crux q-ranker

Usage:

crux q-ranker [options] <protein input> [ --output-dir <psm folder> ]

Description:

Q-ranker is a semi-supervised learning algorithm that dynamically learns to separate target from decoy PSMs. The algorithm is described in this article:

Marina Spivak, Jason Weston, Leon Bottou and William Stafford Noble. "Direct q value optimization methods for peptide identification from shotgun proteomics data sets." Submitted.

Input:

• <protein input > – The name of the file in fasta format or the directory containing the protein index from which to retrieve proteins and peptides.
• <psm folder> – [optional] A folder in which all the PSM result files are located. This is assumed to be crux-output, but it can be set by the user using the --output-dir option. The program looks for files ending in .csm, which are produced by crux search-for-matches. All such files in the given directory are analyzed jointly.

Options:

• --use-index <T|F> Use an index that has already been created if true (T) or use a fasta file if false (F). When using an index the 'protein input' argument will be the name of the directory containing the index files (the same as the 'index name' argument for crux-create-index). Default = F.
• --fileroot <string> – The fileroot string will be added as a prefix to all output file names. Default = none.
• --output-dir <filename> – The name of the directory where output files will be created. Default = crux-output.
• --overwrite <T|F> Replace existing files if true (T) or fail when trying to overwrite a file if false (F). Default = F.
• --parameter-file <filename> – A file containing command-line or additional parameters. See the parameter documentation page for details.
• --feature-file <string> – Optional file in which to write the features. Default = none.
• --verbosity <0-100> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = 30.
• --version T – Print the version number and quit. Please note that you must include the 'T' after --version.

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