip this sample
if (configMap['index1Name'] not in sample) or (sample[configMap['index1Name']] == 'NOINDEX'): if (config_dict['index1Name'] not in sample) or (sample[config_dict['index1Name']] == 'NOINDEX'):
continue continue
index1 = sample[configMap['index1Name']] index1 = sample[config_dict['index1Name']]
index2="" index2=""
if configMap['index2Name'] in sample: if config_dict['index2Name'] in sample:
index2 = sample[configMap['index2Name']] index2 = sample[config_dict['index2Name']]
index1_set.add(len(index1)) index1_set.add(len(index1))
if index2: if index2:
...@@ -599,28 +612,25 @@ def verify_index_length (parentDict, flowCellDict, configMap, logger): ...@@ -599,28 +612,25 @@ def verify_index_length (parentDict, flowCellDict, configMap, logger):
return index_length_dict return index_length_dict
def create_sample_sheet_dict(model, parentDict, flowCellDict, configMap, index1Vocabulary, def create_sample_sheet_dict(model, parentDict, index_length_dict, flowCellDict, config_dict, index1Vocabulary,
index2Vocabulary, flowCellName, logger): index2Vocabulary, flowCellName, logger):
sampleSheetDict = {} sampleSheetDict = {}
separator = configMap['separator'] separator = config_dict['separator']
index_length_dict = verify_index_length(parentDict, flowCellDict, configMap, logger)
print(index_length_dict)
for key in parentDict.keys(): for key in parentDict.keys():
lane = parentDict[key]['LANE'][-1:] lane = parentDict[key]['LANE'][-1:]
# If no index then just skip this sample # If no index then just skip this sample
if (configMap['index1Name'] not in parentDict[key]) or (parentDict[key][configMap['index1Name']] == 'NOINDEX'): if (config_dict['index1Name'] not in parentDict[key]) or (parentDict[key][config_dict['index1Name']] == 'NOINDEX'):
continue continue
index1 = parentDict[key][configMap['index1Name']] index1 = parentDict[key][config_dict['index1Name']]
index2="" index2=""
if configMap['index2Name'] in parentDict[key]: if config_dict['index2Name'] in parentDict[key]:
index2 = parentDict[key][configMap['index2Name']] index2 = parentDict[key][config_dict['index2Name']]
indexNumber = index2Vocabulary[parentDict[key][configMap['index2Name']]].split()[2] indexNumber = index2Vocabulary[parentDict[key][config_dict['index2Name']]].split()[2]
try: try:
kit = parentDict[key][configMap['kit']] kit = parentDict[key][config_dict['kit']]
prefix = kitsDict[kit][0] prefix = kitsDict[kit][0]
except: except:
# print "Missing Kit on " + str(key) # print "Missing Kit on " + str(key)
...@@ -642,7 +652,7 @@ def create_sample_sheet_dict(model, parentDict, flowCellDict, configMap, index1V ...@@ -642,7 +652,7 @@ def create_sample_sheet_dict(model, parentDict, flowCellDict, configMap, index1V
sampleSheetDict[lane + '_' + key] = [ sampleSheetDict[lane + '_' + key] = [
lane_string lane_string
+ key + separator + key + separator
+ key + '_' + sanitize_string(parentDict[key][configMap['externalSampleName']]) + '_' + index1[0:len_index1] + '_' + index2[0:len_index2] + separator + key + '_' + sanitize_string(parentDict[key][config_dict['externalSampleName']]) + '_' + index1[0:len_index1] + '_' + index2[0:len_index2] + separator
+ separator + separator
+ separator + separator
+ index1Vocabulary[index1].split()[1] + separator + index1Vocabulary[index1].split()[1] + separator
...@@ -655,7 +665,7 @@ def create_sample_sheet_dict(model, parentDict, flowCellDict, configMap, index1V ...@@ -655,7 +665,7 @@ def create_sample_sheet_dict(model, parentDict, flowCellDict, configMap, index1V
sampleSheetDict[lane + '_' + key] = [ sampleSheetDict[lane + '_' + key] = [
lane_string lane_string
+ key + separator + key + separator
+ key + '_' + sanitize_string(parentDict[key][configMap['externalSampleName']]) + '_' + index1[0:len_index1] + separator + key + '_' + sanitize_string(parentDict[key][config_dict['externalSampleName']]) + '_' + index1[0:len_index1] + separator
+ separator + separator
+ separator + separator
+ index1Vocabulary[index1].split()[1] + separator + index1Vocabulary[index1].split()[1] + separator
...@@ -663,7 +673,7 @@ def create_sample_sheet_dict(model, parentDict, flowCellDict, configMap, index1V ...@@ -663,7 +673,7 @@ def create_sample_sheet_dict(model, parentDict, flowCellDict, configMap, index1V
+ key + separator + key + separator
] ]
csv_file_name = configMap['SampleSheetFileName'] + '_' + flowCellName csv_file_name = config_dict['SampleSheetFileName'] + '_' + flowCellName
ordered_sample_sheet_dict = OrderedDict(sorted(sampleSheetDict.items(), key=lambda t: t[0])) ordered_sample_sheet_dict = OrderedDict(sorted(sampleSheetDict.items(), key=lambda t: t[0]))
return ordered_sample_sheet_dict, csv_file_name return ordered_sample_sheet_dict, csv_file_name
...@@ -689,8 +699,6 @@ def main (): ...@@ -689,8 +699,6 @@ def main ():
foundFlowCell, containedSamples = get_flowcell(config_dict['illuminaFlowCellTypeName'], flowCellName, foundFlowCell, containedSamples = get_flowcell(config_dict['illuminaFlowCellTypeName'], flowCellName,
service, logger) service, logger)
parentDict, samplesPerLaneDict = get_contained_sample_properties(containedSamples, service) parentDict, samplesPerLaneDict = get_contained_sample_properties(containedSamples, service)
logger.info('Found ' + str(len(parentDict)) + ' samples on the flow cell ' + flowCellName)
flowCellName = foundFlowCell.getCode() flowCellName = foundFlowCell.getCode()
flowCellDict = transform_sample_to_dict(foundFlowCell) flowCellDict = transform_sample_to_dict(foundFlowCell)
model = get_model(flowCellDict['RUN_NAME_FOLDER']) model = get_model(flowCellDict['RUN_NAME_FOLDER'])
...@@ -699,14 +707,15 @@ def main (): ...@@ -699,14 +707,15 @@ def main ():
index1Vocabulary = get_vocabulary(config_dict['index1Name'], service) index1Vocabulary = get_vocabulary(config_dict['index1Name'], service)
index2Vocabulary = get_vocabulary(config_dict['index2Name'], service) index2Vocabulary = get_vocabulary(config_dict['index2Name'], service)
ordered_sample_sheet_dict, csv_file_name = create_sample_sheet_dict(model, parentDict, index_length_dict = verify_index_length(parentDict, flowCellDict, config_dict, logger)
ordered_sample_sheet_dict, csv_file_name = create_sample_sheet_dict(model, parentDict, index_length_dict,
flowCellDict, config_dict, index1Vocabulary, index2Vocabulary, flowCellName, logger) flowCellDict, config_dict, index1Vocabulary, index2Vocabulary, flowCellName, logger)
if myoptions.singlelane: if myoptions.singlelane:
write_sample_sheet_single_lane(ordered_sample_sheet_dict, flowCellDict, write_sample_sheet_single_lane(model, ordered_sample_sheet_dict, flowCellDict, index_length_dict,
parentDict, config_dict, myoptions, logger, csv_file_name) parentDict, config_dict, myoptions, logger, csv_file_name)
else: else:
header_list = create_header_section (config_dict, parentDict, flowCellDict) header_list = create_header_section (model, config_dict, parentDict, flowCellDict, index_length_dict, samplesPerLaneDict.keys()[0])
sampleSheetFile = write_sample_sheet(ordered_sample_sheet_dict, header_list, sampleSheetFile = write_sample_sheet(ordered_sample_sheet_dict, header_list,
myoptions, logger, myoptions.outdir + csv_file_name + CSV) myoptions, logger, myoptions.outdir + csv_file_name + CSV)
if myoptions.maillist: if myoptions.maillist:
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment