class Bio::PSORT::PSORT2::Report
Bio::PSORT::PSORT2::Report¶ ↑
Report parser classe for PSORT II(PSORT2).
Example¶ ↑
Constants
Attributes
definition[RW]
Definition of query sequence.
entry_id[RW]
entry_id of query sequence.
features[RW]
Feature vector used the kNN prediction.
k[RW]
k parameter of k-nearest neighbors classifier.
pred[RW]
Predicted subcellular localization (three letters code).
prob[RW]
Probability vector of kNN prediction.
raw[RW]
Raw text of output report.
scl[RW]
Given subcellular localization (three letters code).
seq[RW]
Sequence of query sequence.
Public Class Methods
default_parser(ent, entry_id = nil)
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Parser for the default report format. “psort report” output.
# File lib/bio/appl/psort/report.rb 273 def self.default_parser(ent, entry_id = nil) 274 report = self.new(ent, entry_id) 275 ent = ent.split(/\n\n/).map {|e| e.chomp } 276 277 report.set_header_line(ent[0]) 278 279 # feature matrix 280 ent[1].gsub(/\n/,' ').strip.split(/ /).map {|fe| 281 pair = fe.split(/: /) 282 report.features[pair[0].strip] = pair[1].strip.to_f 283 } 284 285 report.prob = self.set_kNN_prob(ent[2]) 286 report.set_prediction(ent[3]) 287 288 return report 289 end
divent(entry)
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Divides entry body
# File lib/bio/appl/psort/report.rb 392 def self.divent(entry) 393 boundary = entry.index(BOUNDARY) 394 return entry[0..(boundary - 1)], entry[(boundary + 2)..(entry.length)] 395 end
new(raw = '', entry_id = nil, scl = nil, definition = nil, seq = nil, k = nil, features = {}, prob = {}, pred = nil)
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Constructs aBio::PSORT::PSORT2::Report object.
# File lib/bio/appl/psort/report.rb 227 def initialize(raw = '', entry_id = nil, scl = nil, definition = nil, 228 seq = nil, k = nil, features = {}, prob = {}, pred = nil) 229 @entry_id = entry_id 230 @scl = scl 231 @definition = definition 232 @seq = seq 233 @features = features 234 @prob = prob 235 @pred = pred 236 @k = k 237 @raw = raw 238 end
parser(str, entry_id)
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Parses output report with output format detection automatically.
# File lib/bio/appl/psort/report.rb 242 def self.parser(str, entry_id) 243 case str 244 when /^ psg:/ # default report 245 self.default_parser(str, entry_id) 246 when /^PSG:/ # -v report 247 self.v_parser(str, entry_id) 248 when /: too short length / 249 self.too_short_parser(str, entry_id) 250 when /PSORT II server/ 251 tmp = self.new(ent, entry_id) 252 else 253 raise ArgumentError, "invalid format\n[#{str}]" 254 end 255 end
set_kNN_prob(str)
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Returns @prob value.
# File lib/bio/appl/psort/report.rb 309 def self.set_kNN_prob(str) 310 prob = Hash.new 311 Bio::PSORT::PSORT2::SclNames.keys.each {|a| 312 prob.update( {a => 0.0} ) 313 } 314 str.gsub(/\t/,'').split(/\n/).each {|a| 315 val,scl = a.strip.split(/ %: /) 316 key = Bio::PSORT::PSORT2::SclNames.index(scl) 317 prob[key] = val.to_f 318 } 319 return prob 320 end
too_short_parser(ent, entry_id = nil)
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Parser for “too short length” report.
$id: too short length ($leng), skipped\n";
# File lib/bio/appl/psort/report.rb 260 def self.too_short_parser(ent, entry_id = nil) 261 report = self.new(ent) 262 report.entry_id = entry_id 263 if ent =~ /^(.+)?: too short length/ 264 report.entry_id = $1 unless report.entry_id 265 report.scl = '---' 266 end 267 report 268 end
v_parser(ent, entry_id = nil)
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Parser for the verbose output report format. “psort -v report” and WWW server output.
# File lib/bio/appl/psort/report.rb 338 def self.v_parser(ent, entry_id = nil) 339 report = Bio::PSORT::PSORT2::Report.new(ent, entry_id) 340 341 ent = ent.split(/\n\n/).map {|e| e.chomp } 342 ent.each_with_index {|e, i| 343 unless /^(\w|-|\>|\t)/ =~ e 344 j = self.__send__(:search_j, i, ent) 345 ent[i - j] += e 346 ent[i] = nil 347 end 348 if /^none/ =~ e # psort output bug 349 j = self.__send__(:search_j, i, ent) 350 ent[i - j] += e 351 ent[i] = nil 352 end 353 } 354 ent.compact! 355 356 if /^ PSORT II server/ =~ ent[0] # for WWW version 357 ent.shift 358 delline = '' 359 ent.each {|e| delline = e if /^Results of Subprograms/ =~ e } 360 i = ent.index(delline) 361 ent.delete(delline) 362 ent.delete_at(i - 1) 363 end 364 365 report.set_header_line(ent.shift) 366 report.seq = Bio::Sequence::AA.new(ent.shift) 367 368 fent, pent = self.divent(ent) 369 report.set_features(fent) 370 report.prob = self.set_kNN_prob(pent[0].strip) 371 report.set_prediction(pent[1].strip) 372 373 return report 374 end
Public Instance Methods
set_features(features_ary)
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Sets @features values.
# File lib/bio/appl/psort/report.rb 398 def set_features(features_ary) 399 features_ary.each {|fent| 400 key = fent.split(/\:( |\n)/)[0].strip 401 self.features[key] = fent # unless /^\>/ =~ key 402 } 403 self.features['AA'] = self.seq.length 404 end
set_header_line(str)
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Returns header information.
# File lib/bio/appl/psort/report.rb 292 def set_header_line(str) 293 str.sub!(/^-+\n/,'') 294 tmp = str.split(/\t| /) 295 @entry_id = tmp.shift.sub(/^-+/,'').strip unless @entry_id 296 297 case tmp.join(' ').chomp 298 when /\(\d+ aa\) (.+)$/ 299 @definition = $1 300 else 301 @definition = tmp.join(' ').chomp 302 end 303 scl = @definition.split(' ')[0] 304 305 @scl = scl if SclNames.keys.index(scl) 306 end
set_prediction(str)
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Returns @prob and @k values.
# File lib/bio/appl/psort/report.rb 323 def set_prediction(str) 324 case str 325 when /prediction for (\S+?) is (\w{3}) \(k=(\d+)\)/ 326 @entry_id ||= $1 unless @entry_id 327 @pred = $2 328 @k = $3 329 else 330 raise ArgumentError, 331 "Invalid format at(#{self.entry_id}):\n[#{str}]\n" 332 end 333 end