bio 0.7.0
Sign up to get free protection for your applications and to get access to all the features.
- data/bin/bioruby +107 -0
- data/bin/br_biofetch.rb +59 -0
- data/bin/br_bioflat.rb +294 -0
- data/bin/br_biogetseq.rb +57 -0
- data/bin/br_pmfetch.rb +431 -0
- data/doc/BioRuby.rd.ja +225 -0
- data/doc/Changes-0.7.rd +236 -0
- data/doc/Design.rd.ja +341 -0
- data/doc/KEGG_API.rd +1437 -0
- data/doc/KEGG_API.rd.ja +1399 -0
- data/doc/TODO.rd.ja +138 -0
- data/doc/Tutorial.rd +1138 -0
- data/doc/Tutorial.rd.ja +2110 -0
- data/etc/bioinformatics/seqdatabase.ini +210 -0
- data/lib/bio.rb +256 -0
- data/lib/bio/alignment.rb +1906 -0
- data/lib/bio/appl/bl2seq/report.rb +350 -0
- data/lib/bio/appl/blast.rb +269 -0
- data/lib/bio/appl/blast/format0.rb +1402 -0
- data/lib/bio/appl/blast/format8.rb +95 -0
- data/lib/bio/appl/blast/report.rb +652 -0
- data/lib/bio/appl/blast/rexml.rb +151 -0
- data/lib/bio/appl/blast/wublast.rb +553 -0
- data/lib/bio/appl/blast/xmlparser.rb +222 -0
- data/lib/bio/appl/blat/report.rb +392 -0
- data/lib/bio/appl/clustalw.rb +191 -0
- data/lib/bio/appl/clustalw/report.rb +154 -0
- data/lib/bio/appl/emboss.rb +68 -0
- data/lib/bio/appl/fasta.rb +262 -0
- data/lib/bio/appl/fasta/format10.rb +428 -0
- data/lib/bio/appl/fasta/format6.rb +37 -0
- data/lib/bio/appl/genscan/report.rb +570 -0
- data/lib/bio/appl/hmmer.rb +129 -0
- data/lib/bio/appl/hmmer/report.rb +556 -0
- data/lib/bio/appl/mafft.rb +222 -0
- data/lib/bio/appl/mafft/report.rb +119 -0
- data/lib/bio/appl/psort.rb +555 -0
- data/lib/bio/appl/psort/report.rb +473 -0
- data/lib/bio/appl/sim4.rb +134 -0
- data/lib/bio/appl/sim4/report.rb +501 -0
- data/lib/bio/appl/sosui/report.rb +166 -0
- data/lib/bio/appl/spidey/report.rb +604 -0
- data/lib/bio/appl/targetp/report.rb +283 -0
- data/lib/bio/appl/tmhmm/report.rb +238 -0
- data/lib/bio/command.rb +166 -0
- data/lib/bio/data/aa.rb +354 -0
- data/lib/bio/data/codontable.rb +740 -0
- data/lib/bio/data/na.rb +226 -0
- data/lib/bio/db.rb +340 -0
- data/lib/bio/db/aaindex.rb +280 -0
- data/lib/bio/db/embl/common.rb +332 -0
- data/lib/bio/db/embl/embl.rb +446 -0
- data/lib/bio/db/embl/sptr.rb +954 -0
- data/lib/bio/db/embl/swissprot.rb +32 -0
- data/lib/bio/db/embl/trembl.rb +31 -0
- data/lib/bio/db/embl/uniprot.rb +32 -0
- data/lib/bio/db/fantom.rb +604 -0
- data/lib/bio/db/fasta.rb +869 -0
- data/lib/bio/db/genbank/common.rb +299 -0
- data/lib/bio/db/genbank/ddbj.rb +34 -0
- data/lib/bio/db/genbank/genbank.rb +354 -0
- data/lib/bio/db/genbank/genpept.rb +73 -0
- data/lib/bio/db/genbank/refseq.rb +31 -0
- data/lib/bio/db/gff.rb +106 -0
- data/lib/bio/db/go.rb +497 -0
- data/lib/bio/db/kegg/brite.rb +51 -0
- data/lib/bio/db/kegg/cell.rb +88 -0
- data/lib/bio/db/kegg/compound.rb +130 -0
- data/lib/bio/db/kegg/enzyme.rb +125 -0
- data/lib/bio/db/kegg/expression.rb +173 -0
- data/lib/bio/db/kegg/genes.rb +293 -0
- data/lib/bio/db/kegg/genome.rb +362 -0
- data/lib/bio/db/kegg/glycan.rb +213 -0
- data/lib/bio/db/kegg/keggtab.rb +418 -0
- data/lib/bio/db/kegg/kgml.rb +299 -0
- data/lib/bio/db/kegg/ko.rb +178 -0
- data/lib/bio/db/kegg/reaction.rb +97 -0
- data/lib/bio/db/litdb.rb +131 -0
- data/lib/bio/db/medline.rb +317 -0
- data/lib/bio/db/nbrf.rb +199 -0
- data/lib/bio/db/pdb.rb +38 -0
- data/lib/bio/db/pdb/atom.rb +60 -0
- data/lib/bio/db/pdb/chain.rb +117 -0
- data/lib/bio/db/pdb/model.rb +106 -0
- data/lib/bio/db/pdb/pdb.rb +1682 -0
- data/lib/bio/db/pdb/residue.rb +122 -0
- data/lib/bio/db/pdb/utils.rb +234 -0
- data/lib/bio/db/prosite.rb +616 -0
- data/lib/bio/db/rebase.rb +417 -0
- data/lib/bio/db/transfac.rb +387 -0
- data/lib/bio/feature.rb +201 -0
- data/lib/bio/io/brdb.rb +103 -0
- data/lib/bio/io/das.rb +471 -0
- data/lib/bio/io/dbget.rb +212 -0
- data/lib/bio/io/ddbjxml.rb +614 -0
- data/lib/bio/io/fastacmd.rb +123 -0
- data/lib/bio/io/fetch.rb +114 -0
- data/lib/bio/io/flatfile.rb +496 -0
- data/lib/bio/io/flatfile/bdb.rb +266 -0
- data/lib/bio/io/flatfile/index.rb +1308 -0
- data/lib/bio/io/flatfile/indexer.rb +778 -0
- data/lib/bio/io/higet.rb +92 -0
- data/lib/bio/io/keggapi.rb +863 -0
- data/lib/bio/io/pubmed.rb +189 -0
- data/lib/bio/io/registry.rb +308 -0
- data/lib/bio/io/soapwsdl.rb +114 -0
- data/lib/bio/io/sql.rb +428 -0
- data/lib/bio/location.rb +650 -0
- data/lib/bio/pathway.rb +991 -0
- data/lib/bio/reference.rb +308 -0
- data/lib/bio/sequence.rb +593 -0
- data/lib/bio/shell.rb +51 -0
- data/lib/bio/shell/core.rb +512 -0
- data/lib/bio/shell/plugin/codon.rb +228 -0
- data/lib/bio/shell/plugin/entry.rb +85 -0
- data/lib/bio/shell/plugin/flatfile.rb +119 -0
- data/lib/bio/shell/plugin/keggapi.rb +187 -0
- data/lib/bio/shell/plugin/midi.rb +448 -0
- data/lib/bio/shell/plugin/obda.rb +63 -0
- data/lib/bio/shell/plugin/seq.rb +238 -0
- data/lib/bio/shell/session.rb +214 -0
- data/lib/bio/util/color_scheme.rb +214 -0
- data/lib/bio/util/color_scheme/buried.rb +78 -0
- data/lib/bio/util/color_scheme/helix.rb +78 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +83 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +50 -0
- data/lib/bio/util/color_scheme/strand.rb +78 -0
- data/lib/bio/util/color_scheme/taylor.rb +69 -0
- data/lib/bio/util/color_scheme/turn.rb +78 -0
- data/lib/bio/util/color_scheme/zappo.rb +69 -0
- data/lib/bio/util/contingency_table.rb +337 -0
- data/lib/bio/util/sirna.rb +306 -0
- data/lib/bioruby.rb +34 -0
- data/sample/biofetch.rb +475 -0
- data/sample/color_scheme_na.rb +99 -0
- data/sample/dbget +37 -0
- data/sample/fasta2tab.rb +99 -0
- data/sample/fsplit.rb +51 -0
- data/sample/gb2fasta.rb +31 -0
- data/sample/gb2tab.rb +325 -0
- data/sample/gbtab2mysql.rb +161 -0
- data/sample/genes2nuc.rb +33 -0
- data/sample/genes2pep.rb +33 -0
- data/sample/genes2tab.rb +81 -0
- data/sample/genome2rb.rb +29 -0
- data/sample/genome2tab.rb +76 -0
- data/sample/goslim.rb +311 -0
- data/sample/gt2fasta.rb +47 -0
- data/sample/pmfetch.rb +42 -0
- data/sample/pmsearch.rb +42 -0
- data/sample/psortplot_html.rb +222 -0
- data/sample/ssearch2tab.rb +96 -0
- data/sample/tdiary.rb +158 -0
- data/sample/tfastx2tab.rb +100 -0
- data/sample/vs-genes.rb +212 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/blast/eco:b0002.faa +15 -0
- data/test/data/blast/eco:b0002.faa.m0 +128 -0
- data/test/data/blast/eco:b0002.faa.m7 +65 -0
- data/test/data/blast/eco:b0002.faa.m8 +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/runner.rb +10 -0
- data/test/unit/bio/appl/blast/test_report.rb +427 -0
- data/test/unit/bio/appl/blast/test_xmlparser.rb +400 -0
- data/test/unit/bio/appl/genscan/test_report.rb +195 -0
- data/test/unit/bio/appl/sosui/test_report.rb +94 -0
- data/test/unit/bio/appl/targetp/test_report.rb +159 -0
- data/test/unit/bio/appl/test_blast.rb +159 -0
- data/test/unit/bio/appl/test_fasta.rb +142 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +139 -0
- data/test/unit/bio/data/test_aa.rb +103 -0
- data/test/unit/bio/data/test_codontable.rb +120 -0
- data/test/unit/bio/data/test_na.rb +89 -0
- data/test/unit/bio/db/embl/test_common.rb +130 -0
- data/test/unit/bio/db/embl/test_embl.rb +227 -0
- data/test/unit/bio/db/embl/test_sptr.rb +268 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +44 -0
- data/test/unit/bio/db/kegg/test_genes.rb +58 -0
- data/test/unit/bio/db/test_fasta.rb +263 -0
- data/test/unit/bio/db/test_gff.rb +140 -0
- data/test/unit/bio/db/test_prosite.rb +1450 -0
- data/test/unit/bio/io/test_ddbjxml.rb +87 -0
- data/test/unit/bio/io/test_soapwsdl.rb +45 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +175 -0
- data/test/unit/bio/test_alignment.rb +1028 -0
- data/test/unit/bio/test_command.rb +71 -0
- data/test/unit/bio/test_db.rb +109 -0
- data/test/unit/bio/test_feature.rb +128 -0
- data/test/unit/bio/test_location.rb +51 -0
- data/test/unit/bio/test_pathway.rb +485 -0
- data/test/unit/bio/test_sequence.rb +386 -0
- data/test/unit/bio/test_shell.rb +31 -0
- data/test/unit/bio/util/test_color_scheme.rb +45 -0
- data/test/unit/bio/util/test_contingency_table.rb +106 -0
- data/test/unit/bio/util/test_sirna.rb +258 -0
- metadata +295 -0
@@ -0,0 +1,87 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/io/test_ddbjxml.rb - Unit test for DDBJ XML.
|
3
|
+
#
|
4
|
+
# Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
|
5
|
+
#
|
6
|
+
# This library is free software; you can redistribute it and/or
|
7
|
+
# modify it under the terms of the GNU Lesser General Public
|
8
|
+
# License as published by the Free Software Foundation; either
|
9
|
+
# version 2 of the License, or (at your option) any later version.
|
10
|
+
#
|
11
|
+
# This library is distributed in the hope that it will be useful,
|
12
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
13
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
|
14
|
+
# Lesser General Public License for more details.
|
15
|
+
#
|
16
|
+
# You should have received a copy of the GNU Lesser General Public
|
17
|
+
# License along with this library; if not, write to the Free Software
|
18
|
+
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
19
|
+
#
|
20
|
+
# $Id: test_ddbjxml.rb,v 1.1 2005/12/11 14:59:25 nakao Exp $
|
21
|
+
#
|
22
|
+
|
23
|
+
require 'pathname'
|
24
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
25
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
26
|
+
|
27
|
+
|
28
|
+
require 'test/unit'
|
29
|
+
require 'bio/io/ddbjxml'
|
30
|
+
|
31
|
+
module Bio
|
32
|
+
|
33
|
+
class TestDDBJXMLConstants < Test::Unit::TestCase
|
34
|
+
|
35
|
+
def test_constants
|
36
|
+
constants = ["DDBJ", "TxSearch", "ClustalW", "PML", "Gib", "Fasta", "BASE_URI", "SRS", "Gtop", "GetEntry", "Blast"].sort
|
37
|
+
assert_equal(constants, Bio::DDBJ::XML.constants.sort)
|
38
|
+
end
|
39
|
+
|
40
|
+
def test_base_url
|
41
|
+
assert_equal("http://xml.nig.ac.jp/wsdl/", Bio::DDBJ::XML::BASE_URI)
|
42
|
+
end
|
43
|
+
|
44
|
+
def test_blast_server_rul
|
45
|
+
assert_equal("http://xml.nig.ac.jp/wsdl/Blast.wsdl", Bio::DDBJ::XML::Blast::SERVER_URI)
|
46
|
+
end
|
47
|
+
|
48
|
+
def test_clustalw_server_url
|
49
|
+
assert_equal("http://xml.nig.ac.jp/wsdl/ClustalW.wsdl", Bio::DDBJ::XML::ClustalW::SERVER_URI)
|
50
|
+
end
|
51
|
+
|
52
|
+
def test_ddbj_server_url
|
53
|
+
assert_equal("http://xml.nig.ac.jp/wsdl/DDBJ.wsdl", Bio::DDBJ::XML::DDBJ::SERVER_URI)
|
54
|
+
end
|
55
|
+
|
56
|
+
def test_fasta_server_url
|
57
|
+
assert_equal("http://xml.nig.ac.jp/wsdl/Fasta.wsdl", Bio::DDBJ::XML::Fasta::SERVER_URI)
|
58
|
+
end
|
59
|
+
|
60
|
+
def test_getentry_server_url
|
61
|
+
assert_equal("http://xml.nig.ac.jp/wsdl/GetEntry.wsdl", Bio::DDBJ::XML::GetEntry::SERVER_URI)
|
62
|
+
end
|
63
|
+
|
64
|
+
def test_gib_server_url
|
65
|
+
assert_equal("http://xml.nig.ac.jp/wsdl/Gib.wsdl", Bio::DDBJ::XML::Gib::SERVER_URI)
|
66
|
+
end
|
67
|
+
|
68
|
+
def test_gtop_server_url
|
69
|
+
assert_equal("http://xml.nig.ac.jp/wsdl/Gtop.wsdl", Bio::DDBJ::XML::Gtop::SERVER_URI)
|
70
|
+
end
|
71
|
+
|
72
|
+
def test_pml_server_url
|
73
|
+
assert_equal("http://xml.nig.ac.jp/wsdl/PML.wsdl", Bio::DDBJ::XML::PML::SERVER_URI)
|
74
|
+
end
|
75
|
+
|
76
|
+
def test_srs_server_url
|
77
|
+
assert_equal("http://xml.nig.ac.jp/wsdl/SRS.wsdl", Bio::DDBJ::XML::SRS::SERVER_URI)
|
78
|
+
end
|
79
|
+
|
80
|
+
def test_txsearch_server_url
|
81
|
+
assert_equal("http://xml.nig.ac.jp/wsdl/TxSearch.wsdl", Bio::DDBJ::XML::TxSearch::SERVER_URI)
|
82
|
+
end
|
83
|
+
|
84
|
+
end
|
85
|
+
|
86
|
+
|
87
|
+
end
|
@@ -0,0 +1,45 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
|
3
|
+
#
|
4
|
+
# Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
|
5
|
+
#
|
6
|
+
# This library is free software; you can redistribute it and/or
|
7
|
+
# modify it under the terms of the GNU Lesser General Public
|
8
|
+
# License as published by the Free Software Foundation; either
|
9
|
+
# version 2 of the License, or (at your option) any later version.
|
10
|
+
#
|
11
|
+
# This library is distributed in the hope that it will be useful,
|
12
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
13
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
|
14
|
+
# Lesser General Public License for more details.
|
15
|
+
#
|
16
|
+
# You should have received a copy of the GNU Lesser General Public
|
17
|
+
# License along with this library; if not, write to the Free Software
|
18
|
+
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
19
|
+
#
|
20
|
+
# $Id: test_soapwsdl.rb,v 1.1 2005/12/18 17:09:53 nakao Exp $
|
21
|
+
#
|
22
|
+
|
23
|
+
require 'pathname'
|
24
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
25
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
26
|
+
|
27
|
+
|
28
|
+
require 'test/unit'
|
29
|
+
require 'bio/io/soapwsdl'
|
30
|
+
|
31
|
+
module Bio
|
32
|
+
|
33
|
+
class TestSOAPWSDL < Test::Unit::TestCase
|
34
|
+
|
35
|
+
def setup
|
36
|
+
@obj = Bio::SOAPWSDL
|
37
|
+
end
|
38
|
+
|
39
|
+
def test_methods
|
40
|
+
methods = ['wsdl', 'wsdl=', 'log', 'log=']
|
41
|
+
assert_equal(methods.sort, (@obj.instance_methods - Object.methods).sort)
|
42
|
+
end
|
43
|
+
|
44
|
+
end
|
45
|
+
end
|
@@ -0,0 +1,175 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/shell/plugin/test_seq.rb - Unit test for Bio::Shell plugin for biological sequence manipulations
|
3
|
+
#
|
4
|
+
# Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
|
5
|
+
#
|
6
|
+
# This library is free software; you can redistribute it and/or
|
7
|
+
# modify it under the terms of the GNU Lesser General Public
|
8
|
+
# License as published by the Free Software Foundation; either
|
9
|
+
# version 2 of the License, or (at your option) any later version.
|
10
|
+
#
|
11
|
+
# This library is distributed in the hope that it will be useful,
|
12
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
13
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
|
14
|
+
# Lesser General Public License for more details.
|
15
|
+
#
|
16
|
+
# You should have received a copy of the GNU Lesser General Public
|
17
|
+
# License along with this library; if not, write to the Free Software
|
18
|
+
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
19
|
+
#
|
20
|
+
# $Id: test_seq.rb,v 1.5 2005/12/19 02:44:03 k Exp $
|
21
|
+
#
|
22
|
+
|
23
|
+
require 'pathname'
|
24
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
|
25
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
26
|
+
|
27
|
+
require 'test/unit'
|
28
|
+
require 'bioruby'
|
29
|
+
|
30
|
+
module Bio
|
31
|
+
class TestShellPluginSeq < Test::Unit::TestCase
|
32
|
+
|
33
|
+
# include Bio::Shell
|
34
|
+
# Bio::Shell.instance_variable_set :@config, {}
|
35
|
+
|
36
|
+
def test_naseq
|
37
|
+
str = 'ACGT'
|
38
|
+
assert_equal(Bio::Sequence::NA, seq(str).class)
|
39
|
+
assert_equal(Bio::Sequence::NA.new(str), seq(str))
|
40
|
+
assert_equal('acgt', seq(str))
|
41
|
+
end
|
42
|
+
|
43
|
+
def test_aaseq
|
44
|
+
str = 'WD'
|
45
|
+
assert_equal(Bio::Sequence::AA, seq(str).class)
|
46
|
+
assert_equal(Bio::Sequence::AA.new('WD'), seq(str))
|
47
|
+
assert_equal('WD', seq(str))
|
48
|
+
end
|
49
|
+
|
50
|
+
def test_na_seqstat
|
51
|
+
naseq = 'atgcatgcatgc'
|
52
|
+
output =<<END
|
53
|
+
|
54
|
+
* * * Sequence statistics * * *
|
55
|
+
|
56
|
+
5'->3' sequence : atgcatgcatgc
|
57
|
+
3'->5' sequence : gcatgcatgcat
|
58
|
+
Translation 1 : MHAC
|
59
|
+
Translation 2 : CMH
|
60
|
+
Translation 3 : ACM
|
61
|
+
Translation -1 : ACMH
|
62
|
+
Translation -2 : HAC
|
63
|
+
Translation -3 : MHA
|
64
|
+
Length : 12 bp
|
65
|
+
GC percent : 50 %
|
66
|
+
Composition : a - 3 ( 25.00 %)
|
67
|
+
c - 3 ( 25.00 %)
|
68
|
+
g - 3 ( 25.00 %)
|
69
|
+
t - 3 ( 25.00 %)
|
70
|
+
Codon usage :
|
71
|
+
|
72
|
+
*---------------------------------------------*
|
73
|
+
| | 2nd | |
|
74
|
+
| 1st |-------------------------------| 3rd |
|
75
|
+
| | U | C | A | G | |
|
76
|
+
|-------+-------+-------+-------+-------+-----|
|
77
|
+
| U U |F 0.0%|S 0.0%|Y 0.0%|C 0.0%| u |
|
78
|
+
| U U |F 0.0%|S 0.0%|Y 0.0%|C 25.0%| c |
|
79
|
+
| U U |L 0.0%|S 0.0%|* 0.0%|* 0.0%| a |
|
80
|
+
| UUU |L 0.0%|S 0.0%|* 0.0%|W 0.0%| g |
|
81
|
+
|-------+-------+-------+-------+-------+-----|
|
82
|
+
| CCCC |L 0.0%|P 0.0%|H 25.0%|R 0.0%| u |
|
83
|
+
| C |L 0.0%|P 0.0%|H 0.0%|R 0.0%| c |
|
84
|
+
| C |L 0.0%|P 0.0%|Q 0.0%|R 0.0%| a |
|
85
|
+
| CCCC |L 0.0%|P 0.0%|Q 0.0%|R 0.0%| g |
|
86
|
+
|-------+-------+-------+-------+-------+-----|
|
87
|
+
| A |I 0.0%|T 0.0%|N 0.0%|S 0.0%| u |
|
88
|
+
| A A |I 0.0%|T 0.0%|N 0.0%|S 0.0%| c |
|
89
|
+
| AAAAA |I 0.0%|T 0.0%|K 0.0%|R 0.0%| a |
|
90
|
+
| A A |M 25.0%|T 0.0%|K 0.0%|R 0.0%| g |
|
91
|
+
|-------+-------+-------+-------+-------+-----|
|
92
|
+
| GGGG |V 0.0%|A 0.0%|D 0.0%|G 0.0%| u |
|
93
|
+
| G |V 0.0%|A 0.0%|D 0.0%|G 0.0%| c |
|
94
|
+
| G GGG |V 0.0%|A 25.0%|E 0.0%|G 0.0%| a |
|
95
|
+
| GG G |V 0.0%|A 0.0%|E 0.0%|G 0.0%| g |
|
96
|
+
*---------------------------------------------*
|
97
|
+
|
98
|
+
Molecular weight : 3701.61444
|
99
|
+
Protein weight : 460.565
|
100
|
+
//
|
101
|
+
END
|
102
|
+
$str = ''
|
103
|
+
alias puts_orig puts
|
104
|
+
def puts(*args)
|
105
|
+
args.each do |obj|
|
106
|
+
$str << obj.to_s
|
107
|
+
end
|
108
|
+
end
|
109
|
+
seqstat(naseq)
|
110
|
+
undef puts
|
111
|
+
alias puts puts_orig
|
112
|
+
assert_equal(output, $str)
|
113
|
+
end
|
114
|
+
|
115
|
+
def test_aa_seqstat
|
116
|
+
aaseq = 'WD'
|
117
|
+
output =<<END
|
118
|
+
|
119
|
+
* * * Sequence statistics * * *
|
120
|
+
|
121
|
+
N->C sequence : WD
|
122
|
+
Length : 2 aa
|
123
|
+
Composition : D Asp - 1 ( 50.00 %) aspartic acid
|
124
|
+
W Trp - 1 ( 50.00 %) tryptophan
|
125
|
+
Protein weight : 319.315
|
126
|
+
//
|
127
|
+
END
|
128
|
+
$str = ''
|
129
|
+
alias puts_orig puts
|
130
|
+
def puts(*args)
|
131
|
+
args.each do |obj|
|
132
|
+
$str << obj.to_s
|
133
|
+
end
|
134
|
+
end
|
135
|
+
seqstat(aaseq)
|
136
|
+
undef puts
|
137
|
+
alias puts puts_orig
|
138
|
+
assert_equal(output, $str)
|
139
|
+
end
|
140
|
+
|
141
|
+
def test_doublehelix
|
142
|
+
seq = 'ACGTACGTACGTACGT'
|
143
|
+
output = <<END
|
144
|
+
at
|
145
|
+
c--g
|
146
|
+
g---c
|
147
|
+
t----a
|
148
|
+
a----t
|
149
|
+
c---g
|
150
|
+
g--c
|
151
|
+
ta
|
152
|
+
ta
|
153
|
+
g--c
|
154
|
+
c---g
|
155
|
+
a----t
|
156
|
+
t----a
|
157
|
+
g---c
|
158
|
+
c--g
|
159
|
+
at
|
160
|
+
END
|
161
|
+
$str = ''
|
162
|
+
alias puts_orig puts
|
163
|
+
def puts(*args)
|
164
|
+
args.each do |obj|
|
165
|
+
$str << obj.to_s
|
166
|
+
end
|
167
|
+
end
|
168
|
+
doublehelix(seq)
|
169
|
+
undef puts
|
170
|
+
alias puts puts_orig
|
171
|
+
assert_equal(output, $str)
|
172
|
+
end
|
173
|
+
|
174
|
+
end
|
175
|
+
end
|
@@ -0,0 +1,1028 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/test_alignment.rb - Unit test for Bio::Alignment
|
3
|
+
#
|
4
|
+
# Copyright (C) 2004 Moses Hohman <mmhohman@northwestern.edu>
|
5
|
+
# 2005 Naohisa Goto <ng@bioruby.org>
|
6
|
+
#
|
7
|
+
# This library is free software; you can redistribute it and/or
|
8
|
+
# modify it under the terms of the GNU Lesser General Public
|
9
|
+
# License as published by the Free Software Foundation; either
|
10
|
+
# version 2 of the License, or (at your option) any later version.
|
11
|
+
#
|
12
|
+
# This library is distributed in the hope that it will be useful,
|
13
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
14
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
|
15
|
+
# Lesser General Public License for more details.
|
16
|
+
#
|
17
|
+
# You should have received a copy of the GNU Lesser General Public
|
18
|
+
# License along with this library; if not, write to the Free Software
|
19
|
+
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
20
|
+
#
|
21
|
+
# $Id: test_alignment.rb,v 1.6 2005/12/02 13:01:49 ngoto Exp $
|
22
|
+
#
|
23
|
+
|
24
|
+
require 'pathname'
|
25
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
|
26
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
27
|
+
|
28
|
+
require 'test/unit'
|
29
|
+
require 'bio/alignment'
|
30
|
+
|
31
|
+
module Bio
|
32
|
+
|
33
|
+
class TestAlignmentPropertyMethods < Test::Unit::TestCase
|
34
|
+
|
35
|
+
def setup
|
36
|
+
@obj = Object.new
|
37
|
+
@obj.extend(Alignment::PropertyMethods)
|
38
|
+
end
|
39
|
+
|
40
|
+
def test_is_gap_default_false
|
41
|
+
assert_equal(false, @obj.is_gap?('a'), "\"a\" isn't a gap")
|
42
|
+
end
|
43
|
+
|
44
|
+
def test_is_gap_default_true
|
45
|
+
assert_equal(true, @obj.is_gap?('-'), '"-" is a gap')
|
46
|
+
end
|
47
|
+
|
48
|
+
def test_gap_regexp
|
49
|
+
assert_not_nil(@obj.gap_regexp)
|
50
|
+
end
|
51
|
+
|
52
|
+
def test_gap_regexp_never_nil
|
53
|
+
@obj.gap_regexp = nil
|
54
|
+
assert_not_nil(@obj.gap_regexp)
|
55
|
+
end
|
56
|
+
|
57
|
+
def test_gap_regexp=()
|
58
|
+
@obj.gap_regexp = /[^a-zA-Z0-9]/
|
59
|
+
assert_equal(/[^a-zA-Z0-9]/, @obj.gap_regexp)
|
60
|
+
end
|
61
|
+
|
62
|
+
def test_is_gap_nodefault_false
|
63
|
+
@obj.gap_regexp = /[^a-zA-Z0-9]/
|
64
|
+
assert_equal(false, @obj.is_gap?('3'))
|
65
|
+
end
|
66
|
+
|
67
|
+
def test_is_gap_nodefault_true
|
68
|
+
@obj.gap_regexp = /[^atgc]/
|
69
|
+
assert_equal(true, @obj.is_gap?('z'))
|
70
|
+
end
|
71
|
+
|
72
|
+
def test_gap_char_default
|
73
|
+
assert_not_nil(@obj.gap_char)
|
74
|
+
end
|
75
|
+
|
76
|
+
def test_gap_char_never_nil
|
77
|
+
@obj.gap_char = nil
|
78
|
+
assert_not_nil(@obj.gap_char)
|
79
|
+
end
|
80
|
+
|
81
|
+
def test_gap_char=()
|
82
|
+
@obj.gap_char = '#'
|
83
|
+
assert_equal('#', @obj.gap_char)
|
84
|
+
end
|
85
|
+
|
86
|
+
def test_missing_char_default
|
87
|
+
assert_not_nil(@obj.missing_char)
|
88
|
+
end
|
89
|
+
|
90
|
+
def test_missing_char_never_nil
|
91
|
+
@obj.missing_char = nil
|
92
|
+
assert_not_nil(@obj.missing_char)
|
93
|
+
end
|
94
|
+
|
95
|
+
def test_missing_char=()
|
96
|
+
@obj.missing_char = '_'
|
97
|
+
assert_equal('_', @obj.missing_char)
|
98
|
+
end
|
99
|
+
|
100
|
+
def test_seqclass_default
|
101
|
+
assert_not_nil(@obj.seqclass)
|
102
|
+
end
|
103
|
+
|
104
|
+
def test_seqclass_never_nil
|
105
|
+
@obj.seqclass = nil
|
106
|
+
assert_not_nil(@obj.seqclass)
|
107
|
+
end
|
108
|
+
|
109
|
+
def test_seqclass=()
|
110
|
+
@obj.seqclass = Sequence::NA
|
111
|
+
assert_equal(Sequence::NA, @obj.seqclass)
|
112
|
+
end
|
113
|
+
|
114
|
+
def test_get_all_property_default
|
115
|
+
assert_equal({}, @obj.get_all_property)
|
116
|
+
end
|
117
|
+
|
118
|
+
def test_get_all_property_nodefault
|
119
|
+
@obj.gap_regexp = /[^acgt]/
|
120
|
+
@obj.gap_char = '#'
|
121
|
+
@obj.missing_char = '_'
|
122
|
+
@obj.seqclass = Sequence::NA
|
123
|
+
assert_equal({ :gap_regexp => /[^acgt]/,
|
124
|
+
:gap_char => '#',
|
125
|
+
:missing_char => '_',
|
126
|
+
:seqclass => Sequence::NA },
|
127
|
+
@obj.get_all_property)
|
128
|
+
end
|
129
|
+
|
130
|
+
def test_set_all_property
|
131
|
+
h = { :gap_regexp => /[^acgt]/,
|
132
|
+
:gap_char => '#',
|
133
|
+
:missing_char => '_',
|
134
|
+
:seqclass => Sequence::NA }
|
135
|
+
@obj.set_all_property(h)
|
136
|
+
assert_equal(h, @obj.get_all_property)
|
137
|
+
end
|
138
|
+
end #class TestAlignmentPropertyMethods
|
139
|
+
|
140
|
+
# This is a unit test of Bio::Alignment::Site class and
|
141
|
+
# Bio::Alignment::SiteMethods module.
|
142
|
+
# Since Bio::Alignment::Site includes Bio::Alignment::SiteMethods,
|
143
|
+
# we can test both at a time.
|
144
|
+
class TestAlignmentSite < Test::Unit::TestCase
|
145
|
+
|
146
|
+
def test_has_gap_true
|
147
|
+
site = Alignment::Site[ 'a', '-', 'c', 'g', 't' ]
|
148
|
+
assert_equal(true, site.has_gap?)
|
149
|
+
end
|
150
|
+
|
151
|
+
def test_has_gap_false
|
152
|
+
site = Alignment::Site[ 'a', 'c', 'g', 't' ]
|
153
|
+
assert_equal(false, site.has_gap?)
|
154
|
+
end
|
155
|
+
|
156
|
+
def test_remove_gaps!
|
157
|
+
site = Alignment::Site[ 'a', '-', 'c', '-' ]
|
158
|
+
assert_equal(Alignment::Site['a', 'c'], site.remove_gaps!)
|
159
|
+
end
|
160
|
+
|
161
|
+
def test_remove_gaps_bang_not_removed
|
162
|
+
site = Alignment::Site[ 'a', 'c']
|
163
|
+
assert_equal(nil, site.remove_gaps!)
|
164
|
+
end
|
165
|
+
|
166
|
+
def test_consensus_string_default
|
167
|
+
site = Alignment::Site[ 'a', 'a', 'a', 'a']
|
168
|
+
assert_equal('a', site.consensus_string)
|
169
|
+
end
|
170
|
+
|
171
|
+
def test_consensus_string_default_nil
|
172
|
+
site = Alignment::Site[ 'a', 'a', 'a', 'c']
|
173
|
+
assert_nil(site.consensus_string)
|
174
|
+
end
|
175
|
+
|
176
|
+
def test_consensus_string_50percent
|
177
|
+
site = Alignment::Site[ 'a', 'a', 'c', 'g']
|
178
|
+
assert_equal('a', site.consensus_string(0.5))
|
179
|
+
end
|
180
|
+
|
181
|
+
def test_consensus_string_50percent_nil
|
182
|
+
site = Alignment::Site[ 'a', 'c', 'g', 't']
|
183
|
+
assert_nil(site.consensus_string(0.5))
|
184
|
+
end
|
185
|
+
|
186
|
+
def test_consensus_iupac
|
187
|
+
data = {
|
188
|
+
'a' => [ 'a' ],
|
189
|
+
'c' => [ 'c' ],
|
190
|
+
'g' => [ 'g' ],
|
191
|
+
't' => [ 't' ],
|
192
|
+
't' => [ 't', 'u' ],
|
193
|
+
'm' => [ 'a', 'c' ],
|
194
|
+
'r' => [ 'a', 'g' ],
|
195
|
+
'w' => [ 'a', 't' ],
|
196
|
+
's' => [ 'c', 'g' ],
|
197
|
+
'y' => [ 'c', 't' ],
|
198
|
+
'k' => [ 'g', 't' ],
|
199
|
+
'v' => [ 'a', 'c', 'g' ],
|
200
|
+
'h' => [ 'a', 'c', 't' ],
|
201
|
+
'd' => [ 'a', 'g', 't' ],
|
202
|
+
'b' => [ 'c', 'g', 't' ],
|
203
|
+
'n' => [ 'a', 'c', 'g', 't' ],
|
204
|
+
nil => [ 'z', 'a' ]
|
205
|
+
}
|
206
|
+
data.each do |cons, testdata|
|
207
|
+
site = Alignment::Site[ *testdata ]
|
208
|
+
assert_equal(cons, site.consensus_iupac,
|
209
|
+
"IUPAC consensus of #{testdata.join(',')} is #{cons}")
|
210
|
+
end
|
211
|
+
end
|
212
|
+
|
213
|
+
def test_match_line_amino_missing
|
214
|
+
site = Alignment::Site[ 'P', 'Q', 'R', 'S' ]
|
215
|
+
assert_equal(' ', site.match_line_amino)
|
216
|
+
end
|
217
|
+
|
218
|
+
def test_match_line_amino_100percent
|
219
|
+
site = Alignment::Site[ 'M', 'M', 'M', 'M' ]
|
220
|
+
assert_equal('*', site.match_line_amino)
|
221
|
+
end
|
222
|
+
|
223
|
+
def test_match_line_amino_strong
|
224
|
+
site = Alignment::Site[ 'N', 'E', 'Q', 'K' ]
|
225
|
+
assert_equal(':', site.match_line_amino)
|
226
|
+
end
|
227
|
+
|
228
|
+
def test_match_line_amino_weak
|
229
|
+
site = Alignment::Site[ 'S', 'G', 'N', 'D' ]
|
230
|
+
assert_equal('.', site.match_line_amino)
|
231
|
+
end
|
232
|
+
|
233
|
+
def test_match_line_nuc_missing
|
234
|
+
site = Alignment::Site[ 'A', 'C', 'G', 'T' ]
|
235
|
+
assert_equal(' ', site.match_line_nuc)
|
236
|
+
end
|
237
|
+
|
238
|
+
def test_match_line_nuc_100percent
|
239
|
+
site = Alignment::Site[ 'G', 'G', 'G', 'G' ]
|
240
|
+
assert_equal('*', site.match_line_nuc)
|
241
|
+
end
|
242
|
+
end #class TestAlignmentSite
|
243
|
+
|
244
|
+
# This is sample class for testing Bio::Alignment::EnumerableExtension.
|
245
|
+
class A < Array
|
246
|
+
include Alignment::EnumerableExtension
|
247
|
+
end
|
248
|
+
|
249
|
+
class TestAlignmentEnumerableExtension < Test::Unit::TestCase
|
250
|
+
def test_each_seq
|
251
|
+
expected_results = [ 'atg', 'aag', 'acg' ]
|
252
|
+
a = A[ *expected_results ]
|
253
|
+
a.each_seq do |x|
|
254
|
+
assert_equal(expected_results.shift, x)
|
255
|
+
end
|
256
|
+
assert(expected_results.empty?)
|
257
|
+
end
|
258
|
+
|
259
|
+
def test_seqclass_default
|
260
|
+
a = A.new
|
261
|
+
assert_equal(String, a.seqclass)
|
262
|
+
end
|
263
|
+
|
264
|
+
def test_seqclass
|
265
|
+
a = A[ Bio::Sequence::NA.new('atg') ]
|
266
|
+
assert_equal(Bio::Sequence::NA, a.seqclass)
|
267
|
+
end
|
268
|
+
|
269
|
+
def test_seqclass=()
|
270
|
+
a = A.new
|
271
|
+
assert_equal(String, a.seqclass)
|
272
|
+
a << Bio::Sequence::NA.new('a')
|
273
|
+
assert_equal(Bio::Sequence::NA, a.seqclass)
|
274
|
+
a.seqclass = Bio::Sequence::AA
|
275
|
+
assert_equal(Bio::Sequence::AA, a.seqclass)
|
276
|
+
end
|
277
|
+
|
278
|
+
def test_alignment_length
|
279
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
280
|
+
assert_equal(4, a.alignment_length)
|
281
|
+
end
|
282
|
+
|
283
|
+
def test_private_alignment_site
|
284
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
285
|
+
assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
|
286
|
+
a.instance_eval { _alignment_site(1) })
|
287
|
+
end
|
288
|
+
|
289
|
+
def test_alignment_site
|
290
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
291
|
+
assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
|
292
|
+
a.__send__(:_alignment_site, 1))
|
293
|
+
end
|
294
|
+
|
295
|
+
def test_each_site
|
296
|
+
expected_results = [
|
297
|
+
Alignment::Site[ 'a', 'a', 'a', 'a', '-' ],
|
298
|
+
Alignment::Site[ '-', 't', 't', 't', '-' ],
|
299
|
+
Alignment::Site[ '-', '-', 'g', 'g', '-' ],
|
300
|
+
Alignment::Site[ '-', '-', 'c', '-', '-' ]
|
301
|
+
]
|
302
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
303
|
+
a.each_site do |site|
|
304
|
+
assert_equal(expected_results.shift, site)
|
305
|
+
end
|
306
|
+
assert(expected_results.empty?)
|
307
|
+
end
|
308
|
+
|
309
|
+
def test_each_site_step
|
310
|
+
expected_results = [
|
311
|
+
Alignment::Site[ '-', 't', 't', 't', '-' ], # site 1
|
312
|
+
Alignment::Site[ '-', 'a', 'g', 't', '-' ], # site 3
|
313
|
+
]
|
314
|
+
a = A[ 'a', 'atgatc', 'atggcc', 'atgtga', '' ]
|
315
|
+
a.each_site_step(1, 4, 2) do |site|
|
316
|
+
assert_equal(expected_results.shift, site)
|
317
|
+
end
|
318
|
+
assert(expected_results.empty?)
|
319
|
+
end
|
320
|
+
|
321
|
+
def test_alignment_collect
|
322
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
323
|
+
assert_equal(Alignment::SequenceArray[ 'a', 'au', 'augc', 'aug', '' ],
|
324
|
+
a.alignment_collect { |x| x.gsub(/t/, 'u') })
|
325
|
+
end
|
326
|
+
|
327
|
+
def test_alignment_window
|
328
|
+
a = A[ 'a', 'at', 'atgca', 'atg', '' ]
|
329
|
+
assert_equal(Alignment::SequenceArray[ '', 't', 'tgc', 'tg', '' ],
|
330
|
+
a.alignment_window(1, 3))
|
331
|
+
end
|
332
|
+
|
333
|
+
def test_each_window
|
334
|
+
expected_results = [
|
335
|
+
Alignment::SequenceArray[ 'atg', 'tcg', '' ], # 0..2
|
336
|
+
Alignment::SequenceArray[ 'gca', 'gat', '' ], # 2..4
|
337
|
+
Alignment::SequenceArray[ 'atg', 'tgc', '' ], # 4..6
|
338
|
+
Alignment::SequenceArray[ 'c', 'a', '' ] # 7..7
|
339
|
+
]
|
340
|
+
a = A[ 'atgcatgc', 'tcgatgca', '' ]
|
341
|
+
r = a.each_window(3, 2) do |x|
|
342
|
+
assert_equal(expected_results.shift, x)
|
343
|
+
end
|
344
|
+
assert_equal(expected_results.shift, r)
|
345
|
+
assert(expected_results.empty?)
|
346
|
+
end
|
347
|
+
|
348
|
+
def test_collect_each_site
|
349
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
350
|
+
assert_equal(["aaaa-", "-ttt-", "--gg-", "--c--" ],
|
351
|
+
a.collect_each_site { |x| x.join('') })
|
352
|
+
end
|
353
|
+
|
354
|
+
def test_consensus_each_site_default
|
355
|
+
expected_results = [
|
356
|
+
Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ],
|
357
|
+
Alignment::Site[ 'a', 'c', 'g', 't', '-' ]
|
358
|
+
]
|
359
|
+
|
360
|
+
a = A[ 'aa', 'ac', 'ag', 'at', 'a-' ]
|
361
|
+
result = a.consensus_each_site do |site|
|
362
|
+
assert_equal(expected_results.shift, site)
|
363
|
+
'x'
|
364
|
+
end
|
365
|
+
assert_equal('xx', result)
|
366
|
+
assert(expected_results.empty?)
|
367
|
+
end
|
368
|
+
|
369
|
+
def test_consensus_each_site_gap_mode_1
|
370
|
+
expected_results = [
|
371
|
+
Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ]
|
372
|
+
]
|
373
|
+
|
374
|
+
a = A[ 'aa', 'ac', 'ag', 'at', 'a-' ]
|
375
|
+
result = a.consensus_each_site(:gap_mode => 1) do |site|
|
376
|
+
assert_equal(expected_results.shift, site)
|
377
|
+
'x'
|
378
|
+
end
|
379
|
+
assert_equal('x-', result)
|
380
|
+
assert(expected_results.empty?)
|
381
|
+
end
|
382
|
+
|
383
|
+
def test_consensus_each_site_gap_mode_minus1
|
384
|
+
expected_results = [
|
385
|
+
Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ],
|
386
|
+
Alignment::Site[ 'a', 'c', 'g', 't' ]
|
387
|
+
]
|
388
|
+
|
389
|
+
a = A[ 'aa', 'ac', 'ag', 'at', 'a-' ]
|
390
|
+
result = a.consensus_each_site(:gap_mode => -1) do |site|
|
391
|
+
assert_equal(expected_results.shift, site)
|
392
|
+
'x'
|
393
|
+
end
|
394
|
+
assert_equal('xx', result)
|
395
|
+
assert(expected_results.empty?)
|
396
|
+
end
|
397
|
+
|
398
|
+
def test_consensus_string_default
|
399
|
+
a = A[ 'ata', 'aac', 'aag', 'aat' ]
|
400
|
+
assert_equal('a??', a.consensus_string)
|
401
|
+
end
|
402
|
+
|
403
|
+
def test_consensus_string_half
|
404
|
+
a = A[ 'ata', 'aac', 'aag', 'aat' ]
|
405
|
+
assert_equal('aa?', a.consensus_string(0.5))
|
406
|
+
end
|
407
|
+
|
408
|
+
def test_consensus_iupac
|
409
|
+
a = A[
|
410
|
+
'acgtaaaccgaaacaz',
|
411
|
+
'acgtaaaccgccggcz',
|
412
|
+
'acgtcgtgttgtttgz',
|
413
|
+
'acgtcgtgttaaactz'
|
414
|
+
]
|
415
|
+
assert_equal('acgtmrwsykvhdbn?', a.consensus_iupac)
|
416
|
+
end
|
417
|
+
|
418
|
+
def test_match_line_amino
|
419
|
+
a = A[
|
420
|
+
'M-SNNNQMMHF-CASSSSSNNFH-AW',
|
421
|
+
'M-TEHDHIIYY-STATTGNDEVF-FW',
|
422
|
+
'M-AQQERLLHW-AVGNPNDEQLY-HW',
|
423
|
+
'M-SKKQKVFYF-CASKADEQHIH-LW',
|
424
|
+
'M-TNNNQMMHY-STASSSQHRMF-QW',
|
425
|
+
'M-AEHDHIIYW-AVGTTGKKKFY-YW'
|
426
|
+
#* ::::::::: ........... *
|
427
|
+
]
|
428
|
+
assert_equal('* ::::::::: ........... *', a.match_line_amino)
|
429
|
+
end
|
430
|
+
|
431
|
+
def test_match_line_nuc
|
432
|
+
a = A[ 'aaa', 'aa-','aac', 'at-' ]
|
433
|
+
assert_equal('* ', a.match_line_nuc)
|
434
|
+
end
|
435
|
+
|
436
|
+
def test_match_line
|
437
|
+
a = A[
|
438
|
+
Sequence::AA.new('MNSA'),
|
439
|
+
Sequence::AA.new('MHTL'),
|
440
|
+
Sequence::AA.new('MQNV'),
|
441
|
+
Sequence::AA.new('MKKW'),
|
442
|
+
]
|
443
|
+
assert_equal('*:. ', a.match_line)
|
444
|
+
assert_equal('*:. ', a.match_line(:type => :aa))
|
445
|
+
assert_equal('* ', a.match_line(:type => :na))
|
446
|
+
end
|
447
|
+
|
448
|
+
def test_convert_match
|
449
|
+
a = A[
|
450
|
+
'aaaa',
|
451
|
+
'accc',
|
452
|
+
'acac',
|
453
|
+
'actc'
|
454
|
+
]
|
455
|
+
a.convert_match
|
456
|
+
assert_equal(A[ 'aaaa', '.ccc', '.c.c', '.ctc' ], a)
|
457
|
+
end
|
458
|
+
|
459
|
+
def test_convert_unmatch
|
460
|
+
a = A[ 'aaaa', '.ccc', '.c.c', '.ctc' ]
|
461
|
+
a.convert_unmatch
|
462
|
+
assert_equal(A[ 'aaaa', 'accc', 'acac', 'actc' ], a)
|
463
|
+
end
|
464
|
+
|
465
|
+
def test_alignment_normalize!
|
466
|
+
a = A[ 'a', 'atg', 'atgc', '' ]
|
467
|
+
a.alignment_normalize!
|
468
|
+
assert_equal(A[ 'a---', 'atg-', 'atgc', '----'], a)
|
469
|
+
end
|
470
|
+
|
471
|
+
def test_alignment_rstrip!
|
472
|
+
a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
|
473
|
+
assert(a.alignment_rstrip!)
|
474
|
+
assert_equal(A[ '--aaa', '--t-t', '---g-', '--t' ], a)
|
475
|
+
end
|
476
|
+
|
477
|
+
def test_alignment_rstrip_nil
|
478
|
+
a = A[ 'aa', '-a', 'a-' ]
|
479
|
+
assert_nil(a.alignment_rstrip!)
|
480
|
+
assert_equal(A[ 'aa', '-a', 'a-' ], a)
|
481
|
+
end
|
482
|
+
|
483
|
+
def test_alignment_lstrip!
|
484
|
+
a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
|
485
|
+
assert(a.alignment_lstrip!)
|
486
|
+
assert_equal(A[ 'aaa--', 't-t--', '-g---', 't' ], a)
|
487
|
+
end
|
488
|
+
|
489
|
+
def test_alignment_lstrip_nil
|
490
|
+
a = A[ 'aa', '-a', 'a-' ]
|
491
|
+
assert_nil(a.alignment_lstrip!)
|
492
|
+
assert_equal(A[ 'aa', '-a', 'a-' ], a)
|
493
|
+
end
|
494
|
+
|
495
|
+
def test_alignment_strip!
|
496
|
+
a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
|
497
|
+
assert(a.alignment_strip!)
|
498
|
+
assert_equal(A[ 'aaa', 't-t', '-g-', 't' ], a)
|
499
|
+
end
|
500
|
+
|
501
|
+
def test_alignment_strip_nil
|
502
|
+
a = A[ 'aa', '-a', 'a-' ]
|
503
|
+
assert_nil(a.alignment_strip!)
|
504
|
+
assert_equal(A[ 'aa', '-a', 'a-' ], a)
|
505
|
+
end
|
506
|
+
|
507
|
+
def test_remove_all_gaps!
|
508
|
+
a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
|
509
|
+
assert(a.remove_all_gaps!)
|
510
|
+
assert_equal(A[ 'aaa', 'tt', 'g', 't' ], a)
|
511
|
+
end
|
512
|
+
|
513
|
+
# test of alignment_slice.
|
514
|
+
# Please also refer alignment_window.
|
515
|
+
def test_alignment_slice
|
516
|
+
a = A[ 'a', 'at', 'atgca', 'atg', '' ]
|
517
|
+
assert_equal(Alignment::SequenceArray[ '', 't', 'tgc', 'tg', nil ],
|
518
|
+
a.alignment_slice(1, 3))
|
519
|
+
end
|
520
|
+
|
521
|
+
def test_alignment_subseq
|
522
|
+
a = A[ Sequence.new('a'), Sequence.new('at'), Sequence.new('atgca'),
|
523
|
+
Sequence.new('atg'), Sequence.new('') ]
|
524
|
+
assert_equal(Alignment::SequenceArray[ Sequence.new(''),
|
525
|
+
Sequence.new('t'), Sequence.new('tgc'),
|
526
|
+
Sequence.new('tg'), nil ],
|
527
|
+
a.alignment_subseq(2,4))
|
528
|
+
end
|
529
|
+
|
530
|
+
def test_alignment_concat
|
531
|
+
a = A[ 'aaa', 'c', 'gg', 't' ]
|
532
|
+
a.alignment_concat(A[ 'ttt', 'gg', 'aa', 'cc', 'aa' ])
|
533
|
+
assert_equal(A[ 'aaattt', 'cgg', 'ggaa', 'tcc' ], a)
|
534
|
+
a.alignment_concat([ 'c', 't' ])
|
535
|
+
assert_equal(A[ 'aaatttc', 'cggt', 'ggaa', 'tcc' ], a)
|
536
|
+
end
|
537
|
+
end #class TestAlignmentEnumerableExtension
|
538
|
+
|
539
|
+
class TestAlignmentClustalWFormatter < Test::Unit::TestCase
|
540
|
+
def setup
|
541
|
+
@obj = Object.new
|
542
|
+
@obj.extend(Alignment::ClustalWFormatter)
|
543
|
+
end
|
544
|
+
|
545
|
+
def test_have_same_name_true
|
546
|
+
assert_equal([ 0, 1 ], @obj.instance_eval {
|
547
|
+
have_same_name?([ 'ATP ATG', 'ATP ATA', 'BBB' ]) })
|
548
|
+
end
|
549
|
+
|
550
|
+
def test_have_same_name_false
|
551
|
+
assert_equal(false, @obj.instance_eval {
|
552
|
+
have_same_name?([ 'GTP ATG', 'ATP ATA', 'BBB' ]) })
|
553
|
+
end
|
554
|
+
|
555
|
+
def test_avoid_same_name
|
556
|
+
assert_equal([ 'ATP_ATG', 'ATP_ATA', 'BBB' ],
|
557
|
+
@obj.instance_eval {
|
558
|
+
avoid_same_name([ 'ATP ATG', 'ATP ATA', 'BBB' ]) })
|
559
|
+
end
|
560
|
+
def test_avoid_same_name_numbering
|
561
|
+
assert_equal([ '0_ATP', '1_ATP', '2_BBB' ],
|
562
|
+
@obj.instance_eval {
|
563
|
+
avoid_same_name([ 'ATP', 'ATP', 'BBB' ]) })
|
564
|
+
end
|
565
|
+
|
566
|
+
end #class TestAlignmentClustalWFormatter
|
567
|
+
|
568
|
+
|
569
|
+
class TestAlignment < Test::Unit::TestCase
|
570
|
+
|
571
|
+
# testing helper method
|
572
|
+
def build_na_alignment(*sequences)
|
573
|
+
sequences.inject(Alignment.new) { |alignment, sequence| alignment << Sequence::NA.new(sequence) }
|
574
|
+
end
|
575
|
+
private :build_na_alignment
|
576
|
+
|
577
|
+
def test_equals
|
578
|
+
alignment1 = Alignment.new([Sequence::NA.new("agct"), Sequence::NA.new("tagc")])
|
579
|
+
alignment2 = Alignment.new([Sequence::NA.new("agct"), Sequence::NA.new("tagc")])
|
580
|
+
assert_equal(alignment1, alignment2)
|
581
|
+
end
|
582
|
+
|
583
|
+
# Alignment#store
|
584
|
+
|
585
|
+
def test_store_cannot_override_key
|
586
|
+
alignment = Alignment.new
|
587
|
+
alignment.store("Cat DNA", Sequence::NA.new("cat"))
|
588
|
+
alignment.store("Cat DNA", Sequence::NA.new("gcat"))
|
589
|
+
assert_equal("cat", alignment["Cat DNA"])
|
590
|
+
end
|
591
|
+
|
592
|
+
def test_store_with_nil_key_uses_next_number_for_key
|
593
|
+
alignment = Alignment.new
|
594
|
+
alignment.store(nil, Sequence::NA.new("cat"))
|
595
|
+
alignment.store(nil, Sequence::NA.new("gat"))
|
596
|
+
alignment.store(nil, Sequence::NA.new("tat"))
|
597
|
+
assert_equal({0=>"cat",1=>"gat",2=>"tat"}, alignment.to_hash)
|
598
|
+
end
|
599
|
+
|
600
|
+
def test_store_with_default_keys_and_user_defined_keys
|
601
|
+
alignment = Alignment.new
|
602
|
+
alignment.store("cat key", Sequence::NA.new("cat"))
|
603
|
+
alignment.store(nil, Sequence::NA.new("cag"))
|
604
|
+
alignment.store("gat key", Sequence::NA.new("gat"))
|
605
|
+
alignment.store(nil, Sequence::NA.new("gag"))
|
606
|
+
assert_equal({"gat key"=>"gat",1=>"cag",3=>"gag","cat key"=>"cat"}, alignment.to_hash)
|
607
|
+
end
|
608
|
+
|
609
|
+
# Test append operator
|
610
|
+
|
611
|
+
def test_seqclass_when_sequence_used
|
612
|
+
alignment = Alignment.new
|
613
|
+
alignment << Sequence::NA.new("cat")
|
614
|
+
assert_equal({0=>"cat"}, alignment.to_hash)
|
615
|
+
end
|
616
|
+
|
617
|
+
# Test seqclass
|
618
|
+
|
619
|
+
def test_seqclass_when_sequence_used_no_seqclass_set
|
620
|
+
alignment = Alignment.new
|
621
|
+
alignment << Sequence::NA.new("cat")
|
622
|
+
assert_equal(Sequence::NA, alignment.seqclass)
|
623
|
+
end
|
624
|
+
|
625
|
+
def test_seqclass_String_seq_not_present_no_seqclass_set
|
626
|
+
alignment = Alignment.new
|
627
|
+
alignment << nil
|
628
|
+
assert_equal(String, alignment.seqclass)
|
629
|
+
end
|
630
|
+
|
631
|
+
def test_seqclass_when_seqclass_set
|
632
|
+
alignment = Alignment.new
|
633
|
+
alignment.seqclass = Fixnum
|
634
|
+
alignment << "this doesn't really make sense"
|
635
|
+
assert_equal(Fixnum, alignment.seqclass)
|
636
|
+
end
|
637
|
+
|
638
|
+
# Alignment#gap_char
|
639
|
+
|
640
|
+
def test_default_gap_char
|
641
|
+
alignment = Alignment.new
|
642
|
+
assert_equal("-", alignment.gap_char)
|
643
|
+
end
|
644
|
+
|
645
|
+
def test_set_and_get_gap_char
|
646
|
+
alignment = Alignment.new
|
647
|
+
alignment.gap_char = "+"
|
648
|
+
assert_equal("+", alignment.gap_char)
|
649
|
+
end
|
650
|
+
|
651
|
+
# Alignment#gap_regexp
|
652
|
+
|
653
|
+
def test_default_gap_regexp_matches_default_gap_char
|
654
|
+
alignment = Alignment.new
|
655
|
+
assert(alignment.gap_regexp.match(alignment.gap_char))
|
656
|
+
end
|
657
|
+
|
658
|
+
# Alignment#missing_char
|
659
|
+
|
660
|
+
def test_default_missing_char
|
661
|
+
alignment = Alignment.new
|
662
|
+
assert_equal("?", alignment.missing_char)
|
663
|
+
end
|
664
|
+
|
665
|
+
# Alignment#seq_length
|
666
|
+
|
667
|
+
def test_seq_length_when_one_sequence
|
668
|
+
alignment = build_na_alignment("agt")
|
669
|
+
assert_equal(3, alignment.seq_length)
|
670
|
+
end
|
671
|
+
|
672
|
+
def test_seq_length_is_max_seq_length
|
673
|
+
alignment = build_na_alignment("agt", "agtaa", "agta")
|
674
|
+
assert_equal(5, alignment.seq_length)
|
675
|
+
end
|
676
|
+
|
677
|
+
# Alignment#each_site
|
678
|
+
|
679
|
+
def test_each_site_equal_length
|
680
|
+
alignment = build_na_alignment("acg", "gta")
|
681
|
+
expected_sites = [["a", "g"], ["c", "t"], ["g", "a"]]
|
682
|
+
alignment.each_site do |site|
|
683
|
+
assert_equal expected_sites.shift, site, "site ##{3-expected_sites.size} wrong"
|
684
|
+
end
|
685
|
+
end
|
686
|
+
|
687
|
+
def test_each_site_unequal_length
|
688
|
+
alignment = build_na_alignment("ac", "gta")
|
689
|
+
expected_sites = [["a", "g"], ["c", "t"], ["-", "a"]]
|
690
|
+
alignment.each_site do |site|
|
691
|
+
assert_equal expected_sites.shift, site, "site ##{3-expected_sites.size} wrong"
|
692
|
+
end
|
693
|
+
end
|
694
|
+
|
695
|
+
#TODO: Lots of stuff needing tests here
|
696
|
+
|
697
|
+
# Alignment#add_seq
|
698
|
+
|
699
|
+
def test_add_seq_no_key
|
700
|
+
alignment = Alignment.new
|
701
|
+
alignment.add_seq("agct")
|
702
|
+
assert_equal(String, alignment.seqclass, "wrong class")
|
703
|
+
assert_equal({0=>"agct"}, alignment.to_hash, "wrong hash")
|
704
|
+
end
|
705
|
+
|
706
|
+
def test_add_seq_using_seq_with_seq_method
|
707
|
+
seq = "agtc"
|
708
|
+
class <<seq
|
709
|
+
def seq
|
710
|
+
Sequence::NA.new(self)
|
711
|
+
end
|
712
|
+
end
|
713
|
+
|
714
|
+
alignment = Alignment.new
|
715
|
+
alignment.add_seq(seq, "key")
|
716
|
+
assert_equal(Sequence::NA, alignment.seqclass, "wrong class")
|
717
|
+
assert_equal({"key"=>"agtc"}, alignment.to_hash, "wrong hash")
|
718
|
+
end
|
719
|
+
|
720
|
+
def test_add_seq_using_seq_with_naseq_method
|
721
|
+
seq = "agtc"
|
722
|
+
class <<seq
|
723
|
+
def naseq
|
724
|
+
Sequence::NA.new(self)
|
725
|
+
end
|
726
|
+
end
|
727
|
+
|
728
|
+
alignment = Alignment.new
|
729
|
+
alignment.add_seq(seq, "key")
|
730
|
+
assert_equal(Sequence::NA, alignment.seqclass, "wrong class")
|
731
|
+
assert_equal({"key"=>"agtc"}, alignment.to_hash, "wrong hash")
|
732
|
+
end
|
733
|
+
|
734
|
+
def test_add_seq_using_seq_with_aaseq_method
|
735
|
+
seq = "AVGR"
|
736
|
+
class <<seq
|
737
|
+
def aaseq
|
738
|
+
Sequence::AA.new(self)
|
739
|
+
end
|
740
|
+
end
|
741
|
+
|
742
|
+
alignment = Alignment.new
|
743
|
+
alignment.add_seq(seq, "key")
|
744
|
+
assert_equal(Sequence::AA, alignment.seqclass, "wrong class")
|
745
|
+
assert_equal({"key"=>"AVGR"}, alignment.to_hash, "wrong hash")
|
746
|
+
end
|
747
|
+
|
748
|
+
def test_add_seq_using_seq_with_definition_method
|
749
|
+
seq = "atgc"
|
750
|
+
class <<seq
|
751
|
+
def definition
|
752
|
+
"this is the key"
|
753
|
+
end
|
754
|
+
end
|
755
|
+
|
756
|
+
alignment = Alignment.new
|
757
|
+
alignment.add_seq(seq)
|
758
|
+
assert_equal({"this is the key"=>"atgc"}, alignment.to_hash, "wrong hash")
|
759
|
+
end
|
760
|
+
|
761
|
+
def test_add_seq_using_seq_with_entry_id_method
|
762
|
+
seq = "atgc"
|
763
|
+
class <<seq
|
764
|
+
def entry_id
|
765
|
+
271828
|
766
|
+
end
|
767
|
+
end
|
768
|
+
|
769
|
+
alignment = Alignment.new
|
770
|
+
alignment.add_seq(seq)
|
771
|
+
assert_equal({271828=>"atgc"}, alignment.to_hash, "wrong hash")
|
772
|
+
end
|
773
|
+
|
774
|
+
# Alignment#consensus_string
|
775
|
+
|
776
|
+
def test_consensus_string_no_gaps
|
777
|
+
alignment = build_na_alignment("agtcgattaa",
|
778
|
+
"tttcgatgcc")
|
779
|
+
assert_equal("??tcgat???", alignment.consensus_string)
|
780
|
+
end
|
781
|
+
|
782
|
+
def test_consensus_threshold_two_sequences
|
783
|
+
alignment = build_na_alignment("agtcgattaa",
|
784
|
+
"tttcgatgcc")
|
785
|
+
# the threshold is the fraction of sequences in which a symbol must
|
786
|
+
# occur at a given position to be considered the consensus symbol
|
787
|
+
assert_equal("agtcgattaa", alignment.consensus(0.5))
|
788
|
+
assert_equal("??tcgat???", alignment.consensus(0.500000001))
|
789
|
+
end
|
790
|
+
|
791
|
+
def test_consensus_threshold_four_sequences
|
792
|
+
alignment = build_na_alignment("agtg",
|
793
|
+
"ttag",
|
794
|
+
"actc",
|
795
|
+
"tatc")
|
796
|
+
# ties go to the symbol that occurs in the earliest sequence
|
797
|
+
assert_equal("agtg", alignment.consensus(0.25))
|
798
|
+
assert_equal("a?tg", alignment.consensus(0.26))
|
799
|
+
end
|
800
|
+
|
801
|
+
def test_consensus_opt_gap_mode
|
802
|
+
alignment = build_na_alignment("gt-gt-a",
|
803
|
+
"ttcggc-",
|
804
|
+
"ttcggc-")
|
805
|
+
# using threshold = 0.5, that is a symbol must occur >= half the time in order to be consensus
|
806
|
+
# gap_mode -1 means gaps are ignored
|
807
|
+
assert_equal("ttcggca", alignment.consensus(0.5, :gap_mode => -1), "gap mode -1")
|
808
|
+
# gap_mode 0 means gaps are treated like regular symbols, yielding a gap in the last position
|
809
|
+
assert_equal("ttcggc-", alignment.consensus(0.5, :gap_mode => 0), "gap mode 0")
|
810
|
+
# gap_mode 1 means gaps take precedence over any other symbol, yielding two more gaps
|
811
|
+
assert_equal("tt-gg--", alignment.consensus(0.5, :gap_mode => 1), "gap mode 1")
|
812
|
+
end
|
813
|
+
|
814
|
+
def test_consensus_opt_missing_char
|
815
|
+
alignment = build_na_alignment("agtcgattaa",
|
816
|
+
"tttcgatgcc")
|
817
|
+
assert_equal("**tcgat***", alignment.consensus(1, :missing_char => "*"))
|
818
|
+
end
|
819
|
+
|
820
|
+
# Alignment#consensus_iupac
|
821
|
+
|
822
|
+
def test_consensus_iupac_no_gaps
|
823
|
+
alignment = build_na_alignment("agtcgattaa", "tttcgatgcc")
|
824
|
+
assert_equal("wktcgatkmm", alignment.consensus_iupac)
|
825
|
+
end
|
826
|
+
|
827
|
+
def test_consensus_iupac_of_ambiguous_bases
|
828
|
+
alignment = build_na_alignment("tmrwsykvhdbnd", "uaaaccgaaacab")
|
829
|
+
assert_equal("tmrwsykvhdbnn", alignment.consensus_iupac)
|
830
|
+
end
|
831
|
+
|
832
|
+
def test_consensus_iupac_gap_modes
|
833
|
+
alignment = build_na_alignment("a-t", "acc")
|
834
|
+
# gap_mode -1 means gaps are ignored
|
835
|
+
assert_equal("acy", alignment.consensus_iupac(:gap_mode => -1))
|
836
|
+
# gap_mode 0 means gaps are treated as normal characters, yielding a missing symbol
|
837
|
+
assert_equal("a?y", alignment.consensus_iupac(:gap_mode => 0))
|
838
|
+
# gap_mode 1 means gaps take precedence over everything, yielding a gap
|
839
|
+
assert_equal("a-y", alignment.consensus_iupac(:gap_mode => 1))
|
840
|
+
end
|
841
|
+
|
842
|
+
def test_consensus_iupac_yields_correct_ambiguous_bases
|
843
|
+
assert_equal "t", build_na_alignment("t", "u").consensus_iupac # not really IUPAC
|
844
|
+
|
845
|
+
# m = a c
|
846
|
+
assert_equal "m", build_na_alignment("a", "c").consensus_iupac, "m #1"
|
847
|
+
assert_equal "m", build_na_alignment("m", "c").consensus_iupac, "m #2"
|
848
|
+
assert_equal "m", build_na_alignment("a", "m").consensus_iupac, "m #3"
|
849
|
+
assert_equal "m", build_na_alignment("m", "a", "c").consensus_iupac, "m #4"
|
850
|
+
|
851
|
+
# r = a g
|
852
|
+
assert_equal "r", build_na_alignment("a", "g").consensus_iupac, "r #1"
|
853
|
+
assert_equal "r", build_na_alignment("r", "g").consensus_iupac, "r #2"
|
854
|
+
assert_equal "r", build_na_alignment("a", "r").consensus_iupac, "r #3"
|
855
|
+
assert_equal "r", build_na_alignment("a", "r", "g").consensus_iupac, "r #4"
|
856
|
+
|
857
|
+
# w = a t/u
|
858
|
+
assert_equal "w", build_na_alignment("a", "t").consensus_iupac, "w #1"
|
859
|
+
assert_equal "w", build_na_alignment("a", "u").consensus_iupac, "w #2"
|
860
|
+
assert_equal "w", build_na_alignment("w", "a").consensus_iupac, "w #3"
|
861
|
+
assert_equal "w", build_na_alignment("t", "w").consensus_iupac, "w #4"
|
862
|
+
assert_equal "w", build_na_alignment("w", "u").consensus_iupac, "w #5"
|
863
|
+
assert_equal "w", build_na_alignment("u", "t", "a").consensus_iupac, "w #6"
|
864
|
+
assert_equal "w", build_na_alignment("w", "u", "t", "a").consensus_iupac, "w #7"
|
865
|
+
|
866
|
+
# s = c g
|
867
|
+
assert_equal "s", build_na_alignment("c", "g").consensus_iupac, "s #1"
|
868
|
+
assert_equal "s", build_na_alignment("s", "g").consensus_iupac, "s #2"
|
869
|
+
assert_equal "s", build_na_alignment("c", "s").consensus_iupac, "s #3"
|
870
|
+
assert_equal "s", build_na_alignment("c", "s", "g").consensus_iupac, "s #4"
|
871
|
+
|
872
|
+
# y = c t/u
|
873
|
+
assert_equal "y", build_na_alignment("c", "t").consensus_iupac, "y #1"
|
874
|
+
assert_equal "y", build_na_alignment("c", "u").consensus_iupac, "y #2"
|
875
|
+
assert_equal "y", build_na_alignment("y", "c").consensus_iupac, "y #3"
|
876
|
+
assert_equal "y", build_na_alignment("t", "y").consensus_iupac, "y #4"
|
877
|
+
assert_equal "y", build_na_alignment("y", "u").consensus_iupac, "y #5"
|
878
|
+
assert_equal "y", build_na_alignment("u", "t", "c").consensus_iupac, "y #6"
|
879
|
+
assert_equal "y", build_na_alignment("y", "u", "t", "c").consensus_iupac, "y #7"
|
880
|
+
|
881
|
+
# k = g t/u
|
882
|
+
assert_equal "k", build_na_alignment("g", "t").consensus_iupac, "k #1"
|
883
|
+
assert_equal "k", build_na_alignment("g", "u").consensus_iupac, "k #2"
|
884
|
+
assert_equal "k", build_na_alignment("k", "g").consensus_iupac, "k #3"
|
885
|
+
assert_equal "k", build_na_alignment("t", "k").consensus_iupac, "k #4"
|
886
|
+
assert_equal "k", build_na_alignment("k", "u").consensus_iupac, "k #5"
|
887
|
+
assert_equal "k", build_na_alignment("u", "t", "g").consensus_iupac, "k #6"
|
888
|
+
assert_equal "k", build_na_alignment("k", "u", "t", "g").consensus_iupac, "k #7"
|
889
|
+
|
890
|
+
# v = a c g m r s
|
891
|
+
assert_equal "v", build_na_alignment("a", "c", "g").consensus_iupac, "v #1"
|
892
|
+
assert_equal "v", build_na_alignment("g", "m").consensus_iupac, "v #2"
|
893
|
+
assert_equal "v", build_na_alignment("a", "s").consensus_iupac, "v #3"
|
894
|
+
assert_equal "v", build_na_alignment("c", "r").consensus_iupac, "v #4"
|
895
|
+
assert_equal "v", build_na_alignment("m", "s").consensus_iupac, "v #5"
|
896
|
+
assert_equal "v", build_na_alignment("m", "r").consensus_iupac, "v #6"
|
897
|
+
assert_equal "v", build_na_alignment("s", "r").consensus_iupac, "v #7"
|
898
|
+
assert_equal "v", build_na_alignment("s", "r", "m").consensus_iupac, "v #8"
|
899
|
+
assert_equal "v", build_na_alignment("s", "r", "m", "a", "c", "g").consensus_iupac, "v #9"
|
900
|
+
assert_equal "v", build_na_alignment("v", "g").consensus_iupac, "v #10" # alright, enough
|
901
|
+
|
902
|
+
# b = t/u c g s y k
|
903
|
+
assert_equal "b", build_na_alignment("t", "c", "g").consensus_iupac, "b #1"
|
904
|
+
assert_equal "b", build_na_alignment("g", "y").consensus_iupac, "b #2"
|
905
|
+
assert_equal "b", build_na_alignment("t", "s").consensus_iupac, "b #3"
|
906
|
+
assert_equal "b", build_na_alignment("c", "k").consensus_iupac, "b #4"
|
907
|
+
assert_equal "b", build_na_alignment("y", "s").consensus_iupac, "b #5"
|
908
|
+
assert_equal "b", build_na_alignment("y", "k").consensus_iupac, "b #6"
|
909
|
+
assert_equal "b", build_na_alignment("s", "k").consensus_iupac, "b #7"
|
910
|
+
assert_equal "b", build_na_alignment("s", "k", "y").consensus_iupac, "b #8"
|
911
|
+
assert_equal "b", build_na_alignment("s", "k", "y", "u", "c", "g").consensus_iupac, "b #9"
|
912
|
+
assert_equal "b", build_na_alignment("b", "g").consensus_iupac, "b #10"
|
913
|
+
|
914
|
+
# h = t/u c a y w m
|
915
|
+
assert_equal "h", build_na_alignment("t", "c", "a").consensus_iupac, "h #1"
|
916
|
+
assert_equal "h", build_na_alignment("a", "y").consensus_iupac, "h #2"
|
917
|
+
assert_equal "h", build_na_alignment("c", "w").consensus_iupac, "h #3"
|
918
|
+
assert_equal "h", build_na_alignment("u", "m").consensus_iupac, "h #4"
|
919
|
+
assert_equal "h", build_na_alignment("y", "w").consensus_iupac, "h #5"
|
920
|
+
assert_equal "h", build_na_alignment("y", "m").consensus_iupac, "h #6"
|
921
|
+
assert_equal "h", build_na_alignment("y", "w").consensus_iupac, "h #7"
|
922
|
+
assert_equal "h", build_na_alignment("w", "m", "y").consensus_iupac, "h #8"
|
923
|
+
assert_equal "h", build_na_alignment("w", "m", "y", "t", "c", "a").consensus_iupac, "h #9"
|
924
|
+
assert_equal "h", build_na_alignment("h", "t").consensus_iupac, "h #10"
|
925
|
+
|
926
|
+
# d = t/u g a r w k
|
927
|
+
assert_equal "d", build_na_alignment("t", "g", "a").consensus_iupac, "d #1"
|
928
|
+
assert_equal "d", build_na_alignment("r", "t").consensus_iupac, "d #2"
|
929
|
+
assert_equal "d", build_na_alignment("w", "g").consensus_iupac, "d #3"
|
930
|
+
assert_equal "d", build_na_alignment("k", "a").consensus_iupac, "d #4"
|
931
|
+
assert_equal "d", build_na_alignment("k", "r").consensus_iupac, "d #5"
|
932
|
+
assert_equal "d", build_na_alignment("k", "w").consensus_iupac, "d #6"
|
933
|
+
assert_equal "d", build_na_alignment("r", "w").consensus_iupac, "d #7"
|
934
|
+
assert_equal "d", build_na_alignment("r", "w", "k").consensus_iupac, "d #8"
|
935
|
+
assert_equal "d", build_na_alignment("k", "r", "w", "t", "g", "a").consensus_iupac, "d #9"
|
936
|
+
assert_equal "d", build_na_alignment("d", "t").consensus_iupac, "d #10"
|
937
|
+
|
938
|
+
# n = anything
|
939
|
+
assert_equal "n", build_na_alignment("a", "g", "c", "t").consensus_iupac, "n #1"
|
940
|
+
assert_equal "n", build_na_alignment("a", "g", "c", "u").consensus_iupac, "n #2"
|
941
|
+
assert_equal "n", build_na_alignment("w", "s").consensus_iupac, "n #3"
|
942
|
+
assert_equal "n", build_na_alignment("k", "m").consensus_iupac, "n #4"
|
943
|
+
assert_equal "n", build_na_alignment("r", "y").consensus_iupac, "n #5"
|
944
|
+
end
|
945
|
+
|
946
|
+
def test_consensus_iupac_missing_char
|
947
|
+
alignment = build_na_alignment("a??", "ac?")
|
948
|
+
assert_equal("a??", alignment.consensus_iupac())
|
949
|
+
end
|
950
|
+
|
951
|
+
def test_consensus_iupac_missing_char_option
|
952
|
+
alignment = build_na_alignment("a**t", "ac**")
|
953
|
+
assert_equal("a***", alignment.consensus_iupac(:missing_char => "*"))
|
954
|
+
end
|
955
|
+
|
956
|
+
# Alignment#convert_match
|
957
|
+
|
958
|
+
def test_convert_match
|
959
|
+
alignment = Alignment.new
|
960
|
+
alignment << Sequence::NA.new("agtcgattaa")
|
961
|
+
alignment << Sequence::NA.new("tttcgatgcc")
|
962
|
+
match = alignment.convert_match
|
963
|
+
assert_equal(alignment[0], match[0], "first sequence altered")
|
964
|
+
assert_equal("tt.....gcc", match[1], "wrong match")
|
965
|
+
end
|
966
|
+
|
967
|
+
# Alignment#convert_unmatch
|
968
|
+
|
969
|
+
def test_convert_unmatch
|
970
|
+
alignment = Alignment.new
|
971
|
+
alignment << Sequence::NA.new("agtcgattaa")
|
972
|
+
alignment << Sequence::NA.new("tt.....gcc")
|
973
|
+
unmatched = alignment.convert_unmatch
|
974
|
+
assert_equal("agtcgattaa", unmatched[0], "first changed")
|
975
|
+
assert_equal("tttcgatgcc", unmatched[1], "second wrong")
|
976
|
+
end
|
977
|
+
|
978
|
+
def test_convert_unmatch_multiple_sequences
|
979
|
+
alignment = Alignment.new
|
980
|
+
alignment << Sequence::NA.new("agtcgattaa")
|
981
|
+
alignment << Sequence::NA.new("tt.....gcc")
|
982
|
+
alignment << Sequence::NA.new("c...c..g.c")
|
983
|
+
unmatched = alignment.convert_unmatch
|
984
|
+
assert_equal("agtcgattaa", unmatched[0], "first changed")
|
985
|
+
assert_equal("tttcgatgcc", unmatched[1], "second wrong")
|
986
|
+
assert_equal("cgtccatgac", unmatched[2], "third wrong")
|
987
|
+
end
|
988
|
+
|
989
|
+
def test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched
|
990
|
+
alignment = Alignment.new
|
991
|
+
alignment << Sequence::NA.new("agtcgatta")
|
992
|
+
alignment << Sequence::NA.new("tt.....gc.")
|
993
|
+
unmatched = alignment.convert_unmatch
|
994
|
+
assert_equal("agtcgatta", unmatched[0], "first changed")
|
995
|
+
assert_equal("tttcgatgc", unmatched[1], "second wrong") #TODO: verify this is correct, and not . at end
|
996
|
+
end
|
997
|
+
|
998
|
+
def test_convert_unmatch_different_match_char
|
999
|
+
alignment = Alignment.new
|
1000
|
+
alignment << Sequence::NA.new("agtcga")
|
1001
|
+
alignment << Sequence::NA.new("tt====")
|
1002
|
+
unmatched = alignment.convert_unmatch('=')
|
1003
|
+
assert_equal("agtcga", unmatched[0], "first changed")
|
1004
|
+
assert_equal("tttcga", unmatched[1], "second wrong")
|
1005
|
+
end
|
1006
|
+
|
1007
|
+
# Alignment#match_line
|
1008
|
+
|
1009
|
+
def test_match_line_protein
|
1010
|
+
alignment = Alignment.new
|
1011
|
+
alignment << Sequence::AA.new("AELFMCF")
|
1012
|
+
alignment << Sequence::AA.new("AKLVNNF")
|
1013
|
+
assert_equal "*:*. *", alignment.match_line
|
1014
|
+
end
|
1015
|
+
|
1016
|
+
#TODO: lots more on the consensus, match, etc.
|
1017
|
+
|
1018
|
+
# Alignment#normalize
|
1019
|
+
|
1020
|
+
def test_normalizebang_extends_sequences_with_gaps
|
1021
|
+
alignment = build_na_alignment("a", "ag", "agc", "agct")
|
1022
|
+
alignment.normalize!
|
1023
|
+
assert_equal({0=>"a---",1=>"ag--",2=>"agc-",3=>"agct"}, alignment.to_hash)
|
1024
|
+
end
|
1025
|
+
|
1026
|
+
# Alignment#to_clustal
|
1027
|
+
end
|
1028
|
+
end
|