2.1. taxon_filter.py - tools for taxonomic removal or filtration of readsΒΆ
This script contains a number of utilities for filtering NGS reads based on membership or non-membership in a species / genus / taxonomic grouping.
usage: taxon_filter.py subcommand
- Sub-commands:
- deplete_human
Undocumented
usage: taxon_filter.py deplete_human [-h] [--taxfiltBam TAXFILTBAM] --bmtaggerDbs BMTAGGERDBS [BMTAGGERDBS ...] --blastDbs BLASTDBS [BLASTDBS ...] [--lastDb LASTDB] [--JVMmemory JVMMEMORY] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] [--tmpDir TMPDIR] [--tmpDirKeep] inBam revertBam bmtaggerBam rmdupBam blastnBam
- Positional arguments:
inBam Input BAM file. revertBam Output BAM file. bmtaggerBam Output BAM file. rmdupBam Output BAM file. blastnBam Output BAM file. - Options:
--taxfiltBam Output BAM file. --bmtaggerDbs Reference databases (one or more) to deplete from input. For each db, requires prior creation of db.bitmask by bmtool, and db.srprism.idx, db.srprism.map, etc. by srprism mkindex. --blastDbs One or more reference databases for blast. --lastDb One reference database for last. --JVMmemory=4g 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.
- trim_trimmomatic
Undocumented
usage: taxon_filter.py trim_trimmomatic [-h] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] [--tmpDir TMPDIR] [--tmpDirKeep] inFastq1 inFastq2 pairedOutFastq1 pairedOutFastq2 clipFasta
- Positional arguments:
inFastq1 Input reads 1 inFastq2 Input reads 2 pairedOutFastq1 Paired output 1 pairedOutFastq2 Paired output 2 clipFasta Fasta file with adapters, PCR sequences, etc. to clip off - Options:
--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.
- filter_lastal_bam
Undocumented
usage: taxon_filter.py filter_lastal_bam [-h] [--JVMmemory JVMMEMORY] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] [--tmpDir TMPDIR] [--tmpDirKeep] inBam db outBam
- Positional arguments:
inBam Input reads db Database of taxa we keep outBam Output reads, filtered to refDb - Options:
--JVMmemory=4g 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.
- filter_lastal
Undocumented
usage: taxon_filter.py filter_lastal [-h] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] [--tmpDir TMPDIR] [--tmpDirKeep] inFastq refDb outFastq
- Positional arguments:
inFastq Input fastq file refDb Reference database to retain from input outFastq Output fastq file - Options:
--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.
- partition_bmtagger
Undocumented
usage: taxon_filter.py partition_bmtagger [-h] [--outMatch OUTMATCH OUTMATCH] [--outNoMatch OUTNOMATCH OUTNOMATCH] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] [--tmpDir TMPDIR] [--tmpDirKeep] inFastq1 inFastq2 refDbs [refDbs ...]
- Positional arguments:
inFastq1 Input fastq file; 1st end of paired-end reads. inFastq2 Input fastq file; 2nd end of paired-end reads. Must have same names as inFastq1 refDbs Reference databases (one or more) to deplete from input. For each db, requires prior creation of db.bitmask by bmtool, and db.srprism.idx, db.srprism.map, etc. by srprism mkindex. - Options:
--outMatch Filenames for fastq output of matching reads. --outNoMatch Filenames for fastq output of unmatched reads. --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.
- deplete_bam_bmtagger
Undocumented
usage: taxon_filter.py deplete_bam_bmtagger [-h] [--JVMmemory JVMMEMORY] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] [--tmpDir TMPDIR] [--tmpDirKeep] inBam refDbs [refDbs ...] outBam
- Positional arguments:
inBam Input BAM file. refDbs Reference databases (one or more) to deplete from input. For each db, requires prior creation of db.bitmask by bmtool, and db.srprism.idx, db.srprism.map, etc. by srprism mkindex. outBam Output BAM file. - Options:
--JVMmemory=4g 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.
- deplete_blastn
Undocumented
usage: taxon_filter.py deplete_blastn [-h] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] [--tmpDir TMPDIR] [--tmpDirKeep] inFastq outFastq refDbs [refDbs ...]
- Positional arguments:
inFastq Input fastq file. outFastq Output fastq file with matching reads removed. refDbs One or more reference databases for blast. - Options:
--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.
- deplete_blastn_paired
Undocumented
usage: taxon_filter.py deplete_blastn_paired [-h] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] [--tmpDir TMPDIR] [--tmpDirKeep] infq1 infq2 outfq1 outfq2 refDbs [refDbs ...]
- Positional arguments:
infq1 Input fastq file. infq2 Input fastq file. outfq1 Output fastq file with matching reads removed. outfq2 Output fastq file with matching reads removed. refDbs One or more reference databases for blast. - Options:
--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.
- deplete_blastn_bam
Undocumented
usage: taxon_filter.py deplete_blastn_bam [-h] [--JVMmemory JVMMEMORY] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] [--tmpDir TMPDIR] [--tmpDirKeep] inBam refDbs [refDbs ...] outBam
- Positional arguments:
inBam Input BAM file. refDbs One or more reference databases for blast. outBam Output BAM file with matching reads removed. - Options:
--JVMmemory=4g 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.