Sha256: a0232021bce24590ad30b666be0f5847ba3319fcde1420cb90e06a428549e297
Contents?: true
Size: 1.29 KB
Versions: 2
Compression:
Stored size: 1.29 KB
Contents
module NpSearch # A class to hold sequence data class Sequence DI_NP_CLV = 'KR|KK|RR' MONO_NP_CLV = '[KRH]..R|[KRH]....R|[KRH]......R' attr_reader :id attr_reader :signalp attr_reader :seq attr_reader :html_seq attr_reader :signalp_output attr_reader :translated_frame attr_accessor :score attr_accessor :potential_cleaved_nps def initialize(id, seq, signalp_output, frame = nil) @id = id sp_cleavage_site_idx = signalp_output[:ymax_pos].to_i - 1 @signalp = seq[0..(sp_cleavage_site_idx - 1)] @seq = seq[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
2 entries across 2 versions & 1 rubygems
Version | Path |
---|---|
npsearch-2.0.1 | lib/npsearch/sequence.rb |
npsearch-2.0.0 | lib/npsearch/sequence.rb |