def main():
"""cblaster entry point."""
args = parsers.parse_args(sys.argv[1:])
if args.debug:
LOG.setLevel(logging.DEBUG)
if args.subcommand == "makedb":
makedb(args.genbanks, args.filename, args.indent)
elif args.subcommand == "search":
cblaster(
query_file=args.query_file,
query_ids=args.query_ids,
mode=args.mode,
json_db=args.json_db,
database=args.database,
gap=args.gap,
unique=args.unique,
min_hits=args.min_hits,
require=args.require,
min_identity=args.min_identity,
min_coverage=args.min_coverage,
max_evalue=args.max_evalue,
entrez_query=args.entrez_query,
output=args.output,
output_hide_headers=args.output_hide_headers,
output_delimiter=args.output_delimiter,
output_decimals=args.output_decimals,
binary=args.binary,
binary_hide_headers=args.binary_hide_headers,
binary_delimiter=args.binary_delimiter,
binary_key=args.binary_key,
binary_attr=args.binary_attr,
binary_decimals=args.binary_decimals,
rid=args.rid,
session_file=args.session_file,
indent=args.indent,
recompute=args.recompute,
plot=args.plot,
blast_file=args.blast_file,
ipg_file=args.ipg_file,
hitlist_size=args.hitlist_size,
)
elif args.subcommand == "gui":
from cblaster.gui.main import cblaster_gui
cblaster_gui()
elif args.subcommand == "gne":
gne(
args.session,
args.output,
max_gap=args.max_gap,
samples=args.samples,
scale=args.scale,
delimiter=args.delimiter,
hide_headers=args.hide_headers,
decimals=args.decimals,
plot=args.plot,
)
elif args.subcommand == "extract":
extract.extract(
args.session,
download=args.download,
output=args.output,
queries=args.queries,
organisms=args.organisms,
scaffolds=args.scaffolds,
name_only=args.name_only,
delimiter=args.delimiter,
)
def main():
"""cblaster entry point."""
args = parsers.parse_args(sys.argv[1:])
if args.debug:
LOG.setLevel(logging.DEBUG)
if args.subcommand == "config":
if not args.email and not args.api_key:
LOG.info(
"No e-mail or API key specified; if this is your first time"
" running cblaster config, please make sure you provide one.")
config.write_config_file(
email=args.email,
api_key=args.api_key,
max_tries=args.max_tries,
)
return
# Set BioPython Entrez parameters
set_entrez()
if args.subcommand == "makedb":
database.makedb(
args.paths,
database=args.name,
cpus=args.cpus,
batch=args.batch,
force=args.force,
)
elif args.subcommand == "search":
cblaster(
query_file=args.query_file,
query_ids=args.query_ids,
query_profiles=args.query_profiles,
mode=args.mode,
databases=args.database,
database_pfam=args.database_pfam,
gap=args.gap,
unique=args.unique,
min_hits=args.min_hits,
require=args.require,
percentage=args.percentage,
min_identity=args.min_identity,
min_coverage=args.min_coverage,
max_evalue=args.max_evalue,
entrez_query=args.entrez_query,
output=args.output,
output_hide_headers=args.output_hide_headers,
output_delimiter=args.output_delimiter,
output_decimals=args.output_decimals,
output_sort_clusters=args.sort_clusters,
binary=args.binary,
binary_hide_headers=args.binary_hide_headers,
binary_delimiter=args.binary_delimiter,
binary_key=args.binary_key,
binary_attr=args.binary_attr,
binary_decimals=args.binary_decimals,
rid=args.rid,
session_file=args.session_file,
indent=args.indent,
recompute=args.recompute,
plot=args.plot,
max_plot_clusters=args.max_plot_clusters,
blast_file=args.blast_file,
ipg_file=args.ipg_file,
hitlist_size=args.hitlist_size,
cpus=args.cpus,
intermediate_genes=args.intermediate_genes,
intermediate_gene_distance=args.max_distance,
intermediate_max_clusters=args.maximum_clusters,
testing=args.testing,
)
elif args.subcommand == "gui":
from cblaster.gui.main import cblaster_gui
cblaster_gui()
elif args.subcommand == "gne":
gne(
args.session,
args.output,
max_gap=args.max_gap,
samples=args.samples,
scale=args.scale,
delimiter=args.delimiter,
hide_headers=args.hide_headers,
decimals=args.decimals,
plot=args.plot,
testing=args.testing,
)
elif args.subcommand == "extract":
extract.extract(
args.session,
extract_seqs=args.extract_sequences,
output=args.output,
queries=args.queries,
organisms=args.organisms,
scaffolds=args.scaffolds,
name_only=args.name_only,
delimiter=args.delimiter,
)
elif args.subcommand == "extract_clusters":
extract_clusters.extract_clusters(
args.session,
args.output,
prefix=args.prefix,
cluster_numbers=args.clusters,
score_threshold=args.score_threshold,
organisms=args.organisms,
scaffolds=args.scaffolds,
format_=args.format,
max_clusters=args.maximum_clusters,
)
elif args.subcommand == "plot_clusters":
plot_clusters.plot_clusters(
session=args.session,
cluster_numbers=args.clusters,
score_threshold=args.score_threshold,
organisms=args.organisms,
scaffolds=args.scaffolds,
plot_outfile=args.output,
max_clusters=args.maximum_clusters,
testing=args.testing,
)