3.1. metagenomics.py - metagenomic analysesΒΆ
This script contains a number of utilities for metagenomic analyses.
usage: metagenomics.py subcommand
- Sub-commands:
- kraken
Undocumented
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
usage: metagenomics.py diamond [-h] [--numThreads NUMTHREADS] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] [--tmp_dir TMP_DIR] [--tmp_dirKeep] inBam db outM8
- Positional arguments:
inBam Input unaligned reads, BAM format. db Diamond database directory. outM8 Blast m8 formatted output file. - Options:
--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
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