Argument error (support hmmscan default output)

[ghost]

using bio 1.4.2, ruby 1.9.3, OS X 10.7.4

require 'bio-hmmer3_report'

reportfile = ARGV[0]

report = Bio::HMMER::HMMER3::Report.new(File.open(reportfile))

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

I get this error while reading a hmmscan report.

/.rbenv/versions/1.9.3-p194/lib/ruby/gems/1.9.1/gems/bio-hmmer3_report-0.0.1/lib/bio/appl/hmmer/hmmer3/report.rb:117:in `initialize': line 10 is in an unrecognized format [Query:       1A  [L=127] (ArgumentError)
/.rbenv/versions/1.9.3-p194/lib/ruby/gems/1.9.1/gems/bio-hmmer3_report-0.0.1/lib/bio/appl/hmmer/hmmer3/report.rb:57:in `new'
/.rbenv/versions/1.9.3-p194/lib/ruby/gems/1.9.1/gems/bio-hmmer3_report-0.0.1/lib/bio/appl/hmmer/hmmer3/report.rb:57:in `parse_line'
/.rbenv/versions/1.9.3-p194/lib/ruby/gems/1.9.1/gems/bio-hmmer3_report-0.0.1/lib/bio/appl/hmmer/hmmer3/report.rb:29:in `block in initialize'
/.rbenv/versions/1.9.3-p194/lib/ruby/gems/1.9.1/gems/bio-hmmer3_report-0.0.1/lib/bio/appl/hmmer/hmmer3/report.rb:29:in `each_line'
/.rbenv/versions/1.9.3-p194/lib/ruby/gems/1.9.1/gems/bio-hmmer3_report-0.0.1/lib/bio/appl/hmmer/hmmer3/report.rb:29:in `initialize'
    from hmmer_report.rb:5:in `new'
    from hmmer_report.rb:5:in `<main>'

[wwood]

Thanks for the bug report. Is it possible to supply the report at all, or some small part of it?

[ghost]

Here is a section of the report
http://pastebin.com/ve52iH3m

[wwood]

Hmm. Unfortunately I don't think that the gem currently supports this output format i.e. the default output format from hmmscan. Sorry. It does however support hmmscan with these switches:

• --tblout
• --domtblout

It also supports the default outputs from hmm__search__, maybe you could rerun using that instead?

I'll leave this bug report open as a feature request, hopefully when I get a second I'll implement parsing of this format.