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,
)
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 run_cblaster(values):
"""Handles conversion of PySimpleGUI values to cblaster parameters.
- Know which workflow tab we're on (search or makedb)
- search
- Know which search mode tab we're on
- if remote, use entrez query, database, RID
- if local, jdb and database
Args:
values (dict): Dictionary of values from PySimpleGUI.
"""
if values["cblaster_tabs"] == "Search":
args = dict(
query_file=values["query_file"],
query_ids=values["query_ids"],
session_file=values["session_file"],
mode=values["search_mode"],
gap=int(values["gap"]),
unique=int(values["unique"]),
min_hits=int(values["min_hits"]),
require=values["require"],
min_identity=float(values["min_identity"]),
min_coverage=float(values["min_coverage"]),
max_evalue=float(values["max_evalue"]),
recompute=values["recompute"],
)
if values["search_mode"] == "remote":
args.update(database=values["database"],
entrez_query=values["entrez_query"],
rid=values["rid"])
else:
args.update(database=values["dmnd_database"],
json_db=values["json_db"])
if values["summary_gen"]:
summary = None
if values["summary_text"]:
summary = values["summary_text"]
args.update(output=summary,
output_decimals=values["summary_decimals"],
output_delimiter=values["summary_delimiter"],
output_hide_headers=values["summary_hide_headers"])
if values["binary_gen"]:
args.update(
binary=values["binary_text"],
binary_delimiter=values["binary_delimiter"],
binary_hide_headers=values["binary_hide_headers"],
binary_decimals=values["binary_decimals"],
binary_attr=values["binary_attr"],
binary_key=getattr(builtins, values["binary_key"]),
)
if values["figure_gen"]:
plot = values["figure_text"] if values["figure_text"] else True
args.update(plot=plot)
# Overwrite any placeholder text
for arg, value in args.items():
if isinstance(value, str) and value.startswith("e.g."):
args[arg] = ""
main.cblaster(**args)
elif values["cblaster_tabs"] == "Makedb":
main.makedb(genbanks=values["makedb_genbanks"].split(";"),
filename=values["makedb_filename"],
indent=values["json_indent"])
elif values["cblaster_tabs"] == "Neighbourhood":
main.gne(
session=values["session"],
output=values["output"],
max_gap=int(values["max_gap"]),
samples=int(values["samples"]),
scale=values["scale"],
)
elif values["cblaster_tabs"] == "Extract":
cb_extract.extract(
values["extract_session"],
in_cluster=values["in_cluster"],
delimiter=values["delimiter"],
name_only=values["name_only"],
download=values["download"],
output=values["extract_output"],
queries=values["queries"],
organisms=values["organisms"],
scaffolds=values["scaffolds"],
)
else:
raise ValueError(
"Expected 'Search', 'Makedb', 'Neighbourhood' or 'Extract'")