/
test_tm_hmm_parser.rb
57 lines (52 loc) · 2.77 KB
/
test_tm_hmm_parser.rb
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require 'bio'
require 'helper'
class TmHmmParserTest < Test::Unit::TestCase
include Bio::Transmembrane
def test_parser
result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0635c len=555 ExpAA=0.00 First60=0.00 PredHel=0 Topology=o')
assert result
assert_equal false, result.has_domain?
# test a single TMD
result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0685c len=324 ExpAA=20.36 First60=0.00 PredHel=1 Topology=o281-303i')
assert result
assert_equal 1, result.transmembrane_domains.length
assert_equal 281, result.transmembrane_domains[0].start
assert_equal 303, result.transmembrane_domains[0].stop
assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
result.transmembrane_domains[0].orientation
assert result.transmembrane_type_1?
assert_equal false, result.transmembrane_type_2?
# test 2 TMD
result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0680c len=209 ExpAA=43.03 First60=0.02 PredHel=2 Topology=i137-159o164-183i')
assert result
assert_equal 2, result.transmembrane_domains.length
assert_equal 137, result.transmembrane_domains[0].start
assert_equal 159, result.transmembrane_domains[0].stop
assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::INSIDE_OUT,
result.transmembrane_domains[0].orientation
assert_equal 164, result.transmembrane_domains[1].start
assert_equal 183, result.transmembrane_domains[1].stop
assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
result.transmembrane_domains[1].orientation
assert_equal false, result.transmembrane_type_1?
assert_equal false, result.transmembrane_type_2?
# test 3 TMD
result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0705c len=282 ExpAA=90.97 First60=22.20 PredHel=4 Topology=i22-44o185-207i212-234o259-281i')
assert result
assert_equal 4, result.transmembrane_domains.length
assert_equal 22, result.transmembrane_domains[0].start
assert_equal 44, result.transmembrane_domains[0].stop
assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::INSIDE_OUT,
result.transmembrane_domains[0].orientation
assert_equal 185, result.transmembrane_domains[1].start
assert_equal 207, result.transmembrane_domains[1].stop
assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
result.transmembrane_domains[1].orientation
assert_equal 259, result.transmembrane_domains[3].start
assert_equal 281, result.transmembrane_domains[3].stop
assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
result.transmembrane_domains[3].orientation
assert_equal false, result.transmembrane_type_1?
assert_equal false, result.transmembrane_type_2?
end
end