divvy_proteomics

Takes a DTASelect CSV file, and parses the result so non-unique peptides get accounted for.

Install

Get ruby somehow, if you don’t already have it. Then, install this gem:

$ gem install divvy_proteomics

Or if there is permissions problems e.g. on OSX,

$ sudo gem install divvy_proteomics

Usage

To test it work and to get a full listing of help

$ divvy_spectra -h

To run on a PepXML file e.g.

$ divvy_spectra --pep-xml my.pep.xml

or a DTASelect file

$ divvy_spectra DTASelect_file

Output is a table, with a row for each protein with a few columns, including number of unique spectra and the estimated number of spectral counts after sorting out the non-uniqueness.

Full usage information:

    Usage: divvy_spectra [options] <input_file>

    Takes a tab separated file containing a (possibly modified) output from a DTAselect run (or a pepXML file and add the flag --pep-xml), and use some algorithm to divy up the spectra that match multiple peptides.

        --merge-proteins FILE_OF_IDENTIFIERS
                                     Provide a space/tab separated file where the identifiers on each row should be treated as one protein
        --whitelist FILE_OF_PROTEINS_TO_REPORT
                                     Only report proteins that are in this whitelist, after divvying with everything
        --contaminant-regexes REGEXES
                                     Comma-separated list of regular expressions to apply to protein names. If the protein name matches then all spectra assigned to that protein are considered contaminants. [default: ]

Optional arguments:

        --pep-xml                    Input file is pep XML, rather than a DTA select output file [default: false]

Verbosity:

    -q, --quiet                      Run quietly, set logging to ERROR level [default INFO]
        --logger filename            Log to file [default stderr]
        --trace options              Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG

Contributing to divvy_proteomics

Copyright © 2013-2015 Ben J Woodcroft. See LICENSE.txt for further details.