SpadesAssembly.py 文件源码

def remove_small_large_contigs(self,input_file, output_file):
        with open(input_file, "r") as spades_input_file, open(output_file, "w") as spades_output_file:
            sequences = []
            for record in SeqIO.parse(spades_input_file, "fasta"):
                if self.min_spades_contig_coverage != 0 and self.sequence_coverage(record.id) < self.min_spades_contig_coverage:
                    self.logger.warning("Excluding contig with low coverage of "+ str(self.sequence_coverage(record.id))+ " from "+ self.spades_assembly_file())
                    continue

                if self.max_spades_contig_coverage != 0 and self.sequence_coverage(record.id) > self.max_spades_contig_coverage:
                    self.logger.warning("Excluding contig with high coverage of "+ str(self.sequence_coverage(record.id))+ " from "+ self.spades_assembly_file())
                    continue

                if len(record.seq) > self.minimum_length:
                    sequences.append(record)
                else:
                    self.logger.warning("Excluding contig of length "+ str(len(record.seq))+ " from "+ self.spades_assembly_file() )

            SeqIO.write(sequences, spades_output_file, "fasta")