bio-stockholm
Stockholm format file parser for ruby.
Installation
gem install bio-stockholmUsage
An example stockholm format file, from https://en.wikipedia.org/wiki/Stockholm_format
# STOCKHOLM 1.0
#=GF ID CBS1
#=GF AC PF00571
#=GF DE CBS domain
#=GF AU Bateman A
#=GF CC CBS domains are small intracellular modules mostly found
#=GF CC in 2 or four copies within a protein.
#=GF SQ 5
#=GS O31698/18-71 AC O31698
#=GS O83071/192-246 AC O83071
#=GS O83071/259-312 AC O83071
#=GS O31698/88-139 AC O31698
#=GS O31698/88-139 OS Bacillus subtilis
O83071/192-246 MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS
#=GR O83071/192-246 SA 9998877564535242525515252536463774777
O83071/259-312 MQHVSAPVFVFECTRLAYVQHKLRAHSRAVAIVLDEY
#=GR O83071/259-312 SS CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEE
O31698/18-71 MIEADKVAHVQVGNNLEHALLVLTKTGYTAIPVLDPS
#=GR O31698/18-71 SS CCCHHHHHHHHHHHHHHHEEEEEEEEEEEEEEEEHHH
O31698/88-139 EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
#=GR O31698/88-139 SS CCCCCCCHHHHHHHHHHHHEEEEEEEEEEEEEEEEEH
#=GC SS_cons CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEH
O31699/88-139 EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
#=GR O31699/88-139 AS ________________*____________________
#=GR O31699/88-139 IN ____________1____________2______0____
//
require 'bio-stockholm'
entries = Bio::Stockholm::Reader.parse_from_file('spec/data/wikipedia.sto') #=> Array of 1
cbs = entries[0] #=> Bio::Stockholm::Store object
cbs.gf_features['ID'] #=> 'CBS'
cbs.gf_features['AC'] #=> 'PF00571'
# #=GS O31698/88-139 OS Bacillus subtilis
cbs.records['O31698/88-139'].gs_features['OS'] #=> 'Bacillus subtilis'
# O83071/192-246 MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS
cbs.records['O83071/192-246'].sequence #=> 'MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS'The API doc is online. For more code examples see the test files in the source tree.
Project home page
Information on the source tree, documentation, examples, issues and how to contribute, see
http://github.com/wwood/bioruby-stockholm
The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
Cite
This software is currently unpublished.
Biogems.info
This Biogem is published at (http://biogems.info/index.html#bio-stockholm)
Copyright
Copyright (c) 2013 Ben J. Woodcroft. See LICENSE.txt for further details.