2.1. taxon_filter.py - tools for taxonomic removal or filtration of reads

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.