Usage

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                           Variant Peptides Scoring
          (Annotating the variant peptides using VAS scoring)
                                Version: 1.0
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Program:    PgxSAVy.pl (1.0)
Purpose:    Annotating the variant peptides using VAS scoring.
            Specify a path for file containing variant peptides details and spectra file.

Usage:      PgxSAVy.pl [options] <variant_search_file> <MGF_file>

Options:
            -s <int>        : Search result type (default: 1)
            -e <int>        : Search engine count (default: 1)
            -t <float>      : Fragment tolerance in Da (default: 0.5)
            -f <int>        : Fixed modification (default: 3)
            -v <int>        : Variable modification (default: 1)
            -i <int>        : Instrument type (default: 0)
            -p <int>        : Relative peak intensity in %age (default: 0)
            -m <int>        : Minimum peak (default: 7)
            -b <True|False> : BioAnnotation check (default: TRUE)
            -a <Filename>   : BioAnnotation database file name (default: homo_sapiens_variation.txt)
            -d <True|False> : Keep duplicates (default: FALSE)
            -o <Filename>   : Output file name (default: InputFile_VAS_score_jobtime.tsv)
            -h              : print this usage statement
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Optional Parametres

Search result type

-s    Define the type of input format given for variant search result file. 
      1: tab-separated text file (Default)
      2: MSGF Plus Result file
      3: EuGenoSuite result file

MSGF Plus result need to be converted to tsv from mzid using the converter provided in resources.

Search engine count

-e   Total number of search engines used for the proteogenomic search
     Default: 1

Fragment tolerance

-t   Fragment tolerenace in Da
     Default: 0.5

Fixed Modification

-f   Fixed modification (default: 3)
     A list of modifications is given in modules directory (mods_list.txt).
     Use the code from MOD_ID column for the modification.

Variable Modification

-v    Variable modification (default: 1)
      A list of modifications is given in modules directory (mods_list.txt).
      Use the code from MOD_ID column for the modification.

Instrument type

-i    Instrument type (default: 0)
      0: Low-res LCQ/LTQ (Default), 1: Orbitrap/FTICR/Lumos, 2: TOF, 3: Q-Exactive
      This option is used  when MSGF+ is used as search engine.

Relative peak intensity threshold

-p    Relative peak intensity threshold in percentage (default: 0)
      Minimum peak intensity in spectra to be considered for scoring.

Minimum number of peaks

-m    Minimum peak (default: 7)
      Minimum number of peaks present in spectra to be considered for scoring.

BioAnnotation check

-b    BioAnnotation check (default: TRUE)
      Annotation of scored varinat peptides using variant database downloaded from UniProt.
      By default, annotation is performed using variant database. It takes few minutes to annotate the variant peptides depending upon the number.

BioAnnotation database file name

-a    BioAnnotation database file name (default: homo_sapiens_variation.txt)
      This file is not provided and can be downloaded from UniProt.
      Link: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/variants/homo_sapiens_variation.txt.gz
      After downloading unzip the file and copy it to PgxSAVy directory.

Duplicate scan ID for variant peptide

-d    Keep duplicates (default: FALSE)
      Whether to keep duplicate scans for same varinat peptide. 
      If FALSE, higher scoring scan is kept.