3.9. broad_utils.py - for data generated at the Broad InstituteΒΆ
Utilities for getting sequences out of the Broad walk-up sequencing pipeline. These utilities are probably not of much use outside the Broad.
usage: broad_utils.py subcommand
- Sub-commands:
- get_bustard_dir
Find the basecalls directory from a Picard directory
usage: broad_utils.py get_bustard_dir [-h] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] inDir
- Positional arguments:
inDir Picard directory - Options:
--loglevel=ERROR Verboseness of output. [default: %(default)s]
Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION
- get_run_date
Find the sequencing run date from a Picard directory
usage: broad_utils.py get_run_date [-h] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] inDir
- Positional arguments:
inDir Picard directory - Options:
--loglevel=ERROR Verboseness of output. [default: %(default)s]
Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION
- get_all_names
Get all samples
usage: broad_utils.py get_all_names [-h] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] {samples,libraries,runs} runfile
- Positional arguments:
type Type of name
Possible choices: samples, libraries, runs
runfile File with seq run information - Options:
--loglevel=ERROR Verboseness of output. [default: %(default)s]
Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION