def main(
sample_config: str = typer.Argument(...),
summary_report: str = typer.Argument(...),
output_prefix: str = typer.Argument(...),
min_sample: int = typer.Option(
1, "-S", help="Minimum number of samples as evidence (default: 1)"),
min_transcript: int = typer.Option(
2, "-T",
help="Minimum number of transcripts as evidence (default: 2)"),
# parser.add_argument("-C", "--accept_all_canonical", action="store_true", default=False, help="Accept all canonical jucntions (default: false)")
scrubbed_junction_file: Optional[Union[str, Path]] = typer.Option(
None,
help=
"Scrubbed junction bed --- if given, directly use it to scrub GFFs."),
version: bool = typer.Option(
None,
"--version",
callback=version_callback,
is_eager=True,
help="Prints the version of the SQANTI3 package.",
),
):
(
sample_dirs,
sample_names,
group_filename,
gff_filename,
count_filename,
fastq_filename,
) = sp.read_config(sample_config)
report_filename = summary_report
if scrubbed_junction_file is None:
output_filename = f"{output_prefix}.scrubbed.junction.bed"
tree = scrub_junctions(report_filename, output_filename, min_sample,
min_transcript, True)
logger.info(f"Scrubbed junction written to: {output_filename}")
else:
output_filename = scrubbed_junction_file
logger.info(f"Reading scrubbed junction file: {output_filename}")
tree = read_scrubbed_junction_to_tree(output_filename)
scrub_sample_GFFs(
sample_dirs,
gff_filename,
count_filename,
group_filename,
fastq_filename,
output_prefix,
tree,
)
def main(
config_file: str = typer.Argument(...),
field_to_use: fl_fields = typer.Option(
fl_fields.count_fl,
show_default=False,
help="Which count field to use for chained sample",
),
fuzzy_junction: int = typer.Option(
5,
show_default=False,
help="Max allowed distance in junction to be considered identical",
),
version: bool = typer.Option(
None,
"--version",
callback=version_callback,
is_eager=True,
help="Prints the version of the SQANTI3 package.",
),
) -> None:
(
sample_dirs,
sample_names,
group_filename,
gff_filename,
count_filename,
fastq_filename,
) = read_config(config_file)
chain_fusion_samples(
sample_dirs,
sample_names,
group_filename,
gff_filename,
count_filename,
field_to_use,
fuzzy_junction,
fastq_filename,
)
print(f1.name, file=sys.stderr)
print(f2.name, file=sys.stderr)
if fastq_filename is not None:
print("all_samples.chained.rep.fq", file=sys.stderr)
if __name__ == "__main__":
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument("config_file")
parser.add_argument(
"field_to_use",
choices=['norm_fl', 'count_fl'],
default='count_fl',
help="Which count field to use for chained sample (default: count_fl)")
parser.add_argument(
"--fuzzy_junction",
default=5,
type=int,
help=
"Max allowed distance in junction to be considered identical (default: 5 bp)"
)
#parser.add_argument("--allow_5merge", action="store_true", default=False, help="Allow 5' truncated transcripts (default: off)" )
args = parser.parse_args()
sample_dirs, sample_names, group_filename, gff_filename, count_filename, fastq_filename = read_config(
args.config_file)
chain_fusion_samples(sample_dirs, sample_names, group_filename,
gff_filename, count_filename, args.field_to_use,
args.fuzzy_junction, fastq_filename)
f1.write('\n')
f2.write('\n')
f1.close()
f2.close()
shutil.copyfile('tmp_' + chain[-1] + '.gff', 'all_samples.chained.gff')
if fastq_filename is not None:
shutil.copyfile('tmp_' + chain[-1] + '.rep.fq', 'all_samples.chained.rep.fq')
print >> sys.stderr, "Chained output written to:"
print >> sys.stderr, "all_samples.chained.gff"
print >> sys.stderr, f1.name
print >> sys.stderr, f2.name
if fastq_filename is not None:
print >> sys.stderr, "all_samples.chained.rep.fq"
if __name__ == "__main__":
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument("config_file")
parser.add_argument("field_to_use", choices=['norm_fl', 'norm_nfl', 'norm_nfl_amb', 'count_fl', 'count_nfl', 'count_nfl_amb'], default='norm_nfl', help="Which count field to use for chained sample (default: norm_nfl)")
parser.add_argument("--fuzzy_junction", default=5, type=int, help="Max allowed distance in junction to be considered identical (default: 5 bp)")
#parser.add_argument("--allow_5merge", action="store_true", default=False, help="Allow 5' truncated transcripts (default: off)" )
args = parser.parse_args()
sample_dirs, sample_names, group_filename, gff_filename, count_filename, fastq_filename = read_config(args.config_file)
chain_fusion_samples(sample_dirs, sample_names, group_filename, gff_filename, count_filename, args.field_to_use, args.fuzzy_junction, fastq_filename)