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PSORT(1) User Commands PSORT(1)

NAME

psort - bacterial localization prediction tool

SYNOPSIS

psort [-p|-n] [OPTIONS] [SEQFILE]

DESCRIPTION

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)
--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

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
April 2017 psort 3.0.4