def construct_command(self):
commandline_collection = [
self.binary, "--input-dir", self.config.base_calls_input,
"--output-dir", self.config.output
]
if self.config.barcode_mismatches:
commandline_collection.append("--barcode-mismatches " +
self.config.barcode_mismatches)
if self.config.tiles:
commandline_collection.append("--tiles " + self.config.tiles)
if self.config.use_base_mask:
# Note that for the base mask the "--use-bases-mask" must be included in the
# commandline passed.
commandline_collection.append(self.config.use_base_mask)
else:
length_of_indexes = Bcl2FastqConfig.get_length_of_indexes(
self.config.runfolder_input)
samplesheet = Samplesheet(self.config.samplesheet_file)
lanes_and_base_mask = Bcl2FastqConfig.\
get_bases_mask_per_lane_from_samplesheet(samplesheet, length_of_indexes)
for lane, base_mask in lanes_and_base_mask.iteritems():
commandline_collection.append(
"--use-bases-mask {0}:{1}".format(lane, base_mask))
if self.config.additional_args:
commandline_collection.append(self.config.additional_args)
command = " ".join(commandline_collection)
print("Generated command: " + command)
return command
def test_get_bases_mask_per_lane_from_samplesheet_invalid_length_combo(self):
# These are to short compared to the length indicated in the samplesheet
mock_read_index_lengths = {2: 4, 3: 4}
samplesheet = Samplesheet(TestBcl2FastqConfig.samplesheet_file)
with self.assertRaises(ArteriaUsageException):
Bcl2FastqConfig. \
get_bases_mask_per_lane_from_samplesheet(samplesheet, mock_read_index_lengths, False)
def construct_command(self):
##################################
# First run configureBcl2fastq.pl
##################################
# Assumes configureBclToFastq.pl on path
commandline_collection = [
"configureBclToFastq.pl",
"--input-dir",
self.config.base_calls_input,
"--sample-sheet",
self.config.samplesheet_file,
"--output-dir",
self.config.output,
"--fastq-cluster-count 0", # No upper-limit on number of clusters per output file.
"--force" # overwrite output if it exists.
]
if self.config.barcode_mismatches:
commandline_collection.append("--mismatches " +
self.config.barcode_mismatches)
if self.config.tiles:
commandline_collection.append("--tiles " + self.config.tiles)
if self.config.use_base_mask:
commandline_collection.append("--use_bases_mask " +
self.config.use_base_mask)
else:
length_of_indexes = Bcl2FastqConfig.get_length_of_indexes(
self.config.runfolder_input)
samplesheet = Samplesheet(self.config.samplesheet_file)
lanes_and_base_mask = \
Bcl2FastqConfig.get_bases_mask_per_lane_from_samplesheet(samplesheet, length_of_indexes)
base_masks_as_set = set(lanes_and_base_mask.values())
assert len(base_masks_as_set) is 1, "For bcl2fastq 1.8.4 there is no support for " \
"mixing different bases masks for different lanes"
# Here we are forced to use the same bases mask was always used for all lanes.
commandline_collection.append("--use_bases_mask " +
lanes_and_base_mask.values()[0])
if self.config.additional_args:
commandline_collection.append(self.config.additional_args)
##################################
# Then run make
##################################
commandline_collection.append(" && make -j{0}".format(
self.config.nbr_of_cores))
command = " ".join(commandline_collection)
print("Generated command: " + command)
return command
def test_get_bases_mask_per_lane_from_samplesheet_single_read(self):
mock_read_index_lengths = {2: 9, 3: 9}
expected_bases_mask = {1: "y*,i8n*,i8n*",
2: "y*,i6n*,n*",
3: "y*,i6n*,n*",
4: "y*,i7n*,n*",
5: "y*,i7n*,n*",
6: "y*,i7n*,n*",
7: "y*,i7n*,n*",
8: "y*,i7n*,n*",
}
samplesheet = Samplesheet(TestBcl2FastqConfig.samplesheet_file)
actual_bases_mask = Bcl2FastqConfig. \
get_bases_mask_per_lane_from_samplesheet(samplesheet, mock_read_index_lengths, True)
self.assertEqual(expected_bases_mask, actual_bases_mask)
def test_get_bases_mask_per_lane_from_samplesheet_no_tag(self):
# If we don't have tag for one lane in the samplesheet.
mock_read_index_lengths = {2: 6}
expected_bases_mask = {1: "y*,n*,y*",
2: "y*,n*,y*",
3: "y*,i6,y*",
4: "y*,i6,y*",
5: "y*,i6,y*",
6: "y*,i6,y*",
7: "y*,n*,y*",
8: "y*,n*,y*",
}
samplesheet = Samplesheet(TestBcl2FastqConfig.samplesheet_with_no_tag)
actual_bases_mask = Bcl2FastqConfig. \
get_bases_mask_per_lane_from_samplesheet(samplesheet, mock_read_index_lengths, False)
self.assertEqual(expected_bases_mask, actual_bases_mask)