2.12. broad_utils.py - for data generated at the Broad Institute
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
2.12.2. Sub-commands
2.12.2.1. get_bustard_dir
Find the basecalls directory from a Picard directory
broad_utils.py get_bustard_dir [-h]
[--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
inDir
2.12.2.1.1. Positional Arguments
- inDir
Picard directory
2.12.2.1.2. Named Arguments
- --loglevel
Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION
Verboseness of output. [default: ‘ERROR’]
Default:
'ERROR'
2.12.2.2. get_run_date
Find the sequencing run date from a Picard directory
broad_utils.py get_run_date [-h]
[--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
inDir
2.12.2.2.1. Positional Arguments
- inDir
Picard directory
2.12.2.2.2. Named Arguments
- --loglevel
Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION
Verboseness of output. [default: ‘ERROR’]
Default:
'ERROR'
2.12.2.3. get_all_names
Get all samples
broad_utils.py get_all_names [-h]
[--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
{samples,libraries,runs} runfile
2.12.2.3.1. Positional Arguments
- type
Possible choices: samples, libraries, runs
Type of name
- runfile
File with seq run information
2.12.2.3.2. Named Arguments
- --loglevel
Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION
Verboseness of output. [default: ‘ERROR’]
Default:
'ERROR'