class Bio::HMMER::HMMER3::PerDomainHit

Attributes

acc[R]
ali_coord_from[R]
ali_coord_to[R]
domain_bias[R]
domain_c_e_value[R]
domain_i_e_value[R]
domain_number[R]
domain_score[R]
domain_sum[R]
env_coord_from[R]
env_coord_to[R]
hmm_coord_from[R]
hmm_coord_to[R]
query_length[R]
target_length[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 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