def get_bases_mask(run_info_xml, sample_sheet_file=None):
"""
Get bases mask string
Generates initial bases mask based on data in RunInfo.xml (which
says how many reads there are, how many cycles in each read, and
which are index reads), and optionally updates this using the
barcode information in the sample sheet file.
Arguments:
run_info_xml: name and path of RunInfo.xml file from the
sequencing run
sample_sheet_file: (optional) path to sample sheet file
Returns:
Bases mask string e.g. 'y101,I6'.
"""
# Get initial bases mask
bases_mask = IlluminaData.IlluminaRunInfo(run_info_xml).bases_mask
print "Bases mask: %s (from RunInfo.xml)" % bases_mask
if sample_sheet_file is not None:
# Update bases mask from sample sheet
example_barcode = IlluminaData.samplesheet_index_sequence(
IlluminaData.SampleSheet(sample_sheet_file).data[0])
if example_barcode is None:
example_barcode = ""
if barcode_is_10xgenomics(example_barcode):
print "Bases mask: barcode is 10xGenomics sample set ID"
else:
bases_mask = IlluminaData.fix_bases_mask(bases_mask,
example_barcode)
print "Bases mask: %s (updated for barcode sequence '%s')" % \
(bases_mask,example_barcode)
return bases_mask
