def panel(context, panel, build, bed, version):
"""Export gene panels to .bed like format.
Specify any number of panels on the command line
"""
LOG.info("Running scout export panel")
adapter = context.obj['adapter']
# Save all chromosomes found in the collection if panels
chromosomes_found = set()
if not panel:
LOG.warning("Please provide at least one gene panel")
context.abort()
LOG.info("Exporting panels: {}".format(', '.join(panel)))
if bed:
if version:
version = [version]
lines = export_panels(
adapter=adapter,
panels=panel,
versions=version,
build=build,
)
else:
lines = export_gene_panels(
adapter=adapter,
panels=panel,
version=version,
)
for line in lines:
click.echo(line)
def panel(panel, build, bed, version):
"""Export gene panels to .bed like format.
Specify any number of panels on the command line
"""
LOG.info("Running scout export panel")
adapter = store
# Save all chromosomes found in the collection if panels
chromosomes_found = set()
if not panel:
LOG.warning("Please provide at least one gene panel")
raise click.Abort()
LOG.info("Exporting panels: {}".format(", ".join(panel)))
if bed:
if version:
version = [version]
lines = export_panels(
adapter=adapter, panels=panel, versions=version, build=build
)
else:
lines = export_gene_panels(adapter=adapter, panels=panel, version=version)
for line in lines:
click.echo(line)
def panel_cmd(panel: str, build: str, bed: bool, version: float):
"""Export gene panels to .bed like format.
Specify any number of panels on the command line
"""
LOG.info("Running scout export panel")
adapter = store
if not panel:
LOG.warning("Please provide at least one gene panel")
raise click.Abort()
LOG.info("Exporting panels: {}".format(", ".join(panel)))
if bed:
if version:
version = [version]
lines = export_panels(adapter=adapter,
panels=panel,
versions=version,
build=build)
else:
lines = export_gene_panels(adapter=adapter,
panels=panel,
version=version)
for line in lines:
click.echo(line)
def panel(context, panel, version):
"""Export gene panels to .bed like format.
Specify any number of panels on the command line
"""
LOG.info("Running scout export panel")
adapter = context.obj['adapter']
if not panel:
LOG.warning("Please provide at least one gene panel")
context.abort()
LOG.info("Exporting panels: {}".format(', '.join(panel)))
for line in export_gene_panels(adapter, panel, version):
click.echo(line)