class Proph::ProtSummary
Constants
- Filetype_and_version_re_new
- Filetype_and_version_re_old
if you get this match it’s a protein prophet file and the version is the first match!
Attributes
prot_groups[RW]
the protein groups
version[RW]
Public Class Methods
new(file=nil)
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# File lib/ms/ident/pepxml/prot_summary.rb, line 50 def initialize(file=nil) @prots = nil if file @version = get_version(file) #@prot_groups = ProtSummary::Parser.new.parse_file(file) SpecID::Parser::ProtProph.new(:spec_id).parse(file, :spec_id => self) end end
Public Instance Methods
get_version(file)
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# File lib/ms/ident/pepxml/prot_summary.rb, line 32 def get_version(file) answer = nil File.open(file) do |fh| 5.times do line = fh.gets answer = if line =~ Filetype_and_version_re_new $1.dup elsif line =~ Filetype_and_version_re_old $1.dup end break if answer end end raise(ArgumentError, "couldn't detect version in #{file}") unless answer answer end
hi_prob_best()
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# File lib/ms/ident/pepxml/prot_summary.rb, line 30 def hi_prob_best ; true end
unique_prots(prot_groups)
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returns a set of unique proteins
# File lib/ms/ident/pepxml/prot_summary.rb, line 60 def unique_prots(prot_groups) all_prots = [] prot_groups.each do |pg| pg.prots.each do |prt| all_prots << prt end end all_prots.hash_by(:protein_name).map{|name,prot_arr| prot_arr.first } end