crux subtract-index [options] <tide index 1> <tide index 2> <output index>
This command takes two peptide indices, created by the tide-index command, and subtracts the second index from the first. The result is an output index that contains peptides that appear in the first index but not the second.
tide index 1– A peptide index produced using tide-index
tide index 2– A second peptide index, to be subtracted from the first index.
output index– A new peptide index containing all peptides that occur in thefirst index but not the second.
The program writes files to the folder
crux-output by default. The name of the output folder can be set by the user using the
--output-dir option. The following files will be created:
subtract-index.target.txt– a tab-delimited text file containing the target peptides.
subtract-index.decoy.txt– a tab-delimited text file containing the decoy peptides.
subtract-index.log.txt– a log file containing a copy of all messages that were printed to stderr.
subtract-index.params.txt– a file containing the name and value of all parameters/options 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.
Input and output
--verbosity <integer>– 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 =
--parameter-file <string>– A file containing parameters. See the parameter documentation page for details. Default =
--overwrite T|F– Replace existing files if true or fail when trying to overwrite a file if false. Default =
--peptide-list T|F– Create in the output directory a text file listing of all the peptides in the database, along with their neutral masses, one per line. If decoys are generated, then a second file will be created containing the decoy peptides. Decoys that also appear in the target database are marked with an asterisk in a third column. Default =
--output-dir <string>– The name of the directory where output files will be created. Default =