Data

Tools

Indexes

Applications

Experiments

Open Source Science

scavager

https://github.com/markmipt/scavager

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.4%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: markmipt
  • License: other
  • Language: Python
  • Default Branch: master
  • Size: 252 KB
Statistics
  • Stars: 5
  • Watchers: 2
  • Forks: 2
  • Open Issues: 0
  • Releases: 3
Created about 6 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

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 PSMsfull.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 proteingroups.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

Details on combination of parsimony principle and MS1 information are available at: https://github.com/markmipt/proteininferenceusing_DirectMS1

Protein grouping for indistinguishable proteins

By default, when multiple proteins have the same sets of peptides, the Scavager choose protein group leader using alphabetical order. However, it is possible to choose group leader randomly by using "-sr" option. The same option can be used with MS1 spectra information if multiple proteins have both same sets of MS/MS identifications and DirectMS1 scores.

Links

  • GitHub repo & issue tracker: https://github.com/markmipt/scavager
  • Mailing list: pyteomics@googlegroups.com, markmipt@gmail.com

Owner

  • Name: Mark Ivanov
  • Login: markmipt
  • Kind: user
  • Location: Moscow

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 190
  • Total Committers: 4
  • Avg Commits per committer: 47.5
  • Development Distribution Score (DDS): 0.426
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Mark Ivanov m****t@g****m 109
Lev Levitsky l****y@p****u 77
markmipt m****k@b****n 3
markmipt m****t@l****t 1
Committer Domains (Top 20 + Academic)
bigdata.localdomain: 1 phystech.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: 5 months
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ashwinkallor (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 33 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 10
  • Total maintainers: 1
pypi.org: scavager

Proteomics post-search algorithm

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 33 Last month
Rankings
Dependent packages count: 10.0%
Average: 19.8%
Stargazers count: 21.5%
Dependent repos count: 21.7%
Forks count: 22.6%
Downloads: 23.2%
Maintainers (1)
markmipt
Last synced: 11 months ago

Dependencies

requirements.txt pypi
  • catboost *
  • lxml *
  • matplotlib *
  • numpy *
  • pandas *
  • pyteomics >=3.5
  • scikit-learn *
  • scipy *
setup.py pypi
  • line.strip *