diff --git a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
index 630c5641afceb2b894324895fb1eca468ef257cb..d59d8787e434324f3867da99b60875588c8a28e3 100644
--- a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
+++ b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
@@ -44,15 +44,14 @@ 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
+import argparse
from ConfigParser import SafeConfigParser
-from optparse import OptionParser
from datetime import *
from collections import OrderedDict
@@ -104,55 +103,55 @@ def setUpLogger(logPath, logLevel=logging.INFO):
def parseOptions(logger):
logger.info('Parsing command line parameters')
- parser = OptionParser(version='%prog 1.0')
- parser.add_option('-f', '--flowcell',
+ parser = argparse.ArgumentParser(version='%prog 1.0', description='Process some integers.')
+ parser.add_argument('-f', '--flowcell',
dest='flowcell',
help='The flowcell which is used to create the SampleSheet.csv',
metavar='<flowcell>')
- parser.add_option('-m', '--mailist',
+ parser.add_argument('-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',
+ help='Generated Sample Sheet will be addtionally sent as email to the defined list of recipients')
+ parser.add_argument('-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',
+ parser.add_argument('-o', '--outdir',
dest='outdir',
default='./',
help='Specify the ouput directory. Default: ./' ,
metavar='<outdir>')
- parser.add_option('-s', '--singlelane',
+ parser.add_argument('-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',
+ parser.add_argument('-d', '--debug',
dest='debug',
default=False,
action='store_true',
help='Verbose debug logging. Default: False')
- parser.add_option('-v', '--verbose',
+ parser.add_argument('--verbose',
dest='verbose',
default=False,
action='store_true',
help='Write Sample Sheet to stout. Default: False')
- (options, args) = parser.parse_args()
+ args = parser.parse_args()
+
+ print(type(args))
- if options.outdir[-1] <> '/':
- options.outdir = options.outdir + '/'
+ if args.outdir[-1] <> '/':
+ args.outdir = args.outdir + '/'
- if options.flowcell is None:
+ if args.flowcell is None:
parser.print_help()
exit(-1)
- return options
+ return args
def parseConfigurationFile(propertyFile='etc/createSampleSheet.properties'):
@@ -684,10 +683,10 @@ def main ():
logger.setLevel(logging.DEBUG)
flowCellName = myoptions.flowcell
- configMap = readConfig(logger)
- service = login(logger, configMap)
+ config_dict = readConfig(logger)
+ service = login(logger, config_dict)
- foundFlowCell, containedSamples = get_flowcell(configMap['illuminaFlowCellTypeName'], flowCellName,
+ foundFlowCell, containedSamples = get_flowcell(config_dict['illuminaFlowCellTypeName'], flowCellName,
service, logger)
parentDict, samplesPerLaneDict = get_contained_sample_properties(containedSamples, service)
logger.info('Found ' + str(len(parentDict)) + ' samples on the flow cell ' + flowCellName)
@@ -698,20 +697,20 @@ def main ():
print("Auto-detected: " + model)
logger.info("Auto-detected: " + model)
- index1Vocabulary = get_vocabulary(configMap['index1Name'], service)
- index2Vocabulary = get_vocabulary(configMap['index2Name'], service)
+ index1Vocabulary = get_vocabulary(config_dict['index1Name'], service)
+ index2Vocabulary = get_vocabulary(config_dict['index2Name'], service)
ordered_sample_sheet_dict, csv_file_name = create_sample_sheet_dict(model, parentDict,
- flowCellDict, configMap, index1Vocabulary, index2Vocabulary, flowCellName, logger)
+ flowCellDict, config_dict, index1Vocabulary, index2Vocabulary, flowCellName, logger)
if myoptions.singlelane:
write_sample_sheet_single_lane(ordered_sample_sheet_dict, flowCellDict,
- parentDict, configMap, myoptions, logger, csv_file_name)
+ parentDict, config_dict, myoptions, logger, csv_file_name)
else:
- header_list = create_header_section (configMap, parentDict, flowCellDict)
+ header_list = create_header_section (config_dict, parentDict, flowCellDict)
sampleSheetFile = write_sample_sheet(ordered_sample_sheet_dict, header_list,
myoptions, logger, myoptions.outdir + csv_file_name + CSV)
if myoptions.maillist:
- sendMail(configMap['mailList'], [SampleSheetFile], flowCellName, configMap, logger)
+ sendMail(config_dict['mailList'], [sampleSheetFile], flowCellName, config_dict, logger)
logout(service, logger)
diff --git a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq_Test.py b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq_Test.py
index a5b84e58005a41918cd64ae3b5e6adcd07e0b8ac..62c968ea749460b969e7487f9915180046fa364e 100644
--- a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq_Test.py
+++ b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq_Test.py
@@ -30,62 +30,95 @@ class test_get_reverse_complement(unittest.TestCase):
self.assertNotEqual(get_reverse_complement('ACTG'), 'CAGA')
-class test_get_flowCell(unittest.TestCase):
+class create_sample_sheet(unittest.TestCase):
def setUp(self):
self.myCode = 'C7GMNANXX'
self.logger = setUpLogger('log/')
- configDict = readConfig(self.logger)
- self.service = OpenbisServiceFacadeFactory.tryCreate(configDict['openbisUserName'],
- configDict['openbisPassword'],
- configDict['openbisServer'],
- configDict['connectionTimeout'])
+ self.config_dict = readConfig(self.logger)
+
+# self.options = parseOptions(self.logger)
+
+ import argparse
+ import shlex
+ parser = argparse.ArgumentParser()
+
+ parser.add_argument('--flowcell')
+ parser.add_argument('--lineending')
+ parser.add_argument('--outdir')
+
+ cmd_string = ['--flowcell', self.myCode, '--lineending', 'win32', '--outdir', '../../targets/playground']
+ self.options = parser.parse_args(cmd_string)
+
+ self.service = OpenbisServiceFacadeFactory.tryCreate(self.config_dict['openbisUserName'],
+ self.config_dict['openbisPassword'],
+ self.config_dict['openbisServer'],
+ self.config_dict['connectionTimeout'])
self.flowcell, self.containedSamples = get_flowcell('ILLUMINA_FLOW_CELL',
self.myCode, self.service, self.logger)
+ self.flowCellDict = transform_sample_to_dict(self.flowcell)
+ self.parentDict, self.samplesPerLaneDict = get_contained_sample_properties(
+ self.containedSamples, self.service)
+ self.flowCellName = self.flowcell.getCode()
+ self.index1Vocabulary = get_vocabulary(self.config_dict['index1Name'], self.service)
+ self.index2Vocabulary = get_vocabulary(self.config_dict['index2Name'], self.service)
- def test_get_flowCell (self):
+ def test_get_flowCell (self):
self.assertEqual(self.flowcell.getCode(), self.myCode)
self.assertEqual(self.containedSamples.size(), 8)
fcProp = self.flowcell.getProperties()
self.assertEqual(fcProp['SEQUENCER'], 'D00535')
- self.flowCellDict = transform_sample_to_dict(self.flowcell)
self.assertEqual(self.flowCellDict['FLOWCELLTYPE'], 'HiSeq Flow Cell v4')
-
+
def test_get_contained_sample_properties(self):
- self.parentDict, self.samplesPerLaneDict = get_contained_sample_properties(
- self.containedSamples, self.service)
self.assertEqual(self.parentDict['BSSE_QGF_34778_C7GMNANXX_1']['BARCODE'], 'GTCCGC')
self.assertEqual(self.parentDict['BSSE_QGF_32285_C7GMNANXX_7']['CONTACT_PERSON_EMAIL'], 'yann.bourgeois@unibas.ch')
self.assertEqual(self.samplesPerLaneDict['2'], 23)
-
- def tearDown(self):
- self.service.logout()
- self.logger.info('Logged out')
-
-
-# class test_get_contained_sample_properties(unittest.TestCase):
-# def setUp(self):
-# self.flowcell = test_get_flowCell.setUp(self)
-#
-
+ def test_get_vocabulary(self):
+ self.assertEqual(self.index1Vocabulary['CACTCAA'], 'Illumina A032 CACTCAA')
+ self.assertEqual(self.index2Vocabulary['GTAAGGAG'],'Index2 (i5) 505 GTAAGGAG')
+
+
+ def test_verify_index_length(self):
+ self.index_length_dict = verify_index_length(self.parentDict, self.flowCellDict, self.config_dict, self.logger)
+ self.assertDictEqual(self.index_length_dict, {6: [6, 0], 5: [6, 0], 7: [8, 8], 8: [8, 8], 3: [8, 0], 2: [6, 0], 1: [6, 0], 4: [8, 0]})
+
+
+ def test_create_sample_sheet_dict(self):
+
+ self.model = get_model(self.flowCellDict['RUN_NAME_FOLDER'])
+ self.ordered_sample_sheet_dict, self.csv_file_name = create_sample_sheet_dict(self.model, self.parentDict,
+ self.flowCellDict, self.config_dict, self.index1Vocabulary, self.index2Vocabulary, self.flowCellName, self.logger)
+
+ self.ordered_sample_sheet_dict['5_BSSE_QGF_32303_C7GMNANXX_5'] = \
+ [u'5,BSSE_QGF_32303_C7GMNANXX_5,BSSE_QGF_32303_C7GMNANXX_5_TR_EG_1_GGCTAC,,,SureSelectXT,GGCTAC,BSSE_QGF_32303_C7GMNANXX_5,']
+ self.ordered_sample_sheet_dict['5_BSSE_QGF_36788_C7GMNANXX_5'] = \
+ [u'5,BSSE_QGF_36788_C7GMNANXX_5,BSSE_QGF_36788_C7GMNANXX_5_G_33_run2_TAAGGC,,,N701,TAAGGC,BSSE_QGF_36788_C7GMNANXX_5,']
+
+ self.ordered_sample_sheet_dict['BSSE_QGF_32281_C7GMNANXX_8']= \
+ [u'8,BSSE_QGF_32281_C7GMNANXX_8,BSSE_QGF_32281_C7GMNANXX_8_F2_18_3_P162Nextera_TAGGCATG_CTATTAAG,,,N706,TAGGCATG,518,CTATTAAG,BSSE_QGF_32281_C7GMNANXX_8,']
+
+ def test_write_sample_sheet_single_lane(self):
+ self.model = get_model(self.flowCellDict['RUN_NAME_FOLDER'])
-# class test_verify_index_length(test_get_flowCell):
-#
-# def setUp(self):
-# foundFlowCell, containedSamples = test_get_flowCell()
-#
-#
-# def test_verify_index_length(self):
-# foundFlowCell
+ self.ordered_sample_sheet_dict, self.csv_file_name = create_sample_sheet_dict(self.model, self.parentDict,
+ self.flowCellDict, self.config_dict, self.index1Vocabulary, self.index2Vocabulary, self.flowCellName, self.logger)
+
+ write_sample_sheet_single_lane(self.ordered_sample_sheet_dict, self.flowCellDict,
+ self.parentDict, self.config_dict, self.options, self.logger, self.csv_file_name)
+
+ def tearDown(self):
+ self.service.logout()
+ self.logger.info('Logged out')
def main():
unittest.main()