Metadata-Version: 2.1
Name: Scavager
Version: 0.2.4
Summary: Proteomics post-search algorithm
Home-page: https://github.com/markmipt/scavager
Author: Mark Ivanov & Lev Levitsky & Julia Bubis
Author-email: pyteomics@googlegroups.com
License: License :: OSI Approved :: Apache Software License
Description: Scavager - a proteomics post-search validation tool
        ---------------------------------------------------
        
        The pepXML or MzIdentML files are required for basic operation of the script. Currently supported search engines:
        IdentiPy, X!Tandem, Comet, MSFragger, MSGF+, Morpheus.
        
        FASTA file is required for calculation of NSAF (label-free quantitation index), protein sequence coverage and amino acid statistics.
        
        For MSGF+ and Morpheus search engines it is desirable to provide cleavage rules used in search
        (these search engines do not report number of missed cleavages for peptides).
        
        The output of Scavager contains:
        
        - tab-separated table with unfiltered peptide-spectrum matches (ends with _PSMs_full.tsv)
        - tab-separated table with identified peptide-spectrum matches at 1% PSM FDR (ends with _PSMs.tsv)
        - tab-separated table with identified peptides at 1% peptide FDR (ends with _peptides.tsv)
        - tab-separated table with identified proteins without grouping at 1% protein FDR (ends with _proteins.tsv)
        - tab-separated table with identified protein groups at 1% protein FDR (ends with _protein_groups.tsv)
        - PNG figure with PSM, peptide and protein features distributions
        
        Citing Scavager
        ---------------
        Ivanov et al. Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting. doi: 10.1002/pmic.201800280
        
        Installation
        ------------
        Using pip:
        
            pip install Scavager
        
        
        Usage
        -----
        Algorithm can be run with following command (works with Python2.7/Python3+):
        
            scavager path_to_pepXML/MZID
        
        OR
        
            scavager -h
        
        Protein grouping using DirectMS1 results
        ----------------------------------------
        Protein groups can be generated using parsimony principle combined with information from MS1 spectra:
            scavager path_to_pepXML/MZID -ms1 path_to_DirectMS1_proteins_full_noexclusion.tsv
        
        
        Links
        -----
        
        - GitHub repo & issue tracker: https://github.com/markmipt/scavager
        - Mailing list: pyteomics@googlegroups.com, markmipt@gmail.com
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
