class Bio::SOSUI::Report
SOSUI
output report parsing class¶ ↑
References
¶ ↑
Constants
- DELIMITER
Delimiter
- RS
Attributes
entry_id[R]
Query entry_id
prediction[R]
Returns the prediction result whether “MEMBRANE PROTEIN” or “SOLUBLE PROTEIN”.
tmhs[R]
Transmembrane helixes ary
Public Class Methods
new(output_report)
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Parser for SOSUI
output report.
# File lib/bio/appl/sosui/report.rb 44 def initialize(output_report) 45 entry = output_report.split(/\n/) 46 47 @entry_id = entry[0].strip.sub(/^>/,'') 48 @prediction = entry[1].strip 49 @tms = 0 50 @tmhs = [] 51 parse_tmh(entry) if /MEMBRANE/ =~ @prediction 52 end
Private Instance Methods
parse_tmh(entry)
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Parser for TMH
lines.
# File lib/bio/appl/sosui/report.rb 57 def parse_tmh(entry) 58 entry.each do |line| 59 if /NUMBER OF TM HELIX = (\d+)/ =~ line 60 @tms = $1 61 elsif /TM (\d+) +(\d+)- *(\d+) (\w+) +(\w+)/ =~ line 62 #tmh = $1.to_i 63 range = Range.new($2.to_i, $3.to_i) 64 grade = $4 65 seq = $5 66 @tmhs.push(TMH.new(range, grade, seq)) 67 end 68 end 69 end