def process_feed(args, callback=None):
""" Process feed data """
if callback:
callback("Processing GISAID feed data")
loader = gisaid_utils.load_gisaid(args.infile, minlen=args.minlen, mindate=args.mindate)
batcher = gisaid_utils.batch_fasta(loader, size=args.batchsize)
aligned = gisaid_utils.extract_features(batcher, ref_file=args.ref, binpath=args.mmbin,
nthread=args.mmthreads, minlen=args.minlen)
filtered = gisaid_utils.filter_problematic(aligned, vcf_file=args.vcf, cutoff=args.poisson_cutoff,
callback=callback)
return gisaid_utils.sort_by_lineage(filtered, callback=callback)
def process_local(args, callback=None):
""" Analyze genome sequences from local FASTA file """
with open(args.ref) as handle:
reflen = len(seq_utils.convert_fasta(handle)[0][1])
loader = stream_local(args.infile, args.pangolineages, minlen=args.minlen,
mindate=args.mindate, callback=callback)
batcher = gisaid_utils.batch_fasta(loader, size=args.batchsize)
aligned = gisaid_utils.extract_features(batcher, ref_file=args.ref, binpath=args.mmbin,
nthread=args.mmthreads, minlen=args.minlen)
filtered = gisaid_utils.filter_problematic(aligned, vcf_file=args.vcf, cutoff=args.poisson_cutoff,
callback=callback)
return gisaid_utils.sort_by_lineage(filtered, callback=callback)