psort1
Bacterial localization prediction tool
Usage
psort [{-p | -n}]
[OPTIONS]
[SEQFILE]
Overview
Runs psort on the sequence file SEQFILE . If SEQFILE isn't provided then sequences will be read from STDIN.
-
--help, -h -
Displays usage information
-
--positive, -p -
Gram positive bacteria
-
--negative, -n -
Gram negative bacteria
-
--archaea, -a -
Archaea
-
--cutoff, -c -
Sets a cutoff value for reported results
-
--divergent, -d -
Sets a cutoff value for the multiple localization flag
-
--matrix, -m -
Specifies the path to the pftools installation. If not set, defaults to the value of the PSORT_PFTOOLS environment variable.
-
--format, -f -
Specifies sequence format (default is FASTA)
-
--exact, -e -
Skip SCLBLASTe (useful for batch runs of data against itself in SCLBLAST)
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--output, -o -
Specifies the format for the output (default is 'normal' Value can be one of: terse, long or normal
-
--root, -r -
Specify PSORT_ROOT for running local copies. If not set, defaults to the value of the PSORT_ROOT environment variable.
-
--server, -s -
Specifies the PSort server to use
-
--verbose, -v -
Be verbose while running
--x-skip-localization
-
--version -
Print the version of PSortb
Releases
7 releases since Debian 5.0 (Lenny); the text changed 1 time.
--archaea since Debian 10 (Buster);
--cutoff since Debian 10 (Buster);
--divergent since Debian 10 (Buster);
--exact since Debian 10 (Buster);
--format since Debian 10 (Buster);
--help since Debian 10 (Buster);
--matrix since Debian 10 (Buster);
--negative since Debian 10 (Buster);
--output since Debian 10 (Buster);
--positive since Debian 10 (Buster);
--root since Debian 10 (Buster);
--server since Debian 10 (Buster);
--verbose since Debian 10 (Buster);
--version since Debian 10 (Buster);
-a since Debian 10 (Buster);
-c since Debian 10 (Buster);
-d since Debian 10 (Buster);
-e since Debian 10 (Buster);
-f since Debian 10 (Buster);
-h since Debian 10 (Buster);
-m since Debian 10 (Buster);
-n since Debian 10 (Buster);
-o since Debian 10 (Buster);
-p since Debian 10 (Buster);
-r since Debian 10 (Buster);
-s since Debian 10 (Buster);
-v since Debian 10 (Buster).