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.