README.rdoc

Mascot::MGF¶ ↑

A parser for Mascot Generic Format (MGF) files.

MGF Format ¶ ↑

The Mascot::MGF object represents a file of MSMS spectra. See www.matrixscience.com/help/data_file_help.html#GEN for more information on this file format.

Mascot::MGF¶ ↑

A subclass of File, opens an MGF flat file to read entries using Enumerable syntax.

Mascot::MGF::Query¶ ↑

A simple object that represents individual MS/MS spectrum objects in an MGF file. I use “Query” instead of “Spectrum” to remain consistent with Mascot”s terminology.

Simple Usage Examples¶ ↑

Reading ¶ ↑

require 'mascot/mgf'

# This opens a MGF file and builds an index of the query
# positions. The index is cached to the filesystem.
mgf = Mascot::MGF.open("some/file/path.mgf")

# Same thing as above, but does not cache the index to filesystem
mgf = Mascot::MGF.open("some/file/path.mgf",false)

# How many queries are in this file?
mgf.query_count

# Reads the next query from the read cursor position

query_string = mgf.readquery()

# Create a Mascot::MGF::Query from the query string query = Mascot::Query.new(query_string)

puts query.title

# Read the next query as a Mascot::MGF::Query object query = mgf.query() puts query.title

# puts cursor at begining of MGF file mgf.rewind

mgf.each_query do |query_object|
  # do something with query...
end