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import HTSeq
import sys
class ReadsStatistics(object):
"""
For storing the read counts
"""
def __init__(self, feature_attr, read_io_object):
'''Initialize storage for the read counts
Args:
feature_attr (list of str): Feature names
read_io_object (ReadsIO): Read processor
'''
self.read_io_obj = read_io_object
self.empty = 0
self.ambiguous = 0
self.notaligned = 0
self.lowqual = 0
self.nonunique = 0
self.num_reads_processed = 0
self.counts = {key: 0 for key in feature_attr}
def add_num_reads_processed(self):
self.num_reads_processed += 1
def add_empty_read(self, read_sequence):
self.empty += 1
self.read_io_obj.write_to_samout(read_sequence, "__no_feature")
def add_ambiguous_read(self, read_sequence, assignment):
self.ambiguous += 1
self.read_io_obj.write_to_samout(read_sequence, assignment)
def add_low_quality_read(self, read_sequence):
self.lowqual += 1
self.read_io_obj.write_to_samout(read_sequence, "__too_low_aQual")
def add_not_unique_read(self, read_sequence):
self.nonunique += 1
self.read_io_obj.write_to_samout(read_sequence, "__alignment_not_unique")
def add_not_aligned_read(self, read_sequence):
self.notaligned += 1
self.read_io_obj.write_to_samout(read_sequence, "__not_aligned")
def add_to_count(self, feature, value=1):
self.counts[feature] += value
def add_good_read_assignment(self, read_sequence, assignment):
self.read_io_obj.write_to_samout(read_sequence, assignment)
def print_progress(self, force_print=False):
"""
Simple function to update the progress of reads processing.
Parameters
----------
force_print : boolean
Whether to print progress regardless of number of reads processed
or not.
"""
if force_print:
do_print = True
else:
do_print = (
self.num_reads_processed > 0 and self.num_reads_processed % 100000 == 0
)
if do_print:
sys.stderr.write(
"%d alignment record%s processed.\n"
% (
self.num_reads_processed,
"s" if not self.read_io_obj.pe_mode else " pairs",
)
)
sys.stderr.flush()
def get_output(self, isam):
return {
"isam": isam,
"counts": self.counts,
"empty": self.empty,
"ambiguous": self.ambiguous,
"lowqual": self.lowqual,
"notaligned": self.notaligned,
"nonunique": self.nonunique,
}
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