class Bio::TMHMM::Report
TMHMM report parser class.¶ ↑
Attributes
entry_id[R]
Returns
exp_aas_in_tmhs[R]
Returns
exp_first_60aa[R]
Returns
length[R]
Returns
predicted_tmhs[R]
Returns
query_len[R]
Returns
tmhs[R]
Returns an Array of Bio::TMHMM::TMH.
total_prob_of_N_in[R]
Returns
Public Class Methods
new(entry = nil)
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# File lib/bio/appl/tmhmm/report.rb, line 85 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
Public Instance Methods
helix()
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Returns an Array of Bio::TMHMM::TMH including only “TMhelix”.
# File lib/bio/appl/tmhmm/report.rb, line 98 def helix @tmhs.map {|t| t if t.status == 'TMhelix' }.compact end
to_s()
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# File lib/bio/appl/tmhmm/report.rb, line 103 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 Instance Methods
parse_header(raw)
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# File lib/bio/appl/tmhmm/report.rb, line 120 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
parse_tmhs(raw)
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# File lib/bio/appl/tmhmm/report.rb, line 141 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