3.1. metagenomics.py - metagenomic analysesΒΆ

This script contains a number of utilities for metagenomic analyses.

usage: metagenomics.py subcommand
Sub-commands:
kraken

Undocumented

Classify reads by taxon using Kraken

usage: metagenomics.py kraken [-h] [--outReport OUTREPORT]
                              [--outReads OUTREADS]
                              [--filterThreshold FILTERTHRESHOLD]
                              [--numThreads NUMTHREADS]
                              [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                              [--version] [--tmp_dir TMP_DIR] [--tmp_dirKeep]
                              inBam db
Positional arguments:
inBam Input unaligned reads, BAM format.
db Kraken database directory.
Options:
--outReport Kraken report output file.
--outReads Kraken per read output file.
--filterThreshold=0.05
 Kraken filter threshold (default %(default)s)
--numThreads=1 Number of threads to run. (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
--tmp_dir=/tmp Base directory for temp files. [default: %(default)s]
--tmp_dirKeep=False
 Keep the tmp_dir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.
diamond

Undocumented

Classify reads by the taxon of the Lowest Common Ancestor (LCA)

usage: metagenomics.py diamond [-h] [--outM8 OUTM8] [--outLca OUTLCA]
                               [--numThreads NUMTHREADS]
                               [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                               [--version] [--tmp_dir TMP_DIR] [--tmp_dirKeep]
                               inBam db taxDb outReport
Positional arguments:
inBam Input unaligned reads, BAM format.
db Diamond database directory.
taxDb Taxonomy database directory.
outReport Output taxonomy report.
Options:
--outM8 Blast m8 formatted output file.
--outLca Output LCA assignments for each read.
--numThreads=1 Number of threads (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
--tmp_dir=/tmp Base directory for temp files. [default: %(default)s]
--tmp_dirKeep=False
 Keep the tmp_dir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.
krona

Undocumented

Create an interactive HTML report from a tabular metagenomic report

usage: metagenomics.py krona [-h] [--queryColumn QUERYCOLUMN]
                             [--taxidColumn TAXIDCOLUMN]
                             [--scoreColumn SCORECOLUMN] [--noHits] [--noRank]
                             [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                             [--version]
                             inTsv db outHtml
Positional arguments:
inTsv Input tab delimited file.
db Krona taxonomy database directory.
outHtml Output html report.
Options:
--queryColumn=2
 Column of query id. (default %(default)s)
--taxidColumn=3
 Column of taxonomy id. (default %(default)s)
--scoreColumn Column of score. (default %(default)s)
--noHits=False Include wedge for no hits.
--noRank=False Include no rank assignments.
--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
report_merge

Undocumented

Merge multiple metegenomic reports into a single metagenomic report. Any Krona input files created by this

usage: metagenomics.py report_merge [-h]
                                    [--outSummaryReport OUT_KRAKEN_SUMMARY]
                                    [--krakenDB KRAKEN_DB]
                                    [--outByQueryToTaxonID OUT_KRONA_INPUT]
                                    [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                                    [--version] [--tmp_dir TMP_DIR]
                                    [--tmp_dirKeep]
                                    metagenomic_reports
                                    [metagenomic_reports ...]
Positional arguments:
metagenomic_reports
 Input metagenomic reports with the query ID and taxon ID in the 2nd and 3rd columns (Kraken format)
Options:
--outSummaryReport
 Path of human-readable metagenomic summary report, created by kraken-report
--krakenDB Kraken database (needed for outSummaryReport)
--outByQueryToTaxonID
 Output metagenomic report suitable for Krona input.
--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
--tmp_dir=/tmp Base directory for temp files. [default: %(default)s]
--tmp_dirKeep=False
 Keep the tmp_dir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.