Sha256: 2abca1215749e8cc74f251332061195a5752819d53706bab221e2c5a11744841
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Versions: 8
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Stored size: 1.42 KB
Contents
# Top level module / namespace.
module NpSearch
# Adapted from GeneValidator's Query Class..
# A class to hold sequence data
class Sequence
DI_NP_CLV = 'KR|KK|RR'.freeze
MONO_NP_CLV = '[KRH]..R|[KRH]....R|[KRH]......R'.freeze
attr_reader :id
attr_reader :defline
attr_reader :signalp
attr_reader :seq
attr_reader :html_seq
attr_reader :translated_frame
attr_accessor :score
attr_accessor :potential_cleaved_nps
def initialize(entry, sp, frame = nil)
@id = entry.entry_id
@defline = entry.definition
sp_cleavage_site_idx = sp[:ymax_pos].to_i - 1
@signalp = sp[:orf][0..(sp_cleavage_site_idx - 1)]
@seq = sp[:orf][sp_cleavage_site_idx..-1]
@html_seq = format_seq_for_html
@translated_frame = frame
@score = 0
@potential_cleaved_nps = nil
end
def format_seq_for_html
seq = @seq.gsub(/C/, '<span class=cysteine>C</span>')
seq.gsub!(/#{DI_NP_CLV}/i, '<span class=np_clv>\0</span>')
seq.gsub!(/#{MONO_NP_CLV}/i, '\0::NP_CLV::') # so that we can target 'R'
seq.gsub!('R::NP_CLV::', '<span class=mono_np_clv>R</span>')
seq.gsub!('G<span class=np_clv>',
'<span class=glycine>G</span><span class=np_clv>')
"<span class=signalp>#{@signalp}</span><span class=seq>#{seq}</span>"
end
end
end
Version data entries
8 entries across 8 versions & 1 rubygems