make-pin
Usage:
crux make-pin [options] <search results>
Description:
Make-pin is a utility program that combines a collection of target and decoy peptide-spectrum matches (PSMs) into a single file in pin format, according to this format. The resulting file can be provided as input to
crux percolator
.
make-pin
requires as input two sets of PSMs, one set derived from matching observed spectra against real ("target") peptides and a second set derived from matching the same spectra against "decoy" peptides. The output file contains, for each PSM, a set of features for use by the Percolator algorithm. These features are summarized here.Note that, in the stand-alone version of Percolator, the functionality provided by
crux make-pin
is incorporated into a program calledsqt2pin
. However, a significant difference betweencrux percolator
and the stand-alone version of the program is thatcrux percolator
does not require an explicit call tocrux make-pin
: if input is provided tocrux percolator
in a non-SQT format, then the input will be automatically converted to pin format.Input:
<search results> – A collection of target and decoy peptide-spectrum matches (PSMs). Input may be in one of five formats: SQT, PepXML (obtained from SEQUEST), Crux tab-delimited text, list of files (when
list-of-files=T
, or a tab-delimited table of features (whenfeature-in-file=T
, see below for details).Decoy PSMs can be provided to
make-pin
in two ways: either as a separate file or embedded within the same file as the target PSMs. Percolator will first search for target PSMs in a separate file. The decoy file name is constructed from the target name by replacing "target" with "decoy." For example, ifsearch.target.txt
is provided as input, thenmake-pin
will search for a corresponding file namedsearch.decoy.txt
. If no decoy file is found, then Percolator will assume that the given input file contains a mix of target and decoy PSMs. Within this file, decoys are identified using a prefix (specified via--decoy-prefix
) on the protein name.Output:
The program writes the following files in the
crux-output
directory:
- make-pin.pin: a tab-delimited file containing the input target and decoy PSMs in pin format. This file can be changed to an absolute path (see
--output-file
option).- make-pin.params.txt: a file containing the name and value of all parameters for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the
--parameter-file
option for other crux programs.- make-pin.log.txt: a log file containing a copy of all messages that were printed to standard error.
Options:
--top-match <integer>
The number of psms per spectrum written to the pin file. Default = 5.--list-of-files <T|F>
– Specify that the search results are provided as lists of files, rather than as individual files. Default = F.--decoy-prefix <string>
– Specifies the protein name prefix that indicates a decoy. Default = "decoy_".--fileroot <string>
– Thefileroot
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.--output-file <file>
– Absolute path where pin file will be written. This option overrides crux'soutput-dir
andfileroot
file naming convention. Default = no absolute pathname.--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 for details.--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.
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