bio 1.3.1 → 1.4.0
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- data/ChangeLog +2105 -3728
- data/KNOWN_ISSUES.rdoc +35 -3
- data/README.rdoc +8 -2
- data/RELEASE_NOTES.rdoc +166 -0
- data/bin/bioruby +4 -1
- data/bioruby.gemspec +146 -1
- data/bioruby.gemspec.erb +3 -1
- data/doc/ChangeLog-before-1.3.1 +3961 -0
- data/doc/Tutorial.rd +154 -22
- data/doc/Tutorial.rd.html +125 -68
- data/lib/bio.rb +21 -6
- data/lib/bio/appl/bl2seq/report.rb +11 -202
- data/lib/bio/appl/blast/format0.rb +0 -193
- data/lib/bio/appl/blast/report.rb +2 -147
- data/lib/bio/appl/blast/wublast.rb +0 -208
- data/lib/bio/appl/fasta.rb +4 -19
- data/lib/bio/appl/fasta/format10.rb +0 -14
- data/lib/bio/appl/genscan/report.rb +0 -176
- data/lib/bio/appl/hmmer.rb +1 -15
- data/lib/bio/appl/hmmer/report.rb +0 -100
- data/lib/bio/appl/meme/mast.rb +156 -0
- data/lib/bio/appl/meme/mast/report.rb +91 -0
- data/lib/bio/appl/meme/motif.rb +48 -0
- data/lib/bio/appl/psort.rb +0 -111
- data/lib/bio/appl/psort/report.rb +1 -45
- data/lib/bio/appl/pts1.rb +2 -4
- data/lib/bio/appl/sosui/report.rb +5 -54
- data/lib/bio/appl/targetp/report.rb +1 -104
- data/lib/bio/appl/tmhmm/report.rb +0 -36
- data/lib/bio/command.rb +94 -10
- data/lib/bio/data/aa.rb +1 -77
- data/lib/bio/data/codontable.rb +1 -95
- data/lib/bio/data/na.rb +1 -26
- data/lib/bio/db/aaindex.rb +1 -38
- data/lib/bio/db/fasta.rb +1 -134
- data/lib/bio/db/fasta/format_qual.rb +204 -0
- data/lib/bio/db/fasta/qual.rb +102 -0
- data/lib/bio/db/fastq.rb +645 -0
- data/lib/bio/db/fastq/fastq_to_biosequence.rb +40 -0
- data/lib/bio/db/fastq/format_fastq.rb +175 -0
- data/lib/bio/db/genbank/genbank.rb +1 -86
- data/lib/bio/db/gff.rb +0 -17
- data/lib/bio/db/go.rb +4 -72
- data/lib/bio/db/kegg/common.rb +112 -0
- data/lib/bio/db/kegg/compound.rb +29 -20
- data/lib/bio/db/kegg/drug.rb +74 -34
- data/lib/bio/db/kegg/enzyme.rb +26 -5
- data/lib/bio/db/kegg/genes.rb +128 -15
- data/lib/bio/db/kegg/genome.rb +3 -41
- data/lib/bio/db/kegg/glycan.rb +19 -24
- data/lib/bio/db/kegg/orthology.rb +16 -56
- data/lib/bio/db/kegg/reaction.rb +81 -28
- data/lib/bio/db/kegg/taxonomy.rb +1 -52
- data/lib/bio/db/litdb.rb +1 -16
- data/lib/bio/db/phyloxml/phyloxml.xsd +582 -0
- data/lib/bio/db/phyloxml/phyloxml_elements.rb +1174 -0
- data/lib/bio/db/phyloxml/phyloxml_parser.rb +954 -0
- data/lib/bio/db/phyloxml/phyloxml_writer.rb +228 -0
- data/lib/bio/db/prosite.rb +2 -95
- data/lib/bio/db/rebase.rb +5 -6
- data/lib/bio/db/sanger_chromatogram/abif.rb +120 -0
- data/lib/bio/db/sanger_chromatogram/chromatogram.rb +133 -0
- data/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb +32 -0
- data/lib/bio/db/sanger_chromatogram/scf.rb +210 -0
- data/lib/bio/io/das.rb +0 -44
- data/lib/bio/io/ddbjxml.rb +1 -181
- data/lib/bio/io/flatfile.rb +1 -7
- data/lib/bio/io/flatfile/autodetection.rb +6 -0
- data/lib/bio/io/keggapi.rb +0 -442
- data/lib/bio/io/ncbirest.rb +130 -132
- data/lib/bio/io/ncbisoap.rb +2 -1
- data/lib/bio/io/pubmed.rb +0 -88
- data/lib/bio/location.rb +0 -73
- data/lib/bio/pathway.rb +0 -171
- data/lib/bio/sequence.rb +18 -1
- data/lib/bio/sequence/adapter.rb +3 -0
- data/lib/bio/sequence/format.rb +16 -0
- data/lib/bio/sequence/quality_score.rb +205 -0
- data/lib/bio/tree.rb +70 -5
- data/lib/bio/util/restriction_enzyme/single_strand.rb +3 -2
- data/lib/bio/util/sirna.rb +1 -23
- data/lib/bio/version.rb +1 -1
- data/sample/demo_aaindex.rb +67 -0
- data/sample/demo_aminoacid.rb +101 -0
- data/sample/demo_bl2seq_report.rb +220 -0
- data/sample/demo_blast_report.rb +285 -0
- data/sample/demo_codontable.rb +119 -0
- data/sample/demo_das.rb +105 -0
- data/sample/demo_ddbjxml.rb +212 -0
- data/sample/demo_fasta_remote.rb +51 -0
- data/sample/demo_fastaformat.rb +105 -0
- data/sample/demo_genbank.rb +132 -0
- data/sample/demo_genscan_report.rb +202 -0
- data/sample/demo_gff1.rb +49 -0
- data/sample/demo_go.rb +98 -0
- data/sample/demo_hmmer_report.rb +149 -0
- data/sample/demo_kegg_compound.rb +57 -0
- data/sample/demo_kegg_drug.rb +65 -0
- data/sample/demo_kegg_genome.rb +74 -0
- data/sample/demo_kegg_glycan.rb +72 -0
- data/sample/demo_kegg_orthology.rb +62 -0
- data/sample/demo_kegg_reaction.rb +66 -0
- data/sample/demo_kegg_taxonomy.rb +92 -0
- data/sample/demo_keggapi.rb +502 -0
- data/sample/demo_litdb.rb +42 -0
- data/sample/demo_locations.rb +99 -0
- data/sample/demo_ncbi_rest.rb +130 -0
- data/sample/demo_nucleicacid.rb +49 -0
- data/sample/demo_pathway.rb +196 -0
- data/sample/demo_prosite.rb +120 -0
- data/sample/demo_psort.rb +138 -0
- data/sample/demo_psort_report.rb +70 -0
- data/sample/demo_pubmed.rb +118 -0
- data/sample/demo_sirna.rb +63 -0
- data/sample/demo_sosui_report.rb +89 -0
- data/sample/demo_targetp_report.rb +135 -0
- data/sample/demo_tmhmm_report.rb +68 -0
- data/sample/pmfetch.rb +13 -4
- data/sample/pmsearch.rb +15 -4
- data/sample/test_phyloxml_big.rb +205 -0
- data/test/bioruby_test_helper.rb +61 -0
- data/test/data/KEGG/1.1.1.1.enzyme +935 -0
- data/test/data/KEGG/C00025.compound +102 -0
- data/test/data/KEGG/D00063.drug +104 -0
- data/test/data/KEGG/G00024.glycan +47 -0
- data/test/data/KEGG/G01366.glycan +18 -0
- data/test/data/KEGG/K02338.orthology +902 -0
- data/test/data/KEGG/R00006.reaction +14 -0
- data/test/data/fastq/README.txt +109 -0
- data/test/data/fastq/error_diff_ids.fastq +20 -0
- data/test/data/fastq/error_double_qual.fastq +22 -0
- data/test/data/fastq/error_double_seq.fastq +22 -0
- data/test/data/fastq/error_long_qual.fastq +20 -0
- data/test/data/fastq/error_no_qual.fastq +20 -0
- data/test/data/fastq/error_qual_del.fastq +20 -0
- data/test/data/fastq/error_qual_escape.fastq +20 -0
- data/test/data/fastq/error_qual_null.fastq +0 -0
- data/test/data/fastq/error_qual_space.fastq +21 -0
- data/test/data/fastq/error_qual_tab.fastq +21 -0
- data/test/data/fastq/error_qual_unit_sep.fastq +20 -0
- data/test/data/fastq/error_qual_vtab.fastq +20 -0
- data/test/data/fastq/error_short_qual.fastq +20 -0
- data/test/data/fastq/error_spaces.fastq +20 -0
- data/test/data/fastq/error_tabs.fastq +21 -0
- data/test/data/fastq/error_trunc_at_plus.fastq +19 -0
- data/test/data/fastq/error_trunc_at_qual.fastq +19 -0
- data/test/data/fastq/error_trunc_at_seq.fastq +18 -0
- data/test/data/fastq/error_trunc_in_plus.fastq +19 -0
- data/test/data/fastq/error_trunc_in_qual.fastq +20 -0
- data/test/data/fastq/error_trunc_in_seq.fastq +18 -0
- data/test/data/fastq/error_trunc_in_title.fastq +17 -0
- data/test/data/fastq/illumina_full_range_as_illumina.fastq +8 -0
- data/test/data/fastq/illumina_full_range_as_sanger.fastq +8 -0
- data/test/data/fastq/illumina_full_range_as_solexa.fastq +8 -0
- data/test/data/fastq/illumina_full_range_original_illumina.fastq +8 -0
- data/test/data/fastq/longreads_as_illumina.fastq +40 -0
- data/test/data/fastq/longreads_as_sanger.fastq +40 -0
- data/test/data/fastq/longreads_as_solexa.fastq +40 -0
- data/test/data/fastq/longreads_original_sanger.fastq +120 -0
- data/test/data/fastq/misc_dna_as_illumina.fastq +16 -0
- data/test/data/fastq/misc_dna_as_sanger.fastq +16 -0
- data/test/data/fastq/misc_dna_as_solexa.fastq +16 -0
- data/test/data/fastq/misc_dna_original_sanger.fastq +16 -0
- data/test/data/fastq/misc_rna_as_illumina.fastq +16 -0
- data/test/data/fastq/misc_rna_as_sanger.fastq +16 -0
- data/test/data/fastq/misc_rna_as_solexa.fastq +16 -0
- data/test/data/fastq/misc_rna_original_sanger.fastq +16 -0
- data/test/data/fastq/sanger_full_range_as_illumina.fastq +8 -0
- data/test/data/fastq/sanger_full_range_as_sanger.fastq +8 -0
- data/test/data/fastq/sanger_full_range_as_solexa.fastq +8 -0
- data/test/data/fastq/sanger_full_range_original_sanger.fastq +8 -0
- data/test/data/fastq/solexa_full_range_as_illumina.fastq +8 -0
- data/test/data/fastq/solexa_full_range_as_sanger.fastq +8 -0
- data/test/data/fastq/solexa_full_range_as_solexa.fastq +8 -0
- data/test/data/fastq/solexa_full_range_original_solexa.fastq +8 -0
- data/test/data/fastq/wrapping_as_illumina.fastq +12 -0
- data/test/data/fastq/wrapping_as_sanger.fastq +12 -0
- data/test/data/fastq/wrapping_as_solexa.fastq +12 -0
- data/test/data/fastq/wrapping_original_sanger.fastq +24 -0
- data/test/data/meme/db +0 -0
- data/test/data/meme/mast +0 -0
- data/test/data/meme/mast.out +13 -0
- data/test/data/meme/meme.out +3 -0
- data/test/data/phyloxml/apaf.xml +666 -0
- data/test/data/phyloxml/bcl_2.xml +2097 -0
- data/test/data/phyloxml/made_up.xml +144 -0
- data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +65 -0
- data/test/data/phyloxml/phyloxml_examples.xml +415 -0
- data/test/data/sanger_chromatogram/test_chromatogram_abif.ab1 +0 -0
- data/test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf +0 -0
- data/test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf +0 -0
- data/test/functional/bio/appl/test_pts1.rb +7 -5
- data/test/functional/bio/io/test_ensembl.rb +4 -3
- data/test/functional/bio/io/test_pubmed.rb +9 -3
- data/test/functional/bio/io/test_soapwsdl.rb +5 -4
- data/test/functional/bio/io/test_togows.rb +5 -4
- data/test/functional/bio/sequence/test_output_embl.rb +6 -4
- data/test/functional/bio/test_command.rb +54 -5
- data/test/runner.rb +5 -3
- data/test/unit/bio/appl/bl2seq/test_report.rb +5 -4
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +4 -2
- data/test/unit/bio/appl/blast/test_report.rb +5 -4
- data/test/unit/bio/appl/blast/test_rpsblast.rb +5 -4
- data/test/unit/bio/appl/gcg/test_msf.rb +5 -5
- data/test/unit/bio/appl/genscan/test_report.rb +8 -9
- data/test/unit/bio/appl/hmmer/test_report.rb +5 -4
- data/test/unit/bio/appl/iprscan/test_report.rb +6 -5
- data/test/unit/bio/appl/mafft/test_report.rb +6 -5
- data/test/unit/bio/appl/meme/mast/test_report.rb +46 -0
- data/test/unit/bio/appl/meme/test_mast.rb +103 -0
- data/test/unit/bio/appl/meme/test_motif.rb +38 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +5 -4
- data/test/unit/bio/appl/paml/codeml/test_report.rb +5 -4
- data/test/unit/bio/appl/paml/test_codeml.rb +5 -4
- data/test/unit/bio/appl/sim4/test_report.rb +5 -4
- data/test/unit/bio/appl/sosui/test_report.rb +6 -5
- data/test/unit/bio/appl/targetp/test_report.rb +5 -3
- data/test/unit/bio/appl/test_blast.rb +5 -4
- data/test/unit/bio/appl/test_fasta.rb +4 -2
- data/test/unit/bio/appl/test_pts1.rb +4 -2
- data/test/unit/bio/appl/tmhmm/test_report.rb +6 -5
- data/test/unit/bio/data/test_aa.rb +5 -3
- data/test/unit/bio/data/test_codontable.rb +5 -4
- data/test/unit/bio/data/test_na.rb +5 -3
- data/test/unit/bio/db/biosql/tc_biosql.rb +5 -1
- data/test/unit/bio/db/embl/test_common.rb +4 -2
- data/test/unit/bio/db/embl/test_embl.rb +6 -6
- data/test/unit/bio/db/embl/test_embl_rel89.rb +6 -6
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +7 -8
- data/test/unit/bio/db/embl/test_sptr.rb +6 -8
- data/test/unit/bio/db/embl/test_uniprot.rb +6 -5
- data/test/unit/bio/db/fasta/test_format_qual.rb +346 -0
- data/test/unit/bio/db/kegg/test_compound.rb +146 -0
- data/test/unit/bio/db/kegg/test_drug.rb +194 -0
- data/test/unit/bio/db/kegg/test_enzyme.rb +241 -0
- data/test/unit/bio/db/kegg/test_genes.rb +32 -4
- data/test/unit/bio/db/kegg/test_glycan.rb +260 -0
- data/test/unit/bio/db/kegg/test_orthology.rb +50 -0
- data/test/unit/bio/db/kegg/test_reaction.rb +96 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +4 -2
- data/test/unit/bio/db/sanger_chromatogram/test_abif.rb +76 -0
- data/test/unit/bio/db/sanger_chromatogram/test_scf.rb +98 -0
- data/test/unit/bio/db/test_aaindex.rb +6 -6
- data/test/unit/bio/db/test_fasta.rb +5 -46
- data/test/unit/bio/db/test_fastq.rb +829 -0
- data/test/unit/bio/db/test_gff.rb +4 -2
- data/test/unit/bio/db/test_lasergene.rb +7 -5
- data/test/unit/bio/db/test_medline.rb +4 -2
- data/test/unit/bio/db/test_newick.rb +6 -6
- data/test/unit/bio/db/test_nexus.rb +4 -2
- data/test/unit/bio/db/test_phyloxml.rb +769 -0
- data/test/unit/bio/db/test_phyloxml_writer.rb +328 -0
- data/test/unit/bio/db/test_prosite.rb +6 -5
- data/test/unit/bio/db/test_qual.rb +63 -0
- data/test/unit/bio/db/test_rebase.rb +5 -3
- data/test/unit/bio/db/test_soft.rb +7 -6
- data/test/unit/bio/io/flatfile/test_autodetection.rb +6 -7
- data/test/unit/bio/io/flatfile/test_buffer.rb +6 -5
- data/test/unit/bio/io/flatfile/test_splitter.rb +4 -4
- data/test/unit/bio/io/test_ddbjxml.rb +4 -3
- data/test/unit/bio/io/test_ensembl.rb +5 -3
- data/test/unit/bio/io/test_fastacmd.rb +4 -3
- data/test/unit/bio/io/test_flatfile.rb +6 -5
- data/test/unit/bio/io/test_soapwsdl.rb +4 -3
- data/test/unit/bio/io/test_togows.rb +4 -2
- data/test/unit/bio/sequence/test_aa.rb +5 -3
- data/test/unit/bio/sequence/test_common.rb +4 -2
- data/test/unit/bio/sequence/test_compat.rb +4 -2
- data/test/unit/bio/sequence/test_dblink.rb +5 -3
- data/test/unit/bio/sequence/test_na.rb +4 -2
- data/test/unit/bio/sequence/test_quality_score.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +5 -3
- data/test/unit/bio/test_alignment.rb +5 -3
- data/test/unit/bio/test_command.rb +4 -3
- data/test/unit/bio/test_db.rb +5 -3
- data/test/unit/bio/test_feature.rb +4 -2
- data/test/unit/bio/test_location.rb +4 -2
- data/test/unit/bio/test_map.rb +5 -3
- data/test/unit/bio/test_pathway.rb +4 -2
- data/test/unit/bio/test_reference.rb +4 -2
- data/test/unit/bio/test_sequence.rb +5 -3
- data/test/unit/bio/test_shell.rb +5 -3
- data/test/unit/bio/test_tree.rb +6 -6
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +4 -2
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +17 -13
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +17 -13
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +4 -2
- data/test/unit/bio/util/test_color_scheme.rb +5 -3
- data/test/unit/bio/util/test_contingency_table.rb +5 -3
- data/test/unit/bio/util/test_restriction_enzyme.rb +4 -2
- data/test/unit/bio/util/test_sirna.rb +6 -4
- metadata +147 -2
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'bioruby_test_helper.rb')).cleanpath.to_s
|
|
17
17
|
|
|
18
|
+
# libraries needed for the tests
|
|
18
19
|
require 'test/unit'
|
|
19
20
|
require 'bio/command'
|
|
20
21
|
|
data/test/unit/bio/test_db.rb
CHANGED
|
@@ -4,13 +4,15 @@
|
|
|
4
4
|
# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
|
|
5
5
|
# License:: The Ruby License
|
|
6
6
|
#
|
|
7
|
-
# $Id
|
|
7
|
+
# $Id:$
|
|
8
8
|
#
|
|
9
9
|
|
|
10
|
+
# loading helper routine for testing bioruby
|
|
10
11
|
require 'pathname'
|
|
11
|
-
|
|
12
|
-
|
|
12
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
|
|
13
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
13
14
|
|
|
15
|
+
# libraries needed for the tests
|
|
14
16
|
require 'test/unit'
|
|
15
17
|
require 'bio/db'
|
|
16
18
|
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/feature'
|
|
17
19
|
require 'bio/compat/features'
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/location'
|
|
17
19
|
|
data/test/unit/bio/test_map.rb
CHANGED
|
@@ -5,12 +5,14 @@
|
|
|
5
5
|
# Jan Aerts <jan.aerts@bbsrc.ac.uk>
|
|
6
6
|
# License:: The Ruby License
|
|
7
7
|
#
|
|
8
|
-
# $Id
|
|
8
|
+
# $Id:$
|
|
9
9
|
|
|
10
|
+
# loading helper routine for testing bioruby
|
|
10
11
|
require 'pathname'
|
|
11
|
-
|
|
12
|
-
|
|
12
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
|
|
13
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
13
14
|
|
|
15
|
+
# libraries needed for the tests
|
|
14
16
|
require 'test/unit'
|
|
15
17
|
require 'bio/map'
|
|
16
18
|
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/pathway'
|
|
17
19
|
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/reference'
|
|
17
19
|
require 'bio/compat/references'
|
|
@@ -6,13 +6,15 @@
|
|
|
6
6
|
# 2006 Mitsuteru C. Nakao <n@bioruby.org>
|
|
7
7
|
# License:: The Ruby License
|
|
8
8
|
#
|
|
9
|
-
# $Id
|
|
9
|
+
# $Id:$
|
|
10
10
|
#
|
|
11
11
|
|
|
12
|
+
# loading helper routine for testing bioruby
|
|
12
13
|
require 'pathname'
|
|
13
|
-
|
|
14
|
-
|
|
14
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
|
|
15
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
15
16
|
|
|
17
|
+
# libraries needed for the tests
|
|
16
18
|
require 'test/unit'
|
|
17
19
|
require 'bio/sequence'
|
|
18
20
|
|
data/test/unit/bio/test_shell.rb
CHANGED
|
@@ -4,13 +4,15 @@
|
|
|
4
4
|
# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
|
|
5
5
|
# License:: The Ruby License
|
|
6
6
|
#
|
|
7
|
-
# $Id
|
|
7
|
+
# $Id:$
|
|
8
8
|
#
|
|
9
9
|
|
|
10
|
+
# loading helper routine for testing bioruby
|
|
10
11
|
require 'pathname'
|
|
11
|
-
|
|
12
|
-
|
|
12
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
|
|
13
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
13
14
|
|
|
15
|
+
# libraries needed for the tests
|
|
14
16
|
require 'test/unit'
|
|
15
17
|
require 'bio/shell'
|
|
16
18
|
|
data/test/unit/bio/test_tree.rb
CHANGED
|
@@ -5,16 +5,16 @@
|
|
|
5
5
|
# Naohisa Goto <ng@bioruby.org>
|
|
6
6
|
# License:: The Ruby License
|
|
7
7
|
#
|
|
8
|
-
# $Id
|
|
8
|
+
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
-
|
|
12
|
-
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
13
12
|
require 'pathname'
|
|
14
|
-
|
|
15
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
16
15
|
|
|
17
|
-
|
|
16
|
+
# libraries needed for the tests
|
|
17
|
+
require 'test/unit'
|
|
18
18
|
require 'bio/tree'
|
|
19
19
|
|
|
20
20
|
module Bio
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/range/sequence_range/calculated_cuts'
|
|
17
19
|
require 'bio/util/restriction_enzyme/range/cut_range'
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/range/sequence_range'
|
|
17
19
|
require 'bio/util/restriction_enzyme/range/sequence_range/fragments'
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/range/sequence_range'
|
|
17
19
|
require 'bio/util/restriction_enzyme/range/sequence_range/fragments'
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/sequence'
|
|
17
19
|
require 'bio/util/restriction_enzyme/double_stranded/aligned_strands'
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
|
|
17
19
|
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation'
|
|
17
19
|
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/double_stranded/cut_locations'
|
|
17
19
|
|
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb
CHANGED
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation'
|
|
17
19
|
|
data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb
CHANGED
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation'
|
|
17
19
|
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/analysis'
|
|
17
19
|
require 'bio/sequence'
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/cut_symbol'
|
|
17
19
|
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/double_stranded'
|
|
17
19
|
require 'bio/sequence'
|
|
@@ -8,10 +8,12 @@
|
|
|
8
8
|
# $Id:$
|
|
9
9
|
#
|
|
10
10
|
|
|
11
|
+
# loading helper routine for testing bioruby
|
|
11
12
|
require 'pathname'
|
|
12
|
-
|
|
13
|
-
|
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
|
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
|
14
15
|
|
|
16
|
+
# libraries needed for the tests
|
|
15
17
|
require 'test/unit'
|
|
16
18
|
require 'bio/util/restriction_enzyme/single_strand'
|
|
17
19
|
|
|
@@ -128,17 +130,19 @@ class TestSingleStrand < Test::Unit::TestCase #:nodoc:
|
|
|
128
130
|
assert_raise(ArgumentError) { @t.new('a', [1,1,2]) }
|
|
129
131
|
assert_raise(ArgumentError) { @t.new('a', 1,1,2,2) }
|
|
130
132
|
|
|
131
|
-
|
|
132
|
-
|
|
133
|
-
assert_raise(ArgumentError) { @t.new(
|
|
134
|
-
assert_raise(ArgumentError) { @t.new('
|
|
135
|
-
|
|
136
|
-
assert_raise(ArgumentError) { @t.new('
|
|
137
|
-
|
|
138
|
-
assert_raise(ArgumentError) { @t.new('g', [0,1,
|
|
139
|
-
assert_raise(ArgumentError) { @t.new('g', 0,1,
|
|
140
|
-
assert_raise(ArgumentError) { @t.new(1,2
|
|
141
|
-
assert_raise(ArgumentError) { @t.new(1,2,
|
|
133
|
+
# NOTE t| 2009-09-19 commented out for library efficiency
|
|
134
|
+
# re: validate_args(sequence, c) in util/restriction_enzyme/single_strand/single_strand.rb
|
|
135
|
+
# assert_raise(ArgumentError) { @t.new(1, [1,2,3]) }
|
|
136
|
+
# assert_raise(ArgumentError) { @t.new('gaat^aca', [1,2,3]) }
|
|
137
|
+
# assert_raise(ArgumentError) { @t.new('gaat^^aca') }
|
|
138
|
+
# assert_raise(ArgumentError) { @t.new('z', [1,2,3]) }
|
|
139
|
+
#
|
|
140
|
+
# assert_raise(ArgumentError) { @t.new('g', [0,1,2]) }
|
|
141
|
+
# assert_raise(ArgumentError) { @t.new('g', 0,1,2,0) }
|
|
142
|
+
# assert_raise(ArgumentError) { @t.new('g', [0,1,1,2]) }
|
|
143
|
+
# assert_raise(ArgumentError) { @t.new('g', 0,1,1,2,2) }
|
|
144
|
+
# assert_raise(ArgumentError) { @t.new(1,2,3) }
|
|
145
|
+
# assert_raise(ArgumentError) { @t.new(1,2,'g') }
|
|
142
146
|
end
|
|
143
147
|
|
|
144
148
|
|