Mtrevisan at 14:18, 19 February 2018

2018-02-19T14:18:47Z

Mtrevisan: 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..."

2017-10-03T14:38:24Z

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..."

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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.

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	Do not copy the MSF file to be modified, just remove		Do not copy the MSF file to be modified, just remove
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		+	[[Category:SanXoT software package]]

CataPep - Revision history

Mtrevisan at 14:18, 19 February 2018

Mtrevisan: 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..."