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.