Class | Bio::Fasta::Report::Hit
In: | lib/bio/appl/fasta/format10.rb
Parent: | Object

### Methods

bit_score direction evalue identity lap_at new overlap query_def query_end query_id query_len query_seq query_start query_type sw target_def target_end target_id target_len target_seq target_start target_type

### Classes and Modules

Class Bio::Fasta::Report::Hit::Query
Class Bio::Fasta::Report::Hit::Target

### Attributes

definition | [R] |
query | [R] |
score | [R] |
target | [R] |

### Public Class methods

new(data)

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 201
    201:     def initialize(data)
    202:       score, query, target = data.split(/\n>/)
    203:
    204:       @definition, *score = score.split(/\n/)
    205:       @score = {}
    206:
    207:       pat = /;\s+([^:]+):\s+(.*)/
    208:
    209:       score.each do |x|
    210:         if pat.match(x)
    211:           @score[$1] = $2
    212:         end
    213:       end
    214:
    215:       @query = Query.new(query)
    216:       @target = Target.new(target)
    217:     end

### Public Instance methods

bit_score()

Bit score

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 234
    234:     def bit_score
    235:       if @score['fa_bits']
    236:         @score['fa_bits'].to_f
    237:       elsif @score['sw_bits']
    238:         @score['sw_bits'].to_f
    239:       elsif @score['fx_bits']
    240:         @score['fx_bits'].to_f
    241:       elsif @score['tx_bits']
    242:         @score['tx_bits'].to_f
    243:       end
    244:     end

direction()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 246
    246:     def direction
    247:       @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame']
    248:     end

evalue()

E-value score

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 221
    221:     def evalue
    222:       if @score['fa_expect']
    223:         @score['fa_expect'].to_f
    224:       elsif @score['sw_expect']
    225:         @score['sw_expect'].to_f
    226:       elsif @score['fx_expect']
    227:         @score['fx_expect'].to_f
    228:       elsif @score['tx_expect']
    229:         @score['tx_expect'].to_f
    230:       end
    231:     end

identity()

percent identity

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 256
    256:     def identity
    257:       @score['sw_ident'].to_f
    258:     end

lap_at()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 327
    327:     def lap_at
    328:       [ query_start, query_end, target_start, target_end ]
    329:     end

overlap()

overlap length

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 261
    261:     def overlap
    262:       @score['sw_overlap'].to_i
    263:     end

query_def()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 275
    275:     def query_def
    276:       @query.definition
    277:     end

query_end()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 315
    315:     def query_end
    316:       @query.stop
    317:     end

query_id()

Shortcuts for the methods of Bio::Fasta::Report::Hit::Query

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 267
    267:     def query_id
    268:       @query.entry_id
    269:     end

query_len()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 283
    283:     def query_len
    284:       @query.length
    285:     end

query_seq()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 293
    293:     def query_seq
    294:       @query.sequence
    295:     end

query_start()

Information on matching region

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 311
    311:     def query_start
    312:       @query.start
    313:     end

query_type()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 301
    301:     def query_type
    302:       @query.moltype
    303:     end

sw()

Smith-Waterman score

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 251
    251:     def sw
    252:       @score['sw_score'].to_i
    253:     end

target_def()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 279
    279:     def target_def
    280:       @target.definition
    281:     end

target_end()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 323
    323:     def target_end
    324:       @target.stop
    325:     end

target_id()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 271
    271:     def target_id
    272:       @target.entry_id
    273:     end

target_len()

Shortcuts for the methods of Bio::Fasta::Report::Hit::Target

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 289
    289:     def target_len
    290:       @target.length
    291:     end

target_seq()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 297
    297:     def target_seq
    298:       @target.sequence
    299:     end

target_start()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 319
    319:     def target_start
    320:       @target.start
    321:     end

target_type()

[Source]

         # File lib/bio/appl/fasta/format10.rb, line 305
    305:     def target_type
    306:       @target.moltype
    307:     end

[Validate]