def get_base_masks(rundir):
""" Return a set of base masks to be used when demultiplexing.
:param str rundir: Path to the run directory.
:returns list: Basemasks to be used based on the SampleSeet information.
"""
runsetup = parsers.get_read_configuration(rundir, sort=True)
flowcell_id = parsers.get_flowcell_id(rundir)
base_masks = {}
#Create groups of reads by index length
ss_name = os.path.join(rundir, str(flowcell_id) + '.csv')
if os.path.exists(ss_name):
ss = csv.DictReader(open(ss_name, 'rb'), delimiter=',')
samplesheet = []
[samplesheet.append(read) for read in ss]
for r in samplesheet:
index_length = len(r['Index'].replace('-', '').replace('NoIndex', ''))
if not base_masks.has_key(index_length):
base_masks[index_length] = {'base_mask': [],
'samples': {'fieldnames': ss.fieldnames, 'samples':[]}}
base_masks[index_length]['samples']['samples'].append(r)
#Create the basemask for each group
for index_size, index_group in base_masks.iteritems():
index_size = index_size
group = index_size
bm = []
per_index_size = index_size/(int(last_index_read(rundir)) - 1)
for read in runsetup:
cycles = read['NumCycles']
if read['IsIndexedRead'] == 'N':
bm.append('Y' + cycles)
else:
# I_iN_y(,I_iN_y) or I(,I)
if index_size > int(cycles):
i_remainder = int(cycles) - per_index_size
if i_remainder > 0:
bm.append('I' + str(per_index_size) + 'N' + str(i_remainder))
else:
bm.append('I' + cycles)
# I_iN_y(,N) or I(,N)
else:
if index_size > 0:
to_mask = "I" + str(index_size)
if index_size < int(cycles):
to_mask = to_mask + 'N' + str(int(cycles) - index_size)
bm.append(to_mask)
index_size = 0
else:
bm.append('N' + cycles)
base_masks[group]['base_mask'] = bm
return base_masks
def last_index_read(directory):
"""Parse the number of the highest index read from the RunInfo.xml
"""
read_numbers = [int(read.get("Number", 0)) for read in parsers.get_read_configuration(directory) if read.get("IsIndexedRead", "") == "Y"]
return 0 if len(read_numbers) == 0 else max(read_numbers)
