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Parser for hmmsearch and hmmscan in the HMMER 3 package.
Ruby
branch: master

merge, really a ff in disguise

latest commit 724862b967
Ben J. Woodcroft authored

README.md

bio-hmmer3_report

Build Status

Parser class for hmmsearch and hmmscan in the HMMER 3 package.

Examples

Description

# 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

References

Note: this software is under active development!

Installation

    gem install bio-hmmer3_report

Usage

    require 'bio-hmmer3_report'

The API doc is online. For more code examples see the test files in the source tree.

Project home page

Information on the source tree, documentation, examples, issues and how to contribute, see

http://github.com/wwood/bioruby-hmmer3_report

The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.

Cite

If you use this software, please cite one of

Biogems.info

This Biogem is published at #bio-hmmer3_report

Copyright

Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.

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