IDCONVERT

1 idconvert

idconvert

Convert mass spectrometry identification file formats.

          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

-v | --verbose

- Display detailed processing progress information.

-f | --filelist `filename`

- Uses the contents of `filename` which lists filenames.

-o | --outdir `dir`

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

-c | --config `filename`

- Set the configuration file to `filename`.

-e | --ext `ext`

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

--mzIdentML

- Write `mzIdentML` format (default).

--pepXML

- Write `pepXML` format.

--text

- 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`'.