def filter_phiX(self, reads): filtered_reads = contaminants.pre_filter(self.phiX_bowtie2_index_prefix, reads, self.file_names['phiX_bam'], ) for read in filtered_reads: yield read phiX_length_counts = sam.get_length_counts(self.file_names['phiX_bam']) phiX_lengths = self.zero_padded_array(phiX_length_counts) self.write_file('lengths', {'phiX': phiX_lengths})
def preprocess(self): reads = self.get_reads() trimmed_reads = self.trim_reads(reads) rRNA_filtered_reads = contaminants.pre_filter(self.file_names['rRNA_index'], trimmed_reads, self.file_names['rRNA_bam'], self.file_names['bowtie_error'], ) with open(self.file_names['preprocessed_reads'], 'w') as preprocessed_fh: for read in rRNA_filtered_reads: preprocessed_fh.write(str(read))