# Input from string:
data = String.new
data         << '#                                                                            --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord'
data << "\n" << '# target name        accession   tlen query name           accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target'
data << "\n" << '#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------'
data << "\n" << 'Bcl-2                PF00452.13   101 sp|P10415|BCL2_HUMAN -            239   3.7e-30  103.7   0.1   1   1   7.9e-34   4.9e-30  103.3   0.0     1   101    97   195    97   195 0.99 Apoptosis regulator proteins, Bcl-2 family'
data << "\n" << 'BH4                  PF02180.11    27 sp|P10415|BCL2_HUMAN -            239   3.9e-15   54.6   0.1   1   1   1.3e-18   8.2e-15   53.6   0.1     2    26     8    32     7    33 0.94 Bcl-2 homology region 4'
data << "\n"

report = Bio::HMMER::HMMER3::Report.new(data)
report.hits.each do |hit|
  puts hit.target_name
  puts hit.full_sequence_e_value
end


# Input from file:
report = Bio::HMMER::HMMER3::Report.new(File.open('test/data/HMMER/hmmsearch_domtblout.out'))
report.hits.each do |hit|
  puts hit.target_name
  puts hit.target_accession
  puts hit.query_name
  puts hit.query_accession
  puts hit.query_length
  puts hit.full_sequence_e_value
  puts hit.full_sequence_score
  puts hit.domain_number
  puts hit.domain_sum
  puts hit.domain_c_e_value
  puts hit.domain_i_e_value
  puts hit.domain_score
  puts hit.domain_bias
  puts hit.hmm_coord_from
  puts hit.hmm_coord_to
  puts hit.ali_coord_from
  puts hit.ali_coord_to
  puts hit.env_coord_from
  puts hit.env_coord_to
  puts hit.acc
  puts hit.target_description
end