def run(self):
super(JobConsensus, self).run()
if not os.path.isdir(self.consensus_dir):
os.mkdir(self.consensus_dir)
#split into 1Mb chunks to reduce RAM usage
CHUNK_SIZE = 1000000
chunks_file = os.path.join(self.consensus_dir, "chunks.fasta")
chunks = aln.split_into_chunks(fp.read_sequence_dict(self.in_contigs),
CHUNK_SIZE)
fp.write_fasta_dict(chunks, chunks_file)
logger.info("Running Minimap2")
out_alignment = os.path.join(self.consensus_dir, "minimap.bam")
aln.make_alignment(chunks_file,
self.args.reads,
self.args.threads,
self.consensus_dir,
self.args.platform,
out_alignment,
reference_mode=True,
sam_output=True)
contigs_info = aln.get_contigs_info(chunks_file)
logger.info("Computing consensus")
consensus_fasta = cons.get_consensus(out_alignment, chunks_file,
contigs_info, self.args.threads,
self.args.platform)
#merge chunks back into single sequences
merged_fasta = aln.merge_chunks(consensus_fasta)
fp.write_fasta_dict(merged_fasta, self.out_consensus)
os.remove(chunks_file)
os.remove(out_alignment)
def run(self):
if not os.path.isdir(self.consensus_dir):
os.mkdir(self.consensus_dir)
logger.info("Running Minimap2")
out_alignment = os.path.join(self.consensus_dir, "minimap.sam")
aln.make_alignment(self.in_contigs, self.args.reads, self.args.threads,
self.consensus_dir, self.args.platform,
out_alignment)
contigs_info = aln.get_contigs_info(self.in_contigs)
logger.info("Computing consensus")
consensus_fasta = cons.get_consensus(out_alignment, self.in_contigs,
contigs_info, self.args.threads,
self.args.platform)
fp.write_fasta_dict(consensus_fasta, self.out_consensus)
def run(self):
super(JobConsensus, self).run()
if not os.path.isdir(self.consensus_dir):
os.mkdir(self.consensus_dir)
logger.info("Running Minimap2")
out_alignment = os.path.join(self.consensus_dir, "minimap.bam")
aln.make_alignment(self.in_contigs,
self.args.reads,
self.args.threads,
self.consensus_dir,
self.args.platform,
out_alignment,
reference_mode=True,
sam_output=True)
contigs_info = aln.get_contigs_info(self.in_contigs)
logger.info("Computing consensus")
consensus_fasta = cons.get_consensus(out_alignment, self.in_contigs,
contigs_info, self.args.threads,
self.args.platform)
fp.write_fasta_dict(consensus_fasta, self.out_consensus)
os.remove(out_alignment)
