Difference between revisions of "CataPep"
(Created page with "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...") |
(No difference)
|
Revision as of 16:38, 3 October 2017
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.