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#
# = bio/appl/tmhmm/report.rb - TMHMM report class
#
# Copyright:: Copyright (C) 2003
# Mitsuteru C. Nakao <n@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
# == Description
#
#
# == Example
# == References
#
require 'enumerator'
module Bio
# = TMHMM class for http://www.cbs.dtu.dk/services/TMHMM/
class TMHMM
# Splits multiple reports into a report entry.
def TMHMM.reports(data)
entry = []
ent_state = ''
data.each_line do |line|
if /^\#/ =~ line
if ent_state == 'next'
ent_state = 'entry'
elsif ent_state == 'tmh'
ent_state = 'next'
end
else
ent_state = 'tmh'
end
if ent_state != 'next'
entry << line
else
if block_given?
yield Bio::TMHMM::Report.new(entry)
else
Bio::TMHMM::Report.new(entry)
end
entry = [line]
end
end
if block_given?
yield Bio::TMHMM::Report.new(entry)
else
Bio::TMHMM::Report.new(entry)
end
end
# = TMHMM report parser class.
class Report
# Returns an Array of Bio::TMHMM::TMH.
attr_reader :tmhs
# Returns
attr_reader :entry_id
# Returns
attr_reader :query_len
# Returns
attr_reader :predicted_tmhs
# Returns
attr_reader :exp_aas_in_tmhs
# Returns
attr_reader :exp_first_60aa
# Returns
attr_reader :total_prob_of_N_in
alias length query_len
#
def initialize(entry = nil)
begin
str = entry.to_str
rescue NoMethodError
end
if str then
entry = str.enum_for(:each_line)
end
parse_header(entry)
@tmhs = parse_tmhs(entry)
end
# Returns an Array of Bio::TMHMM::TMH including only "TMhelix".
def helix
@tmhs.map {|t| t if t.status == 'TMhelix' }.compact
end
#
def to_s
[
[
["Length:", @query_len],
["Number of predicted TMHs:", @predicted_tmhs],
["Exp number of AAs in THMs:", @exp_aas_in_tmhs],
["Exp number, first 60 AAs:", @exp_first_60aa],
["Total prob of N-in:", @total_prob_of_N_in]
].map {|e| "\# " + [@entry_id, e].flatten.join("\t") },
tmhs.map {|ent| ent.to_s }
].flatten.join("\n")
end
private
#
def parse_header(raw)
raw.each do |line|
next unless /^#/.match(line)
case line
when / (\S.+) Length: +(\d+)/
@entry_id = $1.strip
@query_len = $2.to_i
when /Number of predicted TMHs: +(\d+)/
@predicted_tmhs = $1.to_i
when /Exp number of AAs in TMHs: +([\d\.]+)/
@exp_aas_in_tmhs = $1.to_f
when /Exp number, first 60 AAs: +([\d\.]+)/
@exp_first_60aa = $1.to_f
when /Total prob of N-in: +([\d\.]+)/
@total_prob_of_N_in = $1.to_f
end
end
end
#
def parse_tmhs(raw)
tmhs = []
raw.each do |line|
case line
when /^[^\#]/
eid,version,status,r0,r1 = line.split(/\s+/)
tmhs << Bio::TMHMM::TMH.new(eid.strip,
version.strip,
status.strip,
Range.new(r0.to_i, r1.to_i))
end
end
tmhs
end
end # class Report
# = Container class of the trainsmembrane helix(TMH) and the other
# segments.
class TMH
# Returns
attr_accessor :entry_id
# Returns
attr_accessor :version
# Returns the status of the TMH. ("outside", "TMhelix" or "inside").
attr_accessor :status
# Returns an Range of TMH position.
attr_accessor :range
alias pos range
#
def initialize(entry_id = nil, version = nil, status = nil, range = nil)
@entry_id = entry_id
@version = version
@status = status
@range = range
end
#
def to_s
[@entry_id, @version, @status, @range.first, @range.last].join("\t")
end
end # class TMH
end # class TMHMM
end # module Bio
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