Class: Bio::HMMER::HMMER3::PerDomainHit

Inherits:
Hit
  • Object
show all
Defined in:
lib/bio/appl/hmmer/hmmer3/tabular_report.rb

Overview

class PerSequenceHit

Instance Attribute Summary collapse

Attributes inherited from Hit

#full_sequence_bias, #full_sequence_e_value, #full_sequence_score, #query_accession, #query_name, #target_accession, #target_description, #target_name

Instance Method Summary collapse

Constructor Details

#initialize(line, line_number) ⇒ PerDomainHit

Sets hit data.



139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 139

def initialize(line, line_number)
    
  # domtblout:
  #                tn     acc    tlen   query     acc    qlen  Evalue   score    bias      #       of     c-E    i-E     score   bias      hf      ht      af      at     ef      et     acc  desc
  #                 1       2       3       4       5       6       7       8       9      10      11      12     13      14      15       16      17      18      19     20      21      22     23
  if  line =~ /^(\S*)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s*(.*)/
    @target_name = $1
    @target_accession = $2
    @target_length = $3.to_i
    @query_name = $4
    @query_accession = $5
    @query_length = $6.to_i
    @full_sequence_e_value = $7.to_f
    @full_sequence_score = $8.to_f
    @full_sequence_bias =  $9.to_f
    @domain_number = $10.to_i
    @domain_sum = $11.to_i
    @domain_c_e_value = $12.to_f
    @domain_i_e_value = $13.to_f
    @domain_score = $14.to_f
    @domain_bias = $15.to_f
    @hmm_coord_from = $16.to_i
    @hmm_coord_to = $17.to_i
    @ali_coord_from = $18.to_i
    @ali_coord_to = $19.to_i
    @env_coord_from = $20.to_i
    @env_coord_to = $21.to_i
    @acc = $22.to_f
    @target_description = $23
  else
    raise ArgumentError, "line "+ line_number.to_s + " is in a unrecognized format [#{line}]"
  end
    
end

Instance Attribute Details

#acc ⇒ Object (readonly)

Returns the value of attribute acc.



188
189
190
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 188

def acc
  @acc
end

#ali_coord_from ⇒ Object (readonly)

Returns the value of attribute ali_coord_from.



184
185
186
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 184

def ali_coord_from
  @ali_coord_from
end

#ali_coord_to ⇒ Object (readonly)

Returns the value of attribute ali_coord_to.



185
186
187
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 185

def ali_coord_to
  @ali_coord_to
end

#domain_bias ⇒ Object (readonly)

Returns the value of attribute domain_bias.



181
182
183
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 181

def domain_bias
  @domain_bias
end

#domain_c_e_value ⇒ Object (readonly)

Returns the value of attribute domain_c_e_value.



178
179
180
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 178

def domain_c_e_value
  @domain_c_e_value
end

#domain_i_e_value ⇒ Object (readonly)

Returns the value of attribute domain_i_e_value.



179
180
181
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 179

def domain_i_e_value
  @domain_i_e_value
end

#domain_number ⇒ Object (readonly)

Returns the value of attribute domain_number.



176
177
178
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 176

def domain_number
  @domain_number
end

#domain_score ⇒ Object (readonly)

Returns the value of attribute domain_score.



180
181
182
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 180

def domain_score
  @domain_score
end

#domain_sum ⇒ Object (readonly)

Returns the value of attribute domain_sum.



177
178
179
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 177

def domain_sum
  @domain_sum
end

#env_coord_from ⇒ Object (readonly)

Returns the value of attribute env_coord_from.



186
187
188
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 186

def env_coord_from
  @env_coord_from
end

#env_coord_to ⇒ Object (readonly)

Returns the value of attribute env_coord_to.



187
188
189
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 187

def env_coord_to
  @env_coord_to
end

#hmm_coord_from ⇒ Object (readonly)

Returns the value of attribute hmm_coord_from.



182
183
184
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 182

def hmm_coord_from
  @hmm_coord_from
end

#hmm_coord_to ⇒ Object (readonly)

Returns the value of attribute hmm_coord_to.



183
184
185
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 183

def hmm_coord_to
  @hmm_coord_to
end

#query_length ⇒ Object (readonly)

Returns the value of attribute query_length.



175
176
177
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 175

def query_length
  @query_length
end

#target_length ⇒ Object (readonly)

initialize



174
175
176
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 174

def target_length
  @target_length
end