CataPep

cataPep v1.03 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to make zero the XCorrs of all the PSMs in an MSF file, excluding those provided in a list.

Usage:

catapep.py [-h] -a ANALYSIS -p PLACE [-L LOGFILE] -d INPUTFILE -M
                 MSFFILE [-r RAWFILECOL] [-s SCANNUMBERCOL] [-q CHARGECOL]
                 [-S PEPSEQUENCECOL] [-x XCORRCOL] [-R INITIALROW] [-v] [-Q]
                 [-O]

Arguments:

 -h, --help            show this help message and exit
 -a ANALYSIS, --analysis ANALYSIS
                       Use a prefix for the output files.
 -p PLACE, --place PLACE
                       To use a different common folder for the output files.
                       If this is not provided, the the folder used will be
                       the same as the FASTA file folder.
 -L LOGFILE, --logfile LOGFILE
                       To use a non-default name for the log file.
 -d INPUTFILE, --inputfile INPUTFILE
                       Name of the text file containing the list of PSMs to
                       keep in the MSF.
 -M MSFFILE, --msffile MSFFILE
                       Name of the MSF file having the PSMs to modify.
 -r RAWFILECOL, --rawfilecol RAWFILECOL
                       Header of the column contaning the name of the RAW
                       files. Default is "RAWFileName".
 -s SCANNUMBERCOL, --scannumbercol SCANNUMBERCOL
                       Header of the column containing the scan numbers.
                       Default is "FirstScan".
 -q CHARGECOL, --chargecol CHARGECOL
                       Header of the column containing the charge. Default is
                       "Charge".
 -S PEPSEQUENCECOL, --pepsequencecol PEPSEQUENCECOL
                       Header of the column containing the identified peptide
                       sequences. Default is "Sequence"
 -x XCORRCOL, --xcorrcol XCORRCOL
                       Header of the column containing the XCorr. Default is
                       "XC1D".
 -R INITIALROW, --initialrow INITIALROW
                       The position of the row containing the headers.
                       Default is 1.
 -v, --verbose         Show extra info while operating.
 -Q, --quixml          Use column headers for QuiXML results tab separated
                       table file (otherwise, pRatio results file headers
                       will be used by default).
 -O, --changeoriginalmsf
                       Do not copy the MSF file to be modified, just remove
                       bad PSMs in the original file.