Scroll to navigation

IDCONVERT (1) General Commands Manual IDCONVERT (1)

NAME

idconvert — Convert mass spectrometry identification file formats.

SYNOPSIS

idconvert [options] [filemasks]

DESCRIPTION

This manual page documents briefly the idconvert software shipped within the libpwiz-tools package. This program allows one to convert mass spectrometry protein identification data files from one format to another.

OPTIONS

Display detailed processing progress information.

Uses the contents of filename which lists filenames.

Set the output directory ('-' for stdout) to dir. By default, the output directory is '.' (that is, the current working directory).

Set the configuration file to filename.

Set the extension of the output files to ext. Can be mzid or pepXML or txt.

Write mzIdentML format (default).

Write pepXML format.

Write hierarchical text format.

EXAMPLES

Convert sequest.pepXML to sequest.mzid

idconvert sequest.pepXML

Convert mascot.mzid to mascot.pepXML

idconvert mascot.mzid --pepXML

Use a configuration file

idconvert xtandem.pep.xml -c config.txt

RETURN VALUE

The number of failed files.

AUTHOR

Filippo Rusconi <lopippo@debian.org>

This manual page was written by Filippo Rusconi <lopippo@debian.org> (initial writing 05 december 2013). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3, published by the Free Software Foundation.

On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'.