MSF Parser

A Thermo MSF file parser using ActiveRecord as ORM. MSF files are SQLite3-based. This library provides a simple API using ActiveRecord that is directly translatable to the database’s schema.

This gem takes heavily from Angel Pizzaro's thermo_msf gem.

https://github.com/itmat/thermo_msf

WARNING

This gem has not been developed to completion. It has only been taken sufficiently far to serve my present needs.

It has not been tested on MSF files other than those generated by my instrument operating my version of Thermo's Proteome Discoverer (1.3).

Installation

gem install msf

API Usage

msf = MSF.new({:path => msf_file})
Peptides.all do |peptide|
  <whatever>
end

CLI Usage

ibspectra msf_file >> msf_file/msf_file.ibspectra.csv

Note

See erd/erd.png for an Entity Relationship Diagram of the MSF schema.

Contributing to msf

Checkout

git clone [email protected]:bioteam/msf.git; cd msf

Fix bugs, add features

<make changes>

Test

rspec

Update version

rake version:bump:patch

Commit changes

git commit

Release

rake release