bioinform 0.1.12 → 0.1.13
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- checksums.yaml +4 -4
- data/.gitignore +17 -17
- data/Gemfile +16 -16
- data/LICENSE +21 -21
- data/README.md +35 -35
- data/Rakefile +4 -4
- data/TODO.txt +37 -37
- data/bin/merge_into_collection +3 -3
- data/bin/pcm2pwm +3 -3
- data/bin/split_motifs +3 -3
- data/bioinform.gemspec +19 -19
- data/lib/bioinform/cli/convert_motif.rb +107 -107
- data/lib/bioinform/cli/merge_into_collection.rb +79 -79
- data/lib/bioinform/cli/pcm2pwm.rb +46 -46
- data/lib/bioinform/cli/split_motifs.rb +46 -46
- data/lib/bioinform/cli.rb +29 -29
- data/lib/bioinform/conversion_algorithms/pcm2ppm_converter.rb +18 -18
- data/lib/bioinform/conversion_algorithms/pcm2pwm_converter.rb +19 -19
- data/lib/bioinform/data_models/collection.rb +74 -74
- data/lib/bioinform/data_models/motif.rb +55 -55
- data/lib/bioinform/data_models/pcm.rb +23 -23
- data/lib/bioinform/data_models/pm.rb +169 -169
- data/lib/bioinform/data_models/ppm.rb +9 -9
- data/lib/bioinform/data_models/pwm.rb +55 -55
- data/lib/bioinform/data_models.rb +10 -10
- data/lib/bioinform/formatters/raw_formatter.rb +40 -40
- data/lib/bioinform/formatters/transfac_formatter.rb +38 -38
- data/lib/bioinform/formatters.rb +1 -1
- data/lib/bioinform/parsers/jaspar_parser.rb +34 -34
- data/lib/bioinform/parsers/parser.rb +87 -87
- data/lib/bioinform/parsers/splittable_parser.rb +56 -56
- data/lib/bioinform/parsers/string_fantom_parser.rb +34 -34
- data/lib/bioinform/parsers/string_parser.rb +71 -71
- data/lib/bioinform/parsers/trivial_parser.rb +33 -33
- data/lib/bioinform/parsers/yaml_parser.rb +34 -34
- data/lib/bioinform/parsers.rb +6 -6
- data/lib/bioinform/support/array_product.rb +5 -5
- data/lib/bioinform/support/array_zip.rb +5 -5
- data/lib/bioinform/support/collect_hash.rb +6 -6
- data/lib/bioinform/support/deep_dup.rb +4 -4
- data/lib/bioinform/support/delete_many.rb +13 -13
- data/lib/bioinform/support/inverf.rb +12 -12
- data/lib/bioinform/support/multiline_squish.rb +5 -5
- data/lib/bioinform/support/parameters.rb +27 -27
- data/lib/bioinform/support/partial_sums.rb +15 -15
- data/lib/bioinform/support/same_by.rb +12 -12
- data/lib/bioinform/support/strip_doc.rb +8 -8
- data/lib/bioinform/support/third_part/active_support/hash_with_indifferent_access.rb +3 -0
- data/lib/bioinform/support.rb +17 -17
- data/lib/bioinform/version.rb +3 -3
- data/lib/bioinform.rb +10 -10
- data/spec/cli/cli_spec.rb +13 -13
- data/spec/cli/convert_motif_spec.rb +106 -106
- data/spec/cli/data/merge_into_collection/GABPA_f1.pwm +14 -14
- data/spec/cli/data/merge_into_collection/KLF4_f2.pwm +11 -11
- data/spec/cli/data/merge_into_collection/SP1_f1.pwm +12 -12
- data/spec/cli/data/merge_into_collection/collection.txt.result +40 -40
- data/spec/cli/data/merge_into_collection/collection.yaml.result +188 -188
- data/spec/cli/data/merge_into_collection/collection_pwm.yaml.result +188 -188
- data/spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm +14 -14
- data/spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm +11 -11
- data/spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm +12 -12
- data/spec/cli/data/pcm2pwm/KLF4 f2 spaced name.pcm +11 -11
- data/spec/cli/data/pcm2pwm/KLF4_f2.pcm +11 -11
- data/spec/cli/data/pcm2pwm/KLF4_f2.pwm.result +11 -11
- data/spec/cli/data/pcm2pwm/SP1_f1.pcm +12 -12
- data/spec/cli/data/pcm2pwm/SP1_f1.pwm.result +12 -12
- data/spec/cli/data/split_motifs/GABPA_f1.mat.result +14 -14
- data/spec/cli/data/split_motifs/KLF4_f2.mat.result +11 -11
- data/spec/cli/data/split_motifs/SP1_f1.mat.result +12 -12
- data/spec/cli/data/split_motifs/collection.yaml +188 -188
- data/spec/cli/data/split_motifs/plain_collection.txt +38 -38
- data/spec/cli/merge_into_collection_spec.rb +99 -99
- data/spec/cli/pcm2pwm_spec.rb +79 -79
- data/spec/cli/shared_examples/convert_motif/motif_list_empty.rb +17 -17
- data/spec/cli/shared_examples/convert_motif/several_motifs_specified.rb +14 -14
- data/spec/cli/shared_examples/convert_motif/single_motif_specified.rb +49 -49
- data/spec/cli/shared_examples/convert_motif/yield_help_string.rb +4 -4
- data/spec/cli/shared_examples/convert_motif/yield_motif_conversion_error.rb +3 -3
- data/spec/cli/split_motifs_spec.rb +76 -76
- data/spec/data_models/collection_spec.rb +97 -97
- data/spec/data_models/motif_spec.rb +223 -223
- data/spec/data_models/pcm_spec.rb +55 -55
- data/spec/data_models/pm_spec.rb +359 -359
- data/spec/data_models/ppm_spec.rb +7 -7
- data/spec/data_models/pwm_spec.rb +82 -82
- data/spec/fabricators/collection_fabricator.rb +7 -7
- data/spec/fabricators/motif_fabricator.rb +32 -32
- data/spec/fabricators/motif_formats_fabricator.rb +124 -124
- data/spec/fabricators/pcm_fabricator.rb +24 -24
- data/spec/fabricators/pm_fabricator.rb +51 -51
- data/spec/fabricators/ppm_fabricator.rb +13 -13
- data/spec/fabricators/pwm_fabricator.rb +16 -16
- data/spec/parsers/parser_spec.rb +152 -152
- data/spec/parsers/string_fantom_parser_spec.rb +69 -69
- data/spec/parsers/string_parser_spec.rb +76 -76
- data/spec/parsers/trivial_parser_spec.rb +63 -63
- data/spec/parsers/yaml_parser_spec.rb +50 -50
- data/spec/spec_helper.rb +10 -10
- data/spec/spec_helper_source.rb +59 -59
- data/spec/support/advanced_scan_spec.rb +31 -31
- data/spec/support/array_product_spec.rb +14 -14
- data/spec/support/array_zip_spec.rb +14 -14
- data/spec/support/collect_hash_spec.rb +14 -14
- data/spec/support/delete_many_spec.rb +43 -43
- data/spec/support/inverf_spec.rb +18 -18
- data/spec/support/multiline_squish_spec.rb +24 -24
- data/spec/support/partial_sums_spec.rb +30 -30
- data/spec/support/same_by_spec.rb +35 -35
- metadata +3 -3
@@ -1,188 +1,188 @@
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--- !ruby/object:Bioinform::Collection
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@@ -1,14 +1,14 @@
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@@ -1,11 +1,11 @@
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1
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KLF4_f2
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@@ -1,12 +1,12 @@
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|
1
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SP1_f1
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@@ -1,12 +1,12 @@
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1
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SP1_f1
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@@ -1,14 +1,14 @@
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|
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GABPA_f1
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@@ -1,11 +1,11 @@
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