def main(argv, cfg_file):
cmd = Command('count', cfg_file=cfg_file)
cmd.parse_args(argv)
database.init_db(cmd.primer_db, create_if_missing=True)
if cmd.input:
kmers = swga.primers.parse_kmer_file(cmd.input)
count_specific_kmers(kmers, **cmd.args)
else:
count_kmers(**cmd.args)
def main(argv, cfg_file):
cmd = Command('find_sets', cfg_file=cfg_file)
score_cmd = Command('score', cfg_file=cfg_file)
cmd.parse_args(argv)
score_cmd.parse_args(argv)
init_db(cmd.primer_db)
# We need to clear all the previously-used sets each time due to uniqueness
# constraints
allsets = Set.select()
if allsets.count() > 0:
if not cmd.force:
click.confirm("Remove all previously-found sets?", abort=True)
for s in progress.bar(allsets, expected_size=allsets.count()):
s.primers.clear()
s.delete_instance()
make_graph(cmd.max_dimer_bp, graph_fname)
swga.message("Now finding sets. If nothing appears, try relaxing your parameters.")
if cmd.workers <= 1:
setlines = setfinder.find_sets(
cmd.min_bg_bind_dist,
cmd.min_size,
cmd.max_size,
cmd.bg_genome_len,
graph_fp=graph_fname)
else:
setlines = setfinder.mp_find_sets(
nprocesses=cmd.workers,
graph_fp=graph_fname,
min_bg_bind_dist=cmd.min_bg_bind_dist,
min_size=cmd.min_size,
max_size=cmd.max_size,
bg_genome_len=cmd.bg_genome_len)
score_sets(
setlines,
cmd.fg_genome_fp,
score_cmd.score_expression,
cmd.max_fg_bind_dist,
cmd.max_sets)
def main(argv, cfg_file):
cmd = Command('export', cfg_file=cfg_file)
cmd.parse_args(argv)
header = not cmd.no_header
what = cmd.what
database.init_db(cmd.primer_db)
if what in ['set', 'sets']:
sets = get_items(Set, cmd.ids, cmd.order_by, cmd.limit, cmd.descending)
export(Set, sets, cmd.output, header)
if what in ['primer', 'primers']:
primers = get_items(
Primer, cmd.ids, cmd.order_by, cmd.limit, cmd.descending)
export(Primer, primers, cmd.output, header)
if "bed" in what:
outpath = cmd.output_folder if cmd.output_folder else os.getcwd()
sets = get_items(Set, cmd.ids, cmd.order_by, cmd.limit, cmd.descending)
if what == "bedfile":
for set in sets:
swga.message(
"Exporting set {} and associated primers as bedfiles..."
.format(set._id))
bedfile = BedFile(set, cmd.fg_genome_fp)
bedfile.write(outpath)
elif what == "bedgraph":
for set in sets:
swga.message("Exporting set {} as bedgraph...".format(set._id))
bedgraph = BedGraph(
set=set,
fg_genome_fp=cmd.fg_genome_fp,
opts_str=cmd.opts_str,
window_size=cmd.window_size,
step_size=cmd.step_size)
bedgraph.write(outpath)
