def main(argv, cfg_file):
cmd = Command('filter', cfg_file=cfg_file)
cmd.parse_args(argv)
swga.database.init_db(cmd.primer_db)
# If we have an input file, use that. Otherwise pull from db
if cmd.input:
with open(cmd.input, 'rb') as infile:
primers = swga.primers.read_primer_list(
infile,
cmd.fg_genome_fp,
cmd.bg_genome_fp)
else:
cmd.skip_filtering = False
primers = Primer.select()
# Undo all active marks, if any
deactivate_all_primers()
if not cmd.skip_filtering:
primers = filter_primers(
primers,
cmd.min_fg_bind,
cmd.max_bg_bind,
cmd.fg_length,
cmd.bg_length,
cmd.min_tm,
cmd.max_tm,
cmd.max_primers)
swga.primers.update_locations(primers, cmd.fg_genome_fp)
n_active = activate_primers(primers)
if n_active < cmd.max_primers:
swga.warn(
"Fewer than {} primers were selected ({} passed all the filters). "
"You may want to try less restrictive filtering parameters."
.format(cmd.max_primers, n_active))
