Class: Bio::HMMER::HMMER3::PerSequenceHit

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

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) ⇒ PerSequenceHit

Sets hit data.



91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 91

def initialize(line, line_number)
    
  # tblout:
  #               tn    tacc      qn    qacc fs_eval fs_scor fs_bias   bst_e bst_scor bst_bias   exp     reg     clu      ov     env      dom     rep     inc   desc
  #                1       2       3       4       5       6       7       8       9      10      11      12      13      14      15       16      17      18     19
  if  line =~ /^(\S*)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(.*)/
    @target_name = $1
    @target_accession = $2
    @query_name = $3
    @query_accession = $4
    @full_sequence_e_value = $5.to_f
    @full_sequence_score = $6.to_f
    @full_sequence_bias =  $7.to_f
    @best_1_domain_e_value = $8.to_f
    @best_1_domain_score = $9.to_f
    @best_1_domain_bias =  $10.to_f
    @domain_number_est_exp = $11.to_i
    @domain_number_est_reg = $12.to_i
    @domain_number_est_clu = $13.to_i
    @domain_number_est_ov  = $14.to_i
    @domain_number_est_env = $15.to_i
    @domain_number_est_dom = $16.to_i
    @domain_number_est_rep = $17.to_i
    @domain_number_est_inc = $18.to_i
    @target_description = $19
  else
    raise ArgumentError, "line "+ line_number.to_s + " is in an unrecognized format [#{line}]"
  end
    
end

Instance Attribute Details

#best_1_domain_bias ⇒ Object (readonly)

Returns the value of attribute best_1_domain_bias.



124
125
126
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 124

def best_1_domain_bias
  @best_1_domain_bias
end

#best_1_domain_e_value ⇒ Object (readonly)

initialize



122
123
124
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 122

def best_1_domain_e_value
  @best_1_domain_e_value
end

#best_1_domain_score ⇒ Object (readonly)

Returns the value of attribute best_1_domain_score.



123
124
125
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 123

def best_1_domain_score
  @best_1_domain_score
end

#domain_number_est_clu ⇒ Object (readonly)

Returns the value of attribute domain_number_est_clu.



127
128
129
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 127

def domain_number_est_clu
  @domain_number_est_clu
end

#domain_number_est_dom ⇒ Object (readonly)

Returns the value of attribute domain_number_est_dom.



130
131
132
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 130

def domain_number_est_dom
  @domain_number_est_dom
end

#domain_number_est_env ⇒ Object (readonly)

Returns the value of attribute domain_number_est_env.



129
130
131
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 129

def domain_number_est_env
  @domain_number_est_env
end

#domain_number_est_exp ⇒ Object (readonly)

Returns the value of attribute domain_number_est_exp.



125
126
127
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 125

def domain_number_est_exp
  @domain_number_est_exp
end

#domain_number_est_inc ⇒ Object (readonly)

Returns the value of attribute domain_number_est_inc.



132
133
134
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 132

def domain_number_est_inc
  @domain_number_est_inc
end

#domain_number_est_ov ⇒ Object (readonly)

Returns the value of attribute domain_number_est_ov.



128
129
130
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 128

def domain_number_est_ov
  @domain_number_est_ov
end

#domain_number_est_reg ⇒ Object (readonly)

Returns the value of attribute domain_number_est_reg.



126
127
128
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 126

def domain_number_est_reg
  @domain_number_est_reg
end

#domain_number_est_rep ⇒ Object (readonly)

Returns the value of attribute domain_number_est_rep.



131
132
133
 
# File 'lib/bio/appl/hmmer/hmmer3/tabular_report.rb', line 131

def domain_number_est_rep
  @domain_number_est_rep
end