http://wikis.cnic.es/proteomica/index.php?action=history&feed=atom&title=TrilogyTrilogy - Revision history2026-04-07T23:12:53ZRevision history for this page on the wikiMediaWiki 1.30.1http://wikis.cnic.es/proteomica/index.php?title=Trilogy&diff=493&oldid=prevMtrevisan at 14:18, 19 February 20182018-02-19T14:18:36Z<p></p>
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<td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 14:18, 19 February 2018</td>
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</table>Mtrevisanhttp://wikis.cnic.es/proteomica/index.php?title=Trilogy&diff=452&oldid=prevMtrevisan: creation2017-11-29T13:57:20Z<p>creation</p>
<p><b>New page</b></p><div>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.<br />
<br />
Usage:<br />
trilogy.py -a paramterTest -i .\data\testParameter.txt -c Corr_Seq-mass<br />
-C fastaDescription -n "[-0.000232]|[1.001701]&D=NonMod"<br />
-p .\data -t "[15.994862]=Oxidation|PTMs" -s Scan -f FileName<br />
<br />
Options:<br />
<br />
--version show program's version number and exit<br />
-h, --help show this help message and exit<br />
-a ANALYSIS, --analysis=ANALYSIS<br />
Use a prefix for the output files. If this is not<br />
provided, then no prefix will be garnered.<br />
-p OUTPUTFOLDER, --place=OUTPUTFOLDER<br />
Provide the output folder location, Id this<br />
notprovided rhen ouput files will be careated in<br />
thesame location as input file.<br />
-i INPUTFILE, --inputFile=INPUTFILE<br />
Enter the path for inputfile, any tab-separated file<br />
can be used as a input. Example: SHIFTS output or<br />
Aljamia output<br />
-c PEPTIDECOLUMN, --peptideHeader=PEPTIDECOLUMN<br />
Identifier for the peptide coloumn<br />
-C PROTEINCOLUMN, --proteinHeader=PROTEINCOLUMN<br />
Identifier for the protein/FastaDescription column<br />
-s SCANCOLUMN, --ScanHeader=SCANCOLUMN<br />
Identifier for the scan coloumn<br />
-f RAWCOLUMN, --RawfileHeader=RAWCOLUMN<br />
Identifier for the raw filename coloumn<br />
-n NMAPEXMASS, --NonmodMass=NMAPEXMASS<br />
This parameter allows to TAG non-modified<br />
peptides.Tagging can be done in a very flexible manner<br />
byusing different Tagging options in combination.Some<br />
defualt tagging options are also includedCheck for<br />
exmaple option below 1)<br />
[-0.000232]|[1.001701]&!D=NonMod<br />
multiple things can be considered to a Null-<br />
hypothesisin eg.1, [-0.000232] and [1.001701] both are<br />
consideredas NH, seprated by a |. In addition,<br />
additional conditionscan be used as [1.001701]&!D,<br />
means,[1.001701] shouldbe in peptide but D should not<br />
be. anythying after = will used as tag for NH<br />
-t PTMTAGS, --PTMtags=PTMTAGS<br />
This parameter allows to TAG modified peptides.Tagging<br />
can be done in a very flexible manner byusing<br />
different Tagging options in combination.Some defualt<br />
tagging options are also included example 1)<br />
[15.994862]=Oxidation,[0.010924]=c13|PTMs , in this eg<br />
multiple things are considered as modification and all<br />
of them have differet label, howeverfor the things<br />
which are not in input can also be tagged as<br />
modification by using |</div>Mtrevisan