bio-hmmer3_report¶ ↑
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¶ ↑
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HMMER hmmer.janelia.org/
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
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 © 2012 Ben J Woodcroft. See LICENSE.txt for further details.