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