[BioRuby-cvs] bioruby/test/unit/bio/appl/hmmer test_report.rb, NONE, 1.1
Mitsuteru C. Nakao
nakao at pub.open-bio.org
Thu Feb 2 17:10:10 UTC 2006
Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/hmmer
In directory pub.open-bio.org:/tmp/cvs-serv1897/test/unit/bio/appl/hmmer
Added Files:
test_report.rb
Log Message:
* Newly added.
--- NEW FILE: test_report.rb ---
#
# test/unit/bio/appl/hmmer/test_report.rb - Unit test for Bio::HMMER::Report
#
# Copyright (C) 2006 Mitsuteru Nakao <n at bioruby.org>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: test_report.rb,v 1.1 2006/02/02 17:10:08 nakao Exp $
#
require 'pathname'
libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)
require 'test/unit'
require 'bio/appl/hmmer/report'
module Bio
class TestHMMERReportData
bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
TestDataHMMER = Pathname.new(File.join(bioruby_root, 'test', 'data', 'HMMER')).cleanpath.to_s
def self.hmmpfam
File.open(File.join(TestDataHMMER, 'hmmpfam.out')).read
end
def self.output
self.hmmpfam
end
def self.hmmsearch
File.open(File.join(TestDataHMMER, 'hmmsearch.out')).read
end
end
class TestHMMERReportClassMethods < Test::Unit::TestCase
def test_reports_ary
ary = Bio::HMMER.reports(Bio::TestHMMERReportData.output)
assert_equal(Array, ary.class)
end
def test_reports_ary
Bio::HMMER.reports(Bio::TestHMMERReportData.output).each do |report|
assert_equal(Bio::HMMER::Report, report.class)
end
end
end
class TestHMMERReportConstants < Test::Unit::TestCase
def test_rs
assert_equal("\n//\n", Bio::HMMER::Report::RS)
assert_equal("\n//\n", Bio::HMMER::Report::DELIMITER)
end
end
class TestHMMERReportHmmpfam < Test::Unit::TestCase
def setup
@obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.hmmpfam)
end
def test_program
assert_equal(Hash, @obj.program.class)
assert_equal("hmmpfam - search one or more sequences against HMM database", @obj.program['name'])
assert_equal("HMMER 2.3.2 (Oct 2003)", @obj.program['version'])
assert_equal("Copyright (C) 1992-2003 HHMI/Washington University School of Medicine", @obj.program['copyright'])
assert_equal("Freely distributed under the GNU General Public License (GPL)", @obj.program['license'])
end
def test_parameter
assert_equal(Hash, @obj.parameter.class)
assert_equal("/Users/nakao/Sites/iprscan/tmp/20050517/iprscan-20050517-16244071/chunk_1/iprscan-20050517-16244071.nocrc", @obj.parameter["Sequence file"])
assert_equal("/Users/nakao/Sites/iprscan/data/Pfam", @obj.parameter['HMM file'])
end
def test_query_info
assert_equal(Hash, @obj.query_info.class)
assert_equal("104K_THEPA", @obj.query_info["Query sequence"])
assert_equal("[none]", @obj.query_info["Accession"])
assert_equal("[none]", @obj.query_info["Description"])
end
def test_hits
assert_equal(Bio::HMMER::Report::Hit, @obj.hits.first.class)
end
def test_hsps
assert_equal(Bio::HMMER::Report::Hsp, @obj.hsps.first.class)
end
def test_histogram
assert_equal(nil, @obj.histogram)
end
def test_statistical_detail
assert_equal(nil, @obj.statistical_detail)
end
def test_total_seq_searched
assert_equal(nil, @obj.total_seq_searched)
end
def test_whole_seq_top_hits
assert_equal(nil, @obj.whole_seq_top_hits)
end
def test_domain_top_hits
assert_equal(nil, @obj.domain_top_hits)
end
def test_each
@obj.each do |hit|
assert_equal(Bio::HMMER::Report::Hit, hit.class)
end
end
def test_each_hit
@obj.each_hit do |hit|
assert_equal(Bio::HMMER::Report::Hit, hit.class)
end
end
end
class TestHMMERReportHit < Test::Unit::TestCase
def setup
@obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.output).hits.first
end
def test_hit
assert_equal(Bio::HMMER::Report::Hit, @obj.class)
end
def test_hsps
assert_equal(Bio::HMMER::Report::Hsp, @obj.hsps.first.class)
end
def test_accession
assert_equal("PF04385.4", @obj.accession)
end
def test_target_id
assert_equal("PF04385.4", @obj.target_id)
end
def test_hit_id
assert_equal("PF04385.4", @obj.hit_id)
end
def test_entry_id
assert_equal("PF04385.4", @obj.entry_id)
end
def test_description
assert_equal("Domain of unknown function, DUF529", @obj.description)
end
def test_definition
assert_equal("Domain of unknown function, DUF529", @obj.definition)
end
def test_score
assert_equal(259.3, @obj.score)
end
def test_bit_score
assert_equal(259.3, @obj.bit_score)
end
def test_evalue
assert_equal(6.6e-75, @obj.evalue)
end
def test_num
assert_equal(4, @obj.num)
end
def test_each
@obj.each do |hsp|
assert_equal(Bio::HMMER::Report::Hsp, hsp.class)
end
end
def test_each_hsp
@obj.each_hsp do |hsp|
assert_equal(Bio::HMMER::Report::Hsp, hsp.class)
end
end
def test_target_def
assert_equal("<4> Domain of unknown function, DUF529", @obj.target_def)
end
def test_append_hsp
hsp = @obj.hsps.first
assert_equal(5, @obj.append_hsp(hsp).size)
end
end
class TestHMMERReportHsp < Test::Unit::TestCase
def setup
@obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.output).hits.first.hsps.first
end
def test_hsp
assert_equal(Bio::HMMER::Report::Hsp, @obj.class)
end
def test_accession
assert_equal("PF04385.4", @obj.accession)
end
def test_domain
assert_equal("1/4", @obj.domain)
end
def test_seq_f
assert_equal(36, @obj.seq_f)
end
def test_seq_t
assert_equal(111, @obj.seq_t)
end
def test_seq_ft
assert_equal("..", @obj.seq_ft)
end
def test_hmm_f
assert_equal(1, @obj.hmm_f)
end
def test_hmm_t
assert_equal(80, @obj.hmm_t)
end
def test_score
assert_equal(65.0, @obj.score)
end
def test_bit_score
assert_equal(65.0, @obj.bit_score)
end
def test_evalue
assert_equal(2.0e-16, @obj.evalue)
end
def test_midline
assert_equal("t+D+n++++ f +v+++g+++ + ++ ++v+++++++Gn+v+We++ + +l++ ++++++++++++++++ +++", @obj.midline)
end
def test_hmmseq
assert_equal("tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvWeseddpefglivtlsfyldsnkfLvlllintak", @obj.hmmseq)
end
def test_flatseq
assert_equal("TFDINSNQTG-PAFLTAVEMAGVKYLQVQHGSNVNIHRLVEGNVVIWENA---STPLYTGAIVTNNDGPYMAYVEVLGDP", @obj.flatseq)
end
def test_query_frame
assert_equal(1, @obj.query_frame)
end
def test_target_frame
assert_equal(1, @obj.target_frame)
end
def test_csline
assert_equal(nil, @obj.csline)
end
def test_rfline
assert_equal(nil, @obj.rfline)
end
def test_set_alignment
end
def test_query_seq
assert_equal("TFDINSNQTG-PAFLTAVEMAGVKYLQVQHGSNVNIHRLVEGNVVIWENA---STPLYTGAIVTNNDGPYMAYVEVLGDP", @obj.query_seq)
end
def test_target_seq
assert_equal("tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvWeseddpefglivtlsfyldsnkfLvlllintak", @obj.target_seq)
end
def test_target_from
assert_equal(1, @obj.target_from)
end
def test_targat_to
assert_equal(80, @obj.target_to)
end
def test_query_from
assert_equal(36, @obj.query_from)
end
def test_query_to
assert_equal(111, @obj.query_to)
end
end
class TestHMMERReportHmmsearch < Test::Unit::TestCase
def setup
@obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.hmmsearch)
end
def test_histogram
hist = "score obs exp (one = represents 1 sequences)\n----- --- ---\n 377 1 0|="
assert_equal(hist, @obj.histogram)
end
def test_statistical_detail
hash = {"P(chi-square)" => 0.0, "chi-sq statistic" => 0.0, "lambda" => 0.7676, "mu" => -10.6639}
assert_equal(hash, @obj.statistical_detail)
hash.keys.each do |key|
assert_equal(hash[key], @obj.statistical_detail[key])
end
end
def test_total_seq_searched
assert_equal(1, @obj.total_seq_searched)
end
def test_whole_seq_top_hit
hash = {"Total memory" => "16K", "Satisfying E cutoff" => 1, "Total hits" => 1}
assert_equal(hash, @obj.whole_seq_top_hits)
hash.keys.each do |key|
assert_equal(hash[key], @obj.whole_seq_top_hits[key])
end
end
def test_domain_top_hits
hash = {"Total memory" => "17K", "Satisfying E cutoff" => 1, "Total hits" => 1}
assert_equal(hash, @obj.domain_top_hits)
hash.keys.each do |key|
assert_equal(hash[key], @obj.domain_top_hits[key])
end
end
end
end # module Bio
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