3.7. 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

Undocumented

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

Undocumented

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

Undocumented

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

make_barcodes_file

Undocumented

usage: broad_utils.py make_barcodes_file [-h] inFile outFile
Positional arguments:
inFile Input tab file w/header and 3-5 named columns (last two are optional): sample, barcode_1, barcode_2, library_id_per_sample, run_id_per_library
outFile Output BARCODE_FILE file for Picard.
extract_barcodes

Undocumented

usage: broad_utils.py extract_barcodes [-h] [--outMetrics OUTMETRICS]
                                       [--read_structure READ_STRUCTURE]
                                       [--max_mismatches MAX_MISMATCHES]
                                       [--minimum_base_quality MINIMUM_BASE_QUALITY]
                                       [--min_mismatch_delta MIN_MISMATCH_DELTA]
                                       [--max_no_calls MAX_NO_CALLS]
                                       [--minimum_quality MINIMUM_QUALITY]
                                       [--compress_outputs COMPRESS_OUTPUTS]
                                       [--num_processors NUM_PROCESSORS]
                                       [--JVMmemory JVMMEMORY]
                                       [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                                       [--version] [--tmpDir TMPDIR]
                                       [--tmpDirKeep]
                                       inDir lane barcodeFile outDir
Positional arguments:
inDir Bustard directory.
lane Lane number.
barcodeFile Input tab file w/header and four named columns: barcode_name, library_name, barcode_sequence_1, barcode_sequence_2
outDir Output directory for barcodes.
Options:
--outMetrics Output metrics file. Default is to dump to a temp file.
--read_structure=101T8B8B101T
 Picard ExtractIlluminaBarcodes READ_STRUCTURE (default: %(default)s)
--max_mismatches=1
 Picard ExtractIlluminaBarcodes MAX_MISMATCHES (default: %(default)s)
--minimum_base_quality=15
 Picard ExtractIlluminaBarcodes MINIMUM_BASE_QUALITY (default: %(default)s)
--min_mismatch_delta
 Picard ExtractIlluminaBarcodes MIN_MISMATCH_DELTA (default: %(default)s)
--max_no_calls Picard ExtractIlluminaBarcodes MAX_NO_CALLS (default: %(default)s)
--minimum_quality
 Picard ExtractIlluminaBarcodes MINIMUM_QUALITY (default: %(default)s)
--compress_outputs
 Picard ExtractIlluminaBarcodes COMPRESS_OUTPUTS (default: %(default)s)
--num_processors=4
 Picard ExtractIlluminaBarcodes NUM_PROCESSORS (default: %(default)s)
--JVMmemory=8g JVM virtual memory size (default: %(default)s)
--loglevel=DEBUG
 

Verboseness of output. [default: %(default)s]

Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION

--version, -V show program’s version number and exit
--tmpDir=/tmp Base directory for temp files. [default: %(default)s]
--tmpDirKeep=False
 Keep the tmpDir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.
make_params_file

Undocumented

usage: broad_utils.py make_params_file [-h] inFile bamDir outFile
Positional arguments:
inFile Input tab file w/header and four named columns: barcode_name, library_name, barcode_sequence_1, barcode_sequence_2
bamDir Directory for output bams
outFile Output LIBRARY_PARAMS file for Picard
illumina_basecalls

Undocumented

usage: broad_utils.py illumina_basecalls [-h]
                                         [--read_structure READ_STRUCTURE]
                                         [--sequencing_center SEQUENCING_CENTER]
                                         [--adapters_to_check [ADAPTERS_TO_CHECK [ADAPTERS_TO_CHECK ...]]]
                                         [--platform PLATFORM]
                                         [--max_reads_in_ram_per_tile MAX_READS_IN_RAM_PER_TILE]
                                         [--max_records_in_ram MAX_RECORDS_IN_RAM]
                                         [--num_processors NUM_PROCESSORS]
                                         [--apply_eamss_filter APPLY_EAMSS_FILTER]
                                         [--force_gc FORCE_GC]
                                         [--first_tile FIRST_TILE]
                                         [--tile_limit TILE_LIMIT]
                                         [--include_non_pf_reads INCLUDE_NON_PF_READS]
                                         [--run_start_date RUN_START_DATE]
                                         [--read_group_id READ_GROUP_ID]
                                         [--JVMmemory JVMMEMORY]
                                         [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                                         [--version] [--tmpDir TMPDIR]
                                         [--tmpDirKeep]
                                         inBustardDir inBarcodesDir flowcell
                                         lane paramsFile
Positional arguments:
inBustardDir Bustard directory.
inBarcodesDir Barcodes directory.
flowcell Flowcell ID
lane Lane number.
paramsFile Input tab file w/header and five named columns: BARCODE_1, BARCODE_2, OUTPUT, SAMPLE_ALIAS, LIBRARY_NAME
Options:
--read_structure=101T8B8B101T
 Picard ExtractIlluminaBarcodes READ_STRUCTURE (default: %(default)s)
--sequencing_center=BI
 Picard ExtractIlluminaBarcodes SEQUENCING_CENTER (default: %(default)s)
--adapters_to_check=('PAIRED_END', 'NEXTERA_V1', 'NEXTERA_V2')
 Picard ExtractIlluminaBarcodes ADAPTERS_TO_CHECK (default: %(default)s)
--platform Picard ExtractIlluminaBarcodes PLATFORM (default: %(default)s)
--max_reads_in_ram_per_tile=100000
 Picard ExtractIlluminaBarcodes MAX_READS_IN_RAM_PER_TILE (default: %(default)s)
--max_records_in_ram=100000
 Picard ExtractIlluminaBarcodes MAX_RECORDS_IN_RAM (default: %(default)s)
--num_processors=4
 Picard ExtractIlluminaBarcodes NUM_PROCESSORS (default: %(default)s)
--apply_eamss_filter
 Picard ExtractIlluminaBarcodes APPLY_EAMSS_FILTER (default: %(default)s)
--force_gc=False
 Picard ExtractIlluminaBarcodes FORCE_GC (default: %(default)s)
--first_tile Picard ExtractIlluminaBarcodes FIRST_TILE (default: %(default)s)
--tile_limit Picard ExtractIlluminaBarcodes TILE_LIMIT (default: %(default)s)
--include_non_pf_reads
 Picard ExtractIlluminaBarcodes INCLUDE_NON_PF_READS (default: %(default)s)
--run_start_date
 Picard ExtractIlluminaBarcodes RUN_START_DATE (default: %(default)s)
--read_group_id
 Picard ExtractIlluminaBarcodes READ_GROUP_ID (default: %(default)s)
--JVMmemory=54g
 JVM virtual memory size (default: %(default)s)
--loglevel=DEBUG
 

Verboseness of output. [default: %(default)s]

Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION

--version, -V show program’s version number and exit
--tmpDir=/tmp Base directory for temp files. [default: %(default)s]
--tmpDirKeep=False
 Keep the tmpDir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.