Trilogy

Trilogy 0.03 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to tag peptides in relations files where non-modified peptides are used as reference in PTM analysis.

Usage:

trilogy.py -a paramterTest -i .\data\testParameter.txt -c Corr_Seq-mass
                  -C fastaDescription -n "[-0.000232]|[1.001701]&D=NonMod"
                  -p .\data -t "[15.994862]=Oxidation|PTMs" -s Scan -f FileName

Options:

 --version             show program's version number and exit
 -h, --help            show this help message and exit
 -a ANALYSIS, --analysis=ANALYSIS
                       Use a prefix for the output files. If this is not
                       provided, then no prefix will be garnered.
 -p OUTPUTFOLDER, --place=OUTPUTFOLDER
                       Provide the output folder location, Id this
                       notprovided rhen ouput files will be careated in
                       thesame location as input file.
 -i INPUTFILE, --inputFile=INPUTFILE
                       Enter the path for inputfile, any tab-separated file
                       can be used as a input. Example: SHIFTS output or
                       Aljamia output
 -c PEPTIDECOLUMN, --peptideHeader=PEPTIDECOLUMN
                       Identifier for the peptide coloumn
 -C PROTEINCOLUMN, --proteinHeader=PROTEINCOLUMN
                       Identifier for the protein/FastaDescription column
 -s SCANCOLUMN, --ScanHeader=SCANCOLUMN
                       Identifier for the scan coloumn
 -f RAWCOLUMN, --RawfileHeader=RAWCOLUMN
                       Identifier for the raw filename coloumn
 -n NMAPEXMASS, --NonmodMass=NMAPEXMASS
                       This parameter allows to TAG non-modified
                       peptides.Tagging can be done in a very flexible manner
                       byusing different Tagging options in combination.Some
                       defualt tagging options are also includedCheck for
                       exmaple option below 1)
                       [-0.000232]|[1.001701]&!D=NonMod
                       multiple things can be considered to a Null-
                       hypothesisin eg.1, [-0.000232] and [1.001701] both are
                       consideredas NH, seprated by a |. In addition,
                       additional conditionscan be used as [1.001701]&!D,
                       means,[1.001701] shouldbe in peptide but D should not
                       be. anythying after = will used as tag for NH
 -t PTMTAGS, --PTMtags=PTMTAGS
                       This parameter allows to TAG modified peptides.Tagging
                       can be done in a very flexible manner byusing
                       different Tagging options in combination.Some defualt
                       tagging options are also included example 1)
                       [15.994862]=Oxidation,[0.010924]=c13|PTMs , in this eg
                       multiple things are considered as modification and all
                       of them have differet label, howeverfor the things
                       which are not in input can also be tagged as
                       modification by using |