def main(argv, cfg_file):
cmd = Command('score', cfg_file=cfg_file)
cmd.parse_args(argv)
swga.database.init_db(cmd.primer_db)
primers = swga.primers.read_primer_list(
cmd.input,
cmd.fg_genome_fp,
cmd.bg_genome_fp)
if len(primers) == 0:
swga.error("No primers specified exist in database, aborting.",
exception=False)
chr_ends = swga.locate.chromosome_ends(cmd.fg_genome_fp)
# Evaluate the user-defined scoring function
score_fun = functools.partial(
swga.score.default_score_set,
expression=cmd.score_expression)
score_set(
set_id=0,
primers=primers,
chr_ends=chr_ends,
score_fun=score_fun,
score_expression=cmd.score_expression,
bg_genome_len=cmd.bg_genome_len,
bg_dist_mean=None,
max_fg_bind_dist=0,
interactive=True)
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("activate", cfg_file=cfg_file)
cmd.parse_args(argv)
swga.database.init_db(cmd.primer_db)
primers = swga.primers.read_primer_list(cmd.input, cmd.fg_genome_fp, cmd.bg_genome_fp)
try:
swga.primers.update_Tms(primers)
swga.primers.update_locations(primers, cmd.fg_genome_fp)
n_activated = swga.primers.activate2(primers)
swga.message("Marked {} primers as active.".format(n_activated))
except AttributeError as e:
swga.warn("Error updating database: '{}'".format(e.message))
swga.warn(
"Sometimes this happens if you're using a database created with "
"an older version of swga. Please try creating a new workspace "
"with `swga init` in another folder and adding these primers to "
"that database instead."
)
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))
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)
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('summary', cfg_file=cfg_file)
cmd.parse_args(argv, quiet=True)
summary(**cmd.args)
