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#!/usr/bin/python3
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import sam_parser
import SeqIO
import sys
class PatternContigFilter:
def __init__(self, contigs, sam, pattern, rc_pattern):
self.sam = sam
reads = []
self.filter = [False] * len(contigs)
for rec in sam:
reads.append(rec)
if len(reads) == 2:
left_sequence = str(reads[0].seq.upper())
right_sequence = str(reads[1].seq.upper())
if left_sequence.find(pattern) != -1 or right_sequence.find(rc_pattern) != -1 or right_sequence.find(pattern) != -1 or left_sequence.find(rc_pattern) != -1:
if not reads[0].is_unmapped:
self.filter[reads[0].tid] = True
if not reads[1].is_unmapped:
self.filter[reads[1].tid] = True
reads = []
def Filter(self, contig):
return self.filter[self.sam.gettid(contig.id)]
class ContigLengthFilter:
def __init__(self, min_length):
self.min_length = min_length
def Filter(self, contig):
return len(contig.seq) >= self.min_length
# def Filter(contigs, left_reads, right_reads, length_threshold, pattern):
# dataset_data = pyyaml.load(yaml_file, 'r')
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