From 47f3903463ea552593ca53b83f2726d15876b41a Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Thu, 15 Dec 2016 12:41:15 +0000
Subject: [PATCH] minor: small code cleanups
SVN: 37508
---
.../Jython/createSampleSheet_bcl2fastq.py | 89 ++++++++++---------
1 file changed, 48 insertions(+), 41 deletions(-)
diff --git a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
index ecebfb2db2b..774f9a843dd 100644
--- a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
+++ b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
@@ -71,8 +71,8 @@ CSV = ".csv"
class Sequencers:
- HISEQ_4000, HISEQ_3000, HISEQ_2500, HISEQ_2000, HISEQ_X, NEXTSEQ_500, MISEQ , UNIDENTIFIED= \
- ('Illumina HiSeq 4000','Illumina HiSeq 3000','Illumina HiSeq 2500','Illumina HiSeq 2000',
+ HISEQ_4000, HISEQ_3000, HISEQ_2500, HISEQ_2000, HISEQ_X, NEXTSEQ_500, MISEQ , UNIDENTIFIED = \
+ ('Illumina HiSeq 4000', 'Illumina HiSeq 3000', 'Illumina HiSeq 2500', 'Illumina HiSeq 2000',
'Illumina HiSeq X', 'Illumina NextSeq 500', 'Illumina MiSeq', 'Unidentified')
HISEQ_LIST = [Sequencers.HISEQ_2000, Sequencers.HISEQ_2500, Sequencers.HISEQ_3000, Sequencers.HISEQ_4000, Sequencers.HISEQ_X]
@@ -249,10 +249,11 @@ def get_vocabulary(vocabulary_code, service):
vocabulary_dict[term.getCode()] = term.getLabel()
else:
print ('No vocabulary found for ' + vocabulary_code)
+ print(vocabulary_dict)
return vocabulary_dict
-def send_email(emails, files, flowCellName, config_dict, logger):
+def send_email(emails, flowCellName, config_dict, logger, subject, body, files=""):
"""
Send out an email to the specified recipients
"""
@@ -263,9 +264,9 @@ def send_email(emails, files, flowCellName, config_dict, logger):
msg['From'] = config_dict['mailFrom']
msg['To'] = COMMASPACE.join(emails_list)
msg['Date'] = formatdate(localtime=True)
- msg['Subject'] = 'Generated Sample Sheet for flowcell ' + flowCellName
+ msg['Subject'] = subject
- msg.attach(MIMEText('Sample Sheet for ' + flowCellName + ' attached.'))
+ msg.attach(MIMEText(body))
for f in files:
part = MIMEBase('application', 'octet-stream')
@@ -486,26 +487,26 @@ def write_sample_sheet_single_lane(model, ordered_sample_sheet_dict, flowCellDic
def create_header_section (model, config_dict, parentDict, flowCellDict, index_length_dict, lane):
- kitsDict = {"CHIP_SEQ_SAMPLE_PREP" : ["",""],
- "TRUSEQ_RNA_SAMPLEPREPKIT_V2_ILLUMINA" : ["A","TruSeq LT"],
+ 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" : ["",""],
+ "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"],
+ "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" : ["",""],
+ "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"]
}
@@ -549,11 +550,11 @@ def create_header_section (model, config_dict, parentDict, flowCellDict, index_l
settings_section = config_dict['settingsSection'].split(separator)
settings_section.reverse()
header_list.append(settings_section.pop())
- if ('nextera' in assay.lower()):
- header_list.append(config_dict['nexteraAdapter'])
- if ('truseq' in assay.lower()):
- header_list.append(config_dict['truSeqAdapter1'])
- header_list.append(config_dict['truSeqAdapter2'])
+# if ('nextera' in assay.lower()):
+# header_list.append(config_dict['nexteraAdapter'])
+# if ('truseq' in assay.lower()):
+# header_list.append(config_dict['truSeqAdapter1'])
+# header_list.append(config_dict['truSeqAdapter2'])
header_list.append('')
if int(flowCellDict['INDEXREAD2']) > 0 and len_index2 > 0:
@@ -583,7 +584,7 @@ def verify_index_length (parentDict, flowCellDict, config_dict, logger):
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 ()
index2_set = set ()
index1_length = 0
@@ -597,7 +598,7 @@ def verify_index_length (parentDict, flowCellDict, config_dict, logger):
if (config_dict['index1Name'] not in sample) or (sample[config_dict['index1Name']] == 'NOINDEX'):
continue
index1 = sample[config_dict['index1Name']]
- index2=""
+ index2 = ""
if config_dict['index2Name'] in sample:
index2 = sample[config_dict['index2Name']]
@@ -622,7 +623,7 @@ def verify_index_length (parentDict, flowCellDict, config_dict, logger):
logger.info("Index2 Length Set: " + str(index2_set))
logger.info("Final length of index1 " + str(index1_length))
logger.info("Final length of index2 " + str(index2_length))
- #print("Lane " + str(lane) + " [" + str(index1_length) + "," + str(index2_length) + "]")
+ # print("Lane " + str(lane) + " [" + str(index1_length) + "," + str(index2_length) + "]")
return index_length_dict
@@ -645,11 +646,11 @@ def create_sample_sheet_dict(service, barcodesPerLaneDict, containedSamples, sam
for key in lane_sample_properties.keys():
if lane_sample_properties[key][u'NCBI_ORGANISM_TAXONOMY'] != u'10847' and not single_index_set:
index1 = ""
- lane_string =""
+ lane_string = ""
if model in HISEQ_LIST or model in Sequencers.MISEQ:
lane_string = lane_int + separator
- line = separator.join([lane_string + key, key + '_' + sanitize_string(lane_sample_properties[key][config_dict['externalSampleName']]),"", "", "", "", key, ""])
+ line = separator.join([lane_string + key, key + '_' + sanitize_string(lane_sample_properties[key][config_dict['externalSampleName']]), "", "", "", "", key, ""])
sampleSheetDict[lane_int + '_' + key] = [line]
single_index_set = True
@@ -660,23 +661,23 @@ def create_sample_sheet_dict(service, barcodesPerLaneDict, containedSamples, sam
if ((config_dict['index1Name'] not in lane_sample_properties[key] or lane_sample_properties[key][config_dict['index1Name']] == 'NOINDEX')):
continue
- index1 = lane_sample_properties[key][config_dict['index1Name']]
- index2=""
+ index1 = index1Vocabulary[lane_sample_properties[key][config_dict['index1Name']]]
+ index2 = ""
if config_dict['index2Name'] in lane_sample_properties[key]:
index2 = lane_sample_properties[key][config_dict['index2Name']]
# Not needed, won't use it any more
indexNumber = index2Vocabulary[lane_sample_properties[key][config_dict['index2Name']]].split()[2]
- #try:
+ # try:
# kit = lane_sample_properties[key][config_dict['kit']]
# prefix = kitsDict[kit][0]
- #except:
+ # except:
# prefix = ""
len_index1 = index_length_dict[int(lane_int)][0]
len_index2 = index_length_dict[int(lane_int)][1]
- lane_string =""
+ lane_string = ""
if model in HISEQ_LIST or model in Sequencers.MISEQ:
lane_string = lane_int + separator
@@ -688,12 +689,12 @@ def create_sample_sheet_dict(service, barcodesPerLaneDict, containedSamples, sam
line = separator.join([lane_string + key,
key + '_' + sanitize_string(lane_sample_properties[key][config_dict['externalSampleName']]) + '_' + index1[0:len_index1] + '_' + index2[0:len_index2],
- "", "","", index1[0:len_index1],"", index2_processed, key, ""])
+ "", "", "", index1[0:len_index1], "", index2_processed, key, ""])
sampleSheetDict[lane_int + '_' + key] = [line]
else:
line = separator.join([lane_string + key, key + '_' + sanitize_string(lane_sample_properties[key][config_dict['externalSampleName']]) + '_' + index1[0:len_index1],
- "", "","", index1[0:len_index1], key, ""])
+ "", "", "", index1[0:len_index1], key, ""])
sampleSheetDict[lane_int + '_' + key] = [line]
csv_file_name = config_dict['SampleSheetFileName'] + '_' + flowCellName
@@ -736,8 +737,14 @@ def main ():
samplesPerLaneDict, model, parentDict, index_length_dict,
flowCellDict, config_dict, index1Vocabulary, index2Vocabulary,
flowCellName, logger)
-
- write_sample_sheet_single_lane(model, ordered_sample_sheet_dict, flowCellDict, index_length_dict,
+ if len(ordered_sample_sheet_dict) < len(containedSamples):
+ subject = "Warning: Creation of Sample Sheet (" + flowCellName + ") failed. No indices found."
+ body = "Warning: No parents/libraries assigned to one of the flowlanes of " + flowCellName + \
+ ". Either it is a non-indexed lane or the parents are not set.\n" + \
+ "Check in the following map for missing lanes:\n" + str(ordered_sample_sheet_dict)
+ send_email(config_dict['mailList'], flowCellName, config_dict, logger, subject, body)
+ else:
+ write_sample_sheet_single_lane(model, ordered_sample_sheet_dict, flowCellDict, index_length_dict,
parentDict, config_dict, myoptions, logger, csv_file_name)
logout(service, logger)
--
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