class Bio::HMMER::HMMER3::PerSequenceHit

Attributes

best_1_domain_bias[R]
best_1_domain_e_value[R]
best_1_domain_score[R]
domain_number_est_clu[R]
domain_number_est_dom[R]
domain_number_est_env[R]
domain_number_est_exp[R]
domain_number_est_inc[R]
domain_number_est_ov[R]
domain_number_est_reg[R]
domain_number_est_rep[R]

Public Class Methods

new(line, line_number) click to toggle source

Sets hit data.

# 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