bioroebe 0.10.80
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- checksums.yaml +7 -0
- data/LICENSE.md +428 -0
- data/README.md +9280 -0
- data/bin/advanced_dotplot +7 -0
- data/bin/align_open_reading_frames +12 -0
- data/bin/all_positions_of_this_nucleotide +7 -0
- data/bin/aminoacid_composition +7 -0
- data/bin/aminoacid_frequencies +12 -0
- data/bin/aminoacid_substitution +7 -0
- data/bin/automatically_rename_this_fasta_file +7 -0
- data/bin/base_composition +7 -0
- data/bin/batch_create_windows_executables +7 -0
- data/bin/biomart_console +11 -0
- data/bin/bioroebe +27 -0
- data/bin/bioroebe_controller +10 -0
- data/bin/bioshell +26 -0
- data/bin/blosum_2D_table +12 -0
- data/bin/calculate_n50_value +12 -0
- data/bin/chunked_display +12 -0
- data/bin/codon_frequency +9 -0
- data/bin/codon_to_aminoacid +30 -0
- data/bin/colourize_this_fasta_sequence +14 -0
- data/bin/compact_fasta_file +7 -0
- data/bin/complement +7 -0
- data/bin/complementary_dna_strand +12 -0
- data/bin/complementary_rna_strand +12 -0
- data/bin/compseq +7 -0
- data/bin/consensus_sequence +17 -0
- data/bin/count_AT +12 -0
- data/bin/count_GC +12 -0
- data/bin/create_random_aminoacids +7 -0
- data/bin/decode_this_aminoacid_sequence +20 -0
- data/bin/deduce_aminoacid_sequence +13 -0
- data/bin/deduce_most_likely_aminoacid_sequence +7 -0
- data/bin/display_aminoacid_table +12 -0
- data/bin/display_open_reading_frames +7 -0
- data/bin/dna_to_aminoacid_sequence +7 -0
- data/bin/dna_to_rna +7 -0
- data/bin/downcase_chunked_display +12 -0
- data/bin/download_this_pdb +7 -0
- data/bin/fasta_index +7 -0
- data/bin/fetch_data_from_uniprot +12 -0
- data/bin/filter_away_invalid_nucleotides +12 -0
- data/bin/find_substring +19 -0
- data/bin/genbank_to_fasta +7 -0
- data/bin/hamming_distance +12 -0
- data/bin/input_as_dna +12 -0
- data/bin/is_palindrome +13 -0
- data/bin/leading_five_prime +7 -0
- data/bin/levensthein +7 -0
- data/bin/longest_ORF +14 -0
- data/bin/longest_substring +12 -0
- data/bin/n_stop_codons_in_this_sequence +15 -0
- data/bin/open_reading_frames +14 -0
- data/bin/overwrite_fasta_header +7 -0
- data/bin/palindrome_2D_structure +7 -0
- data/bin/palindrome_generator +7 -0
- data/bin/parse_fasta +7 -0
- data/bin/partner_nucleotide +9 -0
- data/bin/possible_codons_for_this_aminoacid +12 -0
- data/bin/random_dna_sequence +12 -0
- data/bin/random_sequence +12 -0
- data/bin/raw_hamming_distance +12 -0
- data/bin/return_longest_substring_via_LCS_algorithm +7 -0
- data/bin/reverse_complement +7 -0
- data/bin/reverse_sequence +7 -0
- data/bin/ruler +12 -0
- data/bin/scan_this_input_for_startcodons +12 -0
- data/bin/short_aminoacid_letter_from_long_aminoacid_name +7 -0
- data/bin/show_atomic_composition +7 -0
- data/bin/show_codon_usage +12 -0
- data/bin/show_fasta_header +7 -0
- data/bin/show_nucleotide_sequence +7 -0
- data/bin/show_this_codon_table +7 -0
- data/bin/show_this_dna_sequence +7 -0
- data/bin/showorf +14 -0
- data/bin/simplify_fasta +7 -0
- data/bin/sort_aminoacid_based_on_its_hydrophobicity +7 -0
- data/bin/split_this_fasta_file_into_chromosomes +7 -0
- data/bin/strict_filter_away_invalid_aminoacids +7 -0
- data/bin/taxonomy +63 -0
- data/bin/three_to_one +7 -0
- data/bin/to_rna +7 -0
- data/bin/trailing_three_prime +7 -0
- data/bin/trypsin_digest +7 -0
- data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +7 -0
- data/bioroebe.gemspec +97 -0
- data/doc/IUPAC_aminoacids_code.md +36 -0
- data/doc/IUPAC_nucleotide_code.md +19 -0
- data/doc/README.gen +9237 -0
- data/doc/blosum.md +5 -0
- data/doc/compatibility/BIO_PHP.md +37 -0
- data/doc/compatibility/README.md +3 -0
- data/doc/compatibility/emboss.md +56 -0
- data/doc/extensive_usage_example.md +35 -0
- data/doc/german_names_for_the_aminoacids.md +27 -0
- data/doc/instructions_for_the_taxonomy_subproject.md +504 -0
- data/doc/legacy_paths.md +9 -0
- data/doc/pdb_ATOM_entry.md +33 -0
- data/doc/quality_control/README.md +2 -0
- data/doc/quality_control/commandline_applications.md +13 -0
- data/doc/resources.md +23 -0
- data/doc/setup.rb +1655 -0
- data/doc/statistics/statistics.md +41 -0
- data/doc/todo/README.md +5 -0
- data/doc/todo/bioroebe_GUI_todo.md +15 -0
- data/doc/todo/bioroebe_todo.md +2823 -0
- data/doc/using_biomart.md +258 -0
- data/html/test.html +144 -0
- data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +118 -0
- data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +118 -0
- data/lib/bioroebe/aminoacids/codon_percentage.rb +189 -0
- data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb +110 -0
- data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +221 -0
- data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +460 -0
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +231 -0
- data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +184 -0
- data/lib/bioroebe/annotations/README.md +2 -0
- data/lib/bioroebe/annotations/create_annotation_format.rb +208 -0
- data/lib/bioroebe/autoinclude.rb +7 -0
- data/lib/bioroebe/base/base.rb +35 -0
- data/lib/bioroebe/base/colours.rb +14 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +275 -0
- data/lib/bioroebe/base/commandline_application/README.md +7 -0
- data/lib/bioroebe/base/commandline_application/aminoacids.rb +33 -0
- data/lib/bioroebe/base/commandline_application/commandline_application.rb +37 -0
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +144 -0
- data/lib/bioroebe/base/commandline_application/directory.rb +33 -0
- data/lib/bioroebe/base/commandline_application/extract.rb +22 -0
- data/lib/bioroebe/base/commandline_application/misc.rb +485 -0
- data/lib/bioroebe/base/commandline_application/opn.rb +47 -0
- data/lib/bioroebe/base/commandline_application/reset.rb +40 -0
- data/lib/bioroebe/base/commandline_application/warnings.rb +36 -0
- data/lib/bioroebe/base/commandline_application/write_what_into.rb +29 -0
- data/lib/bioroebe/base/initialize.rb +18 -0
- data/lib/bioroebe/base/misc.rb +94 -0
- data/lib/bioroebe/base/namespace.rb +16 -0
- data/lib/bioroebe/base/prototype/README.md +12 -0
- data/lib/bioroebe/base/prototype/e_and_ee.rb +24 -0
- data/lib/bioroebe/base/prototype/misc.rb +108 -0
- data/lib/bioroebe/base/prototype/mkdir.rb +20 -0
- data/lib/bioroebe/base/prototype/prototype.rb +21 -0
- data/lib/bioroebe/base/prototype/reset.rb +26 -0
- data/lib/bioroebe/base/reset.rb +11 -0
- data/lib/bioroebe/biomart/LICENSE.md +27 -0
- data/lib/bioroebe/biomart/attribute.rb +77 -0
- data/lib/bioroebe/biomart/biomart.rb +227 -0
- data/lib/bioroebe/biomart/database.rb +128 -0
- data/lib/bioroebe/biomart/dataset.rb +572 -0
- data/lib/bioroebe/biomart/filter.rb +97 -0
- data/lib/bioroebe/biomart/server.rb +152 -0
- data/lib/bioroebe/blosum/blosum.rb +88 -0
- data/lib/bioroebe/calculate/calculate_blosum_score.rb +145 -0
- data/lib/bioroebe/calculate/calculate_gc_content.rb +301 -0
- data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +100 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature.rb +398 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +304 -0
- data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +166 -0
- data/lib/bioroebe/cell/README.md +1 -0
- data/lib/bioroebe/cell/cell.rb +63 -0
- data/lib/bioroebe/cleave_and_digest/README.md +2 -0
- data/lib/bioroebe/cleave_and_digest/cleave.rb +80 -0
- data/lib/bioroebe/cleave_and_digest/digestion.rb +75 -0
- data/lib/bioroebe/cleave_and_digest/trypsin.rb +192 -0
- data/lib/bioroebe/codon_tables/README.md +9 -0
- data/lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml +101 -0
- data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml +77 -0
- data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml +71 -0
- data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml +123 -0
- data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml +78 -0
- data/lib/bioroebe/codon_tables/frequencies/README.md +10 -0
- data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +337 -0
- data/lib/bioroebe/codons/README.md +28 -0
- data/lib/bioroebe/codons/codon_table.rb +416 -0
- data/lib/bioroebe/codons/codon_tables.rb +123 -0
- data/lib/bioroebe/codons/codons.rb +517 -0
- data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +102 -0
- data/lib/bioroebe/codons/detect_minimal_codon.rb +180 -0
- data/lib/bioroebe/codons/determine_optimal_codons.rb +74 -0
- data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +380 -0
- data/lib/bioroebe/codons/sanitize_codon_frequency.rb +144 -0
- data/lib/bioroebe/codons/show_codon_tables.rb +130 -0
- data/lib/bioroebe/codons/show_codon_usage.rb +197 -0
- data/lib/bioroebe/codons/show_this_codon_table.rb +573 -0
- data/lib/bioroebe/codons/start_codons.rb +105 -0
- data/lib/bioroebe/colours/colour_schemes/README.md +10 -0
- data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +38 -0
- data/lib/bioroebe/colours/colour_schemes/buried.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +101 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +262 -0
- data/lib/bioroebe/colours/colour_schemes/helix.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/nucleotide.rb +47 -0
- data/lib/bioroebe/colours/colour_schemes/score.rb +112 -0
- data/lib/bioroebe/colours/colour_schemes/simple.rb +42 -0
- data/lib/bioroebe/colours/colour_schemes/strand.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/taylor.rb +58 -0
- data/lib/bioroebe/colours/colour_schemes/turn.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/zappo.rb +59 -0
- data/lib/bioroebe/colours/colourize_sequence.rb +262 -0
- data/lib/bioroebe/colours/colours.rb +119 -0
- data/lib/bioroebe/colours/misc_colours.rb +80 -0
- data/lib/bioroebe/colours/rev.rb +41 -0
- data/lib/bioroebe/colours/sdir.rb +21 -0
- data/lib/bioroebe/colours/sfancy.rb +21 -0
- data/lib/bioroebe/colours/sfile.rb +21 -0
- data/lib/bioroebe/colours/simp.rb +21 -0
- data/lib/bioroebe/colours/swarn.rb +29 -0
- data/lib/bioroebe/colours/use_colours.rb +27 -0
- data/lib/bioroebe/configuration/configuration.rb +114 -0
- data/lib/bioroebe/configuration/constants.rb +35 -0
- data/lib/bioroebe/constants/GUIs.rb +79 -0
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +146 -0
- data/lib/bioroebe/constants/base_directory.rb +120 -0
- data/lib/bioroebe/constants/carriage_return.rb +14 -0
- data/lib/bioroebe/constants/codon_tables.rb +77 -0
- data/lib/bioroebe/constants/database_constants.rb +107 -0
- data/lib/bioroebe/constants/files_and_directories.rb +579 -0
- data/lib/bioroebe/constants/misc.rb +189 -0
- data/lib/bioroebe/constants/newline.rb +14 -0
- data/lib/bioroebe/constants/nucleotides.rb +114 -0
- data/lib/bioroebe/constants/regex.rb +28 -0
- data/lib/bioroebe/constants/roebe.rb +38 -0
- data/lib/bioroebe/constants/row_terminator.rb +16 -0
- data/lib/bioroebe/constants/tabulator.rb +14 -0
- data/lib/bioroebe/constants/unicode.rb +12 -0
- data/lib/bioroebe/constants/urls.rb +50 -0
- data/lib/bioroebe/conversions/README.md +3 -0
- data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +298 -0
- data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +569 -0
- data/lib/bioroebe/count/README.md +1 -0
- data/lib/bioroebe/count/count_amount_of_aminoacids.rb +352 -0
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +491 -0
- data/lib/bioroebe/count/count_at.rb +39 -0
- data/lib/bioroebe/count/count_gc.rb +43 -0
- data/lib/bioroebe/css/README.md +5 -0
- data/lib/bioroebe/css/project.css +121 -0
- data/lib/bioroebe/data/README.md +10 -0
- data/lib/bioroebe/data/bam/README.md +1 -0
- data/lib/bioroebe/data/data.txt +192 -0
- data/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta +12 -0
- data/lib/bioroebe/data/fasta/alu_elements.fasta +42 -0
- data/lib/bioroebe/data/fasta/lady_slippers_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/loxP.fasta +2 -0
- data/lib/bioroebe/data/fasta/ls_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/pax6_in_mouse.fasta +1 -0
- data/lib/bioroebe/data/fasta/test.fasta +7 -0
- data/lib/bioroebe/data/fasta/test_DNA.fasta +1 -0
- data/lib/bioroebe/data/fastq/fastq_example_file.fastq +32 -0
- data/lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq +1000 -0
- data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq +4 -0
- data/lib/bioroebe/data/genbank/sample_file.genbank +15 -0
- data/lib/bioroebe/data/genbank/standard.fasta +3 -0
- data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 +345 -0
- data/lib/bioroebe/data/gff/sample.gff +2 -0
- data/lib/bioroebe/data/gff/test_gene.gff +4 -0
- data/lib/bioroebe/data/gff/transcripts.gff +16 -0
- data/lib/bioroebe/data/gtf/README.md +1 -0
- data/lib/bioroebe/data/json/example_config.json +48 -0
- data/lib/bioroebe/data/pdb/1VII.pdb +754 -0
- data/lib/bioroebe/data/pdb/ala_phe_ala.pdb +228 -0
- data/lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta +2 -0
- data/lib/bioroebe/data/phylip/README.md +11 -0
- data/lib/bioroebe/data/phylip/example.phylip +7 -0
- data/lib/bioroebe/data/svg/example.svg +301 -0
- data/lib/bioroebe/databases/README.md +1 -0
- data/lib/bioroebe/databases/download_taxonomy_database.rb +102 -0
- data/lib/bioroebe/dotplots/README.md +5 -0
- data/lib/bioroebe/dotplots/advanced_dotplot.rb +256 -0
- data/lib/bioroebe/dotplots/dotplot.rb +184 -0
- data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +191 -0
- data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +102 -0
- data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +122 -0
- data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +197 -0
- data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +282 -0
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +131 -0
- data/lib/bioroebe/encoding/README.md +2 -0
- data/lib/bioroebe/encoding/encoding.rb +45 -0
- data/lib/bioroebe/enzymes/README.md +2 -0
- data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +46 -0
- data/lib/bioroebe/enzymes/restriction_enzyme.rb +200 -0
- data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +72 -0
- data/lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb +80 -0
- data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +65 -0
- data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +119 -0
- data/lib/bioroebe/exceptions/README.md +2 -0
- data/lib/bioroebe/exceptions/exceptions.rb +17 -0
- data/lib/bioroebe/ext/LICENCE.md +5 -0
- data/lib/bioroebe/ext/README.md +7 -0
- data/lib/bioroebe/ext/main.cpp +45 -0
- data/lib/bioroebe/ext/nucleotide.cpp +24 -0
- data/lib/bioroebe/ext/nussinov_algorithm.cpp +348 -0
- data/lib/bioroebe/ext/sequence +0 -0
- data/lib/bioroebe/ext/sequence.cpp +162 -0
- data/lib/bioroebe/fasta_and_fastq/README.md +6 -0
- data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +88 -0
- data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +151 -0
- data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +248 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/README.md +2 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +113 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_parser.rb +167 -0
- data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +131 -0
- data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +87 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +50 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +86 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +117 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +981 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +27 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +156 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +128 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb +20 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +83 -0
- data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +112 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +135 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +188 -0
- data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +26 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/menu.rb +41 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/misc.rb +23 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +68 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +290 -0
- data/lib/bioroebe/genbank/README.md +1 -0
- data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +275 -0
- data/lib/bioroebe/genbank/genbank_parser.rb +291 -0
- data/lib/bioroebe/gene/gene.rb +64 -0
- data/lib/bioroebe/genomes/genome_pattern.rb +165 -0
- data/lib/bioroebe/genomes/genome_retriever.rb +79 -0
- data/lib/bioroebe/gui/experimental/README.md +1 -0
- data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +147 -0
- data/lib/bioroebe/gui/gtk3/README.md +2 -0
- data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +337 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb +510 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb +55 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.config +6 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +29 -0
- data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +196 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +6 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +106 -0
- data/lib/bioroebe/gui/gtk3/controller/controller.rb +406 -0
- data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +609 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +6 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +189 -0
- data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +245 -0
- data/lib/bioroebe/gui/gtk3/format_converter/format_converter.rb +346 -0
- data/lib/bioroebe/gui/gtk3/gene/gene.rb +182 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +370 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +175 -0
- data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +428 -0
- data/lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb +342 -0
- data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb +580 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.config +6 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +182 -0
- data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +566 -0
- data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.config +6 -0
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- data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb +556 -0
- data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +171 -0
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- data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +60 -0
- data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +161 -0
- data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +76 -0
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- data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +216 -0
- data/lib/bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb +284 -0
- data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +402 -0
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +192 -0
- data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +72 -0
- data/lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb +213 -0
- data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +206 -0
- data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +140 -0
- data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +262 -0
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- data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +199 -0
- data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +519 -0
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- data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +556 -0
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- data/lib/bioroebe/palindromes/palindrome_finder.rb +208 -0
- data/lib/bioroebe/palindromes/palindrome_generator.rb +272 -0
- data/lib/bioroebe/parsers/biolang_parser.rb +156 -0
- data/lib/bioroebe/parsers/blosum_parser.rb +222 -0
- data/lib/bioroebe/parsers/genbank_parser.rb +78 -0
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- data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +149 -0
- data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +66 -0
- data/lib/bioroebe/patterns/profile_pattern.rb +182 -0
- data/lib/bioroebe/patterns/rgg_scanner.rb +160 -0
- data/lib/bioroebe/patterns/scan_for_repeat.rb +157 -0
- data/lib/bioroebe/pdb/download_this_pdb.rb +67 -0
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- data/lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb +225 -0
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- data/lib/bioroebe/project/project.rb +264 -0
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- data/lib/bioroebe/regexes/README.md +2 -0
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- data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +57 -0
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- data/lib/bioroebe/toplevel_methods/complement.rb +58 -0
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- data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +101 -0
- data/lib/bioroebe/toplevel_methods/levensthein.rb +63 -0
- data/lib/bioroebe/toplevel_methods/log_directory.rb +109 -0
- data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +55 -0
- data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +88 -0
- data/lib/bioroebe/toplevel_methods/matches.rb +259 -0
- data/lib/bioroebe/toplevel_methods/misc.rb +432 -0
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +715 -0
- data/lib/bioroebe/toplevel_methods/number_of_clones.rb +63 -0
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +77 -0
- data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +236 -0
- data/lib/bioroebe/toplevel_methods/opn.rb +34 -0
- data/lib/bioroebe/toplevel_methods/palindromes.rb +127 -0
- data/lib/bioroebe/toplevel_methods/parse.rb +59 -0
- data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rds.rb +24 -0
- data/lib/bioroebe/toplevel_methods/remove.rb +86 -0
- data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +35 -0
- data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rna_splicing.rb +73 -0
- data/lib/bioroebe/toplevel_methods/rnalfold.rb +69 -0
- data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +116 -0
- data/lib/bioroebe/toplevel_methods/shuffleseq.rb +37 -0
- data/lib/bioroebe/toplevel_methods/statistics.rb +53 -0
- data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +62 -0
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +187 -0
- data/lib/bioroebe/toplevel_methods/three_delimiter.rb +34 -0
- data/lib/bioroebe/toplevel_methods/time_and_date.rb +53 -0
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +26 -0
- data/lib/bioroebe/toplevel_methods/truncate.rb +48 -0
- data/lib/bioroebe/toplevel_methods/url.rb +36 -0
- data/lib/bioroebe/toplevel_methods/verbose.rb +59 -0
- data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +191 -0
- data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +119 -0
- data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +230 -0
- data/lib/bioroebe/utility_scripts/compacter.rb +131 -0
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +529 -0
- data/lib/bioroebe/utility_scripts/consensus_sequence.rb +374 -0
- data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +130 -0
- data/lib/bioroebe/utility_scripts/determine_antigenic_areas.rb +115 -0
- data/lib/bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb +137 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb +73 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +31 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb +37 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb +49 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +471 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +113 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb +56 -0
- data/lib/bioroebe/utility_scripts/dot_alignment.rb +177 -0
- data/lib/bioroebe/utility_scripts/download_files_from_rebase.rb +72 -0
- data/lib/bioroebe/utility_scripts/find_gene.rb +202 -0
- data/lib/bioroebe/utility_scripts/mirror_repeat.rb +235 -0
- data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +151 -0
- data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +168 -0
- data/lib/bioroebe/utility_scripts/pathways.rb +152 -0
- data/lib/bioroebe/utility_scripts/permutations.rb +145 -0
- data/lib/bioroebe/utility_scripts/punnet/punnet.rb +126 -0
- data/lib/bioroebe/utility_scripts/show_this_dna_sequence.rb +148 -0
- data/lib/bioroebe/utility_scripts/showorf/constants.rb +36 -0
- data/lib/bioroebe/utility_scripts/showorf/help.rb +33 -0
- data/lib/bioroebe/utility_scripts/showorf/initialize.rb +52 -0
- data/lib/bioroebe/utility_scripts/showorf/menu.rb +68 -0
- data/lib/bioroebe/utility_scripts/showorf/reset.rb +39 -0
- data/lib/bioroebe/utility_scripts/showorf/run.rb +152 -0
- data/lib/bioroebe/utility_scripts/showorf/show.rb +97 -0
- data/lib/bioroebe/utility_scripts/showorf/showorf.rb +488 -0
- data/lib/bioroebe/version/version.rb +44 -0
- data/lib/bioroebe/viennarna/README.md +3 -0
- data/lib/bioroebe/viennarna/rnafold_wrapper.rb +196 -0
- data/lib/bioroebe/with_gui.rb +18 -0
- data/lib/bioroebe/www/bioroebe.cgi +44 -0
- data/lib/bioroebe/www/embeddable_interface.rb +686 -0
- data/lib/bioroebe/www/sinatra/sinatra.rb +1013 -0
- data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +21 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids.yml +92 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_abbreviations.yml +31 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_average_mass_table.yml +33 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_classification.yml +18 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_english.yml +26 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_frequency.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +61 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_molecular_formula.yml +32 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_monoisotopic_mass_table.yml +38 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_reste.yml +35 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml +34 -0
- data/lib/bioroebe/yaml/aminoacids/hydropathy_table.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/molecular_weight.yml +29 -0
- data/lib/bioroebe/yaml/aminoacids/simple_aminoacids.yml +66 -0
- data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +33 -0
- data/lib/bioroebe/yaml/antisense/antisense.yml +9 -0
- data/lib/bioroebe/yaml/base_composition_of_dna.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum45.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum50.yml +34 -0
- data/lib/bioroebe/yaml/blosum/blosum62.yml +35 -0
- data/lib/bioroebe/yaml/blosum/blosum80.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum90.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum_matrix.yml +200 -0
- data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +30 -0
- data/lib/bioroebe/yaml/codon_tables/1.yml +113 -0
- data/lib/bioroebe/yaml/codon_tables/10.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/11.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/12.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/13.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/14.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/15.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/16.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/2.yml +86 -0
- data/lib/bioroebe/yaml/codon_tables/21.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/22.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/23.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/24.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/25.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/26.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/27.yml +104 -0
- data/lib/bioroebe/yaml/codon_tables/28.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/29.yml +93 -0
- data/lib/bioroebe/yaml/codon_tables/3.yml +98 -0
- data/lib/bioroebe/yaml/codon_tables/30.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/31.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/33.yml +101 -0
- data/lib/bioroebe/yaml/codon_tables/4.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/5.yml +100 -0
- data/lib/bioroebe/yaml/codon_tables/6.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/9.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/overview.yml +42 -0
- data/lib/bioroebe/yaml/configuration/README.md +12 -0
- data/lib/bioroebe/yaml/configuration/browser.yml +1 -0
- data/lib/bioroebe/yaml/configuration/colourize_fasta_sequences.yml +14 -0
- data/lib/bioroebe/yaml/configuration/default_colours_for_the_aminoacids.yml +28 -0
- data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -0
- data/lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_opn.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_this_database.yml +1 -0
- data/lib/bioroebe/yaml/create_these_directories_on_startup/create_these_directories_on_startup.yml +9 -0
- data/lib/bioroebe/yaml/default_dna_input.yml +3 -0
- data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +15 -0
- data/lib/bioroebe/yaml/enzymes/pH-Optima.yml +11 -0
- data/lib/bioroebe/yaml/fasta_and_fastq/fastq_quality_schemes.yml +44 -0
- data/lib/bioroebe/yaml/genomes/README.md +16 -0
- data/lib/bioroebe/yaml/humans/README.md +2 -0
- data/lib/bioroebe/yaml/humans/human_chromosomes.yml +53 -0
- data/lib/bioroebe/yaml/laboratory/README.md +1 -0
- data/lib/bioroebe/yaml/laboratory/pipettes.yml +8 -0
- data/lib/bioroebe/yaml/mRNA/mRNA.yml +16 -0
- data/lib/bioroebe/yaml/nuclear_localization_sequences.yml +15 -0
- data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +29 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +10 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +34 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides_weight.yml +12 -0
- data/lib/bioroebe/yaml/pathways/README.md +2 -0
- data/lib/bioroebe/yaml/pathways/citric_acid_cycle.yml +16 -0
- data/lib/bioroebe/yaml/pathways/glycolysis.yml +20 -0
- data/lib/bioroebe/yaml/pathways/shikimate_pathway.yml +23 -0
- data/lib/bioroebe/yaml/pathways/urea_cycle.yml +11 -0
- data/lib/bioroebe/yaml/primers/README.md +4 -0
- data/lib/bioroebe/yaml/primers/primers.yml +3 -0
- data/lib/bioroebe/yaml/promoters/35S.yml +15 -0
- data/lib/bioroebe/yaml/promoters/strong_promoters.yml +24 -0
- data/lib/bioroebe/yaml/proteases/proteases.yml +3 -0
- data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -0
- data/lib/bioroebe/yaml/remote_urls/README.md +4 -0
- data/lib/bioroebe/yaml/remote_urls/remote_urls.yml +3 -0
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +630 -0
- data/lib/bioroebe/yaml/sequences/JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta +14 -0
- data/lib/bioroebe/yaml/sequences/README.md +2 -0
- data/lib/bioroebe/yaml/talens.yml +22 -0
- data/lib/bioroebe/yaml/viruses/ecoli_phages.yml +63 -0
- data/lib/bioroebe/yaml/viruses/viruses.yml +6 -0
- data/lib/bioroebe.rb +5 -0
- data/spec/testing_toplevel_method_editor.rb +20 -0
- data/spec/testing_toplevel_method_url.rb +15 -0
- data/spec/testing_toplevel_method_verbose.rb +13 -0
- data/test/advanced_svg_example.rb +307 -0
- data/test/testing_bioroebe.rb +25 -0
- data/test/testing_codons.rb +45 -0
- data/test/testing_dna_to_rna_conversion.rb +15 -0
- data/test/testing_parse_pdb_file.rb +23 -0
- data/test/testing_reverse_complement.rb +32 -0
- data/test/testing_svg_component_of_bioroebe.rb +311 -0
- data/test/testing_svg_component_of_bioroebe_from_json_dataset.rb +34 -0
- data/test/testing_taxonomy.rb +22 -0
- metadata +1059 -0
@@ -0,0 +1,53 @@
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# =========================================================================== #
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# === Bioroebe::Taxonomy::Helpline
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#
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# This class will display a single helpline, for use in the Taxonomy project.
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# =========================================================================== #
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module Bioroebe
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module Taxonomy
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class Helpline # === Bioroebe::Taxonomy::Helpline
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begin
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require 'colours'
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include Colours
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extend Colours::E
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rescue LoadError; end
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# === PADDING
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# === LJUST
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#
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def self.[](
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a = 'Hello',
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b = 'World'
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)
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a = a.to_s.ljust(LJUST, ' ')
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a = ::Colours.sfancy(a)
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Colours.e PADDING+a+' '+b
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end
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end; end; end
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if __FILE__ == $PROGRAM_NAME
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Bioroebe::Taxonomy::Helpline[]
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end
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# =========================================================================== #
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# === Bioroebe::Taxonomy::CheckAvailable
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#
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# We try to find out which .INFO files are available.
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# =========================================================================== #
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module Bioroebe
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module Taxonomy
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include FileUtils::Verbose
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# Whether we shall copy or not.
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# ========================================================================= #
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SHALL_WE_COPY = true
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# ========================================================================= #
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# === initialize
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# ========================================================================= #
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def initialize(
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optional_input = nil,
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run_already = true
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)
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reset
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set_input(optional_input)
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run if run_already
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end
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# ========================================================================= #
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# === set_input
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# ========================================================================= #
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def set_input(i)
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i = i.first if i.is_a? Array
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i = i.to_s.dup if i
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@input = i
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end
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# ========================================================================= #
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# === reset
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# ========================================================================= #
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def reset
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# === @shall_we_copy
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@shall_we_copy = SHALL_WE_COPY
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# === @array_duplicates
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@array_duplicates = []
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# === @array_no_match
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@array_no_match = []
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end
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# ========================================================================= #
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# === show_important_directories
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# ========================================================================= #
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def show_important_directories
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e 'We will now run through some important local directories.'
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e
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e ' '+sfancy(INFO_DIR)
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e ' '+sfancy(AA_DIR)
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e ' '+sfancy(LOCALOME_DIR)
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e
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end
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# ========================================================================= #
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# === scan_info_directory
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# ========================================================================= #
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def scan_info_directory
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Dir[INFO_DIR+'*.INFO'].each {|entry|
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e ' → '+sfile(entry)+' ('+sfancy(File.basename(entry))+')'
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show_similar_entries_in_aa_dir(entry)
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}
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end
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# ========================================================================= #
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# === show_similar_entries_in_aa_dir
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# ========================================================================= #
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def show_similar_entries_in_aa_dir(i)
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original_input = i.dup # Keep a copy of the original input.
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i = File.basename(i)
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_ = i.gsub(File.extname(i), '')
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query_string = AA_DIR+_+'*'
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result = Dir[query_string]
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unless result.empty?
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e 'The corresponding match should be '+sfile(result.first.to_s)
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if result.size > 1
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e red('!!!')+' At least one more entry was '+
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'found though, at '+sfile(result[1])
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@array_duplicates << original_input
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else
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if @shall_we_copy
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e 'We will now copy these two entries.'
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copy(original_input, TEST_DIR)
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copy(result.first, TEST_DIR)
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end
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end
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else
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ewarn 'Warning: no match was found for '+sfile(query_string)
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ewarn '(Original input was: '+sfancy(original_input)+')'
|
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@array_no_match << original_input
|
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|
+
end
|
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+
e
|
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end
|
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+
|
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|
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# ========================================================================= #
|
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# === report_status_to_the_user
|
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# ========================================================================= #
|
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|
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def report_status_to_the_user
|
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|
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unless @array_duplicates.empty?
|
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e 'We found duplicates for these entries:'
|
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+
pp @array_duplicates
|
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|
+
end
|
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unless @array_no_match.empty?
|
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e 'We found no match for these entries:'
|
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|
+
pp @array_no_match
|
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|
+
end
|
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|
+
end
|
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+
|
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|
+
# ========================================================================= #
|
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+
# === run
|
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# ========================================================================= #
|
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+
def run
|
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if @input.nil?
|
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+
else
|
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@shall_we_copy = false
|
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+
end
|
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+
show_important_directories
|
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|
+
scan_info_directory
|
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+
report_status_to_the_user
|
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|
+
end
|
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+
|
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|
+
end; end; end
|
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+
|
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|
+
if __FILE__ == $PROGRAM_NAME
|
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|
+
Bioroebe::Taxonomy::CheckAvailable.new(ARGV)
|
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|
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end # taxonomy_check_available
|
@@ -0,0 +1,337 @@
|
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#!/usr/bin/ruby -w
|
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|
+
# Encoding: UTF-8
|
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|
+
# frozen_string_literal: true
|
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|
+
# =========================================================================== #
|
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|
+
# === Bioroebe::Taxonomy::Info
|
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|
+
#
|
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|
+
# This file will attempt to parse (and display) information from
|
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|
+
# .nfo or .INFO files.
|
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|
+
#
|
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|
+
# These files are normally stored in the local directory:
|
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|
+
#
|
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|
+
# cd /data/curated/sequences/INFO
|
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|
+
#
|
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|
+
# If however had an .INFO file is found in localomes, we will instead
|
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|
+
# assume that a fasta file will also be nearby.
|
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|
+
# =========================================================================== #
|
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|
+
# require 'taxonomy/info.rb'
|
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|
+
# =========================================================================== #
|
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|
+
require 'bioroebe/base/commandline_application/commandline_application.rb'
|
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|
+
|
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|
+
module Bioroebe
|
22
|
+
|
23
|
+
module Taxonomy
|
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|
+
|
25
|
+
class Info < ::Bioroebe::CommandlineApplication
|
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|
+
|
27
|
+
require 'bioroebe/taxonomy/constants.rb'
|
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|
+
require 'bioroebe/taxonomy/shared.rb'
|
29
|
+
|
30
|
+
# ========================================================================= #
|
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|
+
# === NAMESPACE
|
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|
+
# ========================================================================= #
|
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|
+
NAMESPACE = inspect
|
34
|
+
|
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|
+
# ========================================================================= #
|
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|
+
# === DEFAULT_TARGET
|
37
|
+
# ========================================================================= #
|
38
|
+
DEFAULT_TARGET =
|
39
|
+
"#{Constants::INFO_DIR}Nematostella_vectensis.INFO"
|
40
|
+
|
41
|
+
attr_accessor :location
|
42
|
+
alias location? location
|
43
|
+
attr_accessor :taxonomy_id
|
44
|
+
|
45
|
+
# ========================================================================= #
|
46
|
+
# === initialize
|
47
|
+
# ========================================================================= #
|
48
|
+
def initialize(
|
49
|
+
i = DEFAULT_TARGET,
|
50
|
+
run_already = true
|
51
|
+
)
|
52
|
+
reset
|
53
|
+
set_location(i)
|
54
|
+
if run_already.is_a?(Hash) or run_already == :silent
|
55
|
+
@be_verbose = false
|
56
|
+
run_already = true
|
57
|
+
end
|
58
|
+
run if run_already
|
59
|
+
end
|
60
|
+
|
61
|
+
# ========================================================================= #
|
62
|
+
# === set_location
|
63
|
+
# ========================================================================= #
|
64
|
+
def set_location(i = nil)
|
65
|
+
i = DEFAULT_TARGET if i.nil?
|
66
|
+
i = i.to_s # Should always be a String.
|
67
|
+
if File.exist?(i)
|
68
|
+
@data = File.read(i)
|
69
|
+
elsif File.exist? INFO_DIR+File.basename(i)
|
70
|
+
@data = File.read(INFO_DIR+File.basename(i))
|
71
|
+
else
|
72
|
+
opnn; e 'No file was found at `'+sfile(i)+'`.'
|
73
|
+
end
|
74
|
+
i = return_pwd+i unless i.include? '/'
|
75
|
+
@location = i
|
76
|
+
end
|
77
|
+
|
78
|
+
# ========================================================================= #
|
79
|
+
# === corresponding_datafile?
|
80
|
+
# ========================================================================= #
|
81
|
+
def corresponding_datafile?
|
82
|
+
@corresponding_datafile
|
83
|
+
end; alias corresponding_datafile corresponding_datafile? # === corresponding_datafile
|
84
|
+
|
85
|
+
# ========================================================================= #
|
86
|
+
# === reset (reset tag)
|
87
|
+
# ========================================================================= #
|
88
|
+
def reset
|
89
|
+
super()
|
90
|
+
# ======================================================================= #
|
91
|
+
# === @namespace
|
92
|
+
# ======================================================================= #
|
93
|
+
@namespace = NAMESPACE
|
94
|
+
# ======================================================================= #
|
95
|
+
# === @be_verbose
|
96
|
+
# ======================================================================= #
|
97
|
+
@be_verbose = true
|
98
|
+
# ======================================================================= #
|
99
|
+
# === @location
|
100
|
+
# ======================================================================= #
|
101
|
+
@location = nil
|
102
|
+
# ======================================================================= #
|
103
|
+
# === @data
|
104
|
+
# ======================================================================= #
|
105
|
+
@data = nil
|
106
|
+
# ======================================================================= #
|
107
|
+
# === @taxonomy_id
|
108
|
+
# ======================================================================= #
|
109
|
+
@taxonomy_id = false # By default we will assume that this file has no taxonomy id.
|
110
|
+
# ======================================================================= #
|
111
|
+
# === @genbank_common_name
|
112
|
+
# ======================================================================= #
|
113
|
+
@genbank_common_name = nil
|
114
|
+
# ======================================================================= #
|
115
|
+
# === @corresponding_datafile
|
116
|
+
# ======================================================================= #
|
117
|
+
@corresponding_datafile = nil
|
118
|
+
end
|
119
|
+
|
120
|
+
# ========================================================================= #
|
121
|
+
# === location?
|
122
|
+
# ========================================================================= #
|
123
|
+
def location?
|
124
|
+
@location
|
125
|
+
end
|
126
|
+
|
127
|
+
# ========================================================================= #
|
128
|
+
# === filename
|
129
|
+
#
|
130
|
+
# This will return the filename of the .INFO file in question.
|
131
|
+
# ========================================================================= #
|
132
|
+
def filename(
|
133
|
+
i = location?
|
134
|
+
)
|
135
|
+
return sfile(File.basename(i))
|
136
|
+
end
|
137
|
+
|
138
|
+
# ========================================================================= #
|
139
|
+
# === show_info
|
140
|
+
#
|
141
|
+
# Show info here. This will delegate to the method show_info_output.
|
142
|
+
# We decide whether we will use cliner or not.
|
143
|
+
# ========================================================================= #
|
144
|
+
def show_info(use_cliner = true)
|
145
|
+
if use_cliner
|
146
|
+
cliner { show_info_output }
|
147
|
+
else
|
148
|
+
show_info_output
|
149
|
+
end
|
150
|
+
end; alias show show_info # === show
|
151
|
+
|
152
|
+
# ========================================================================= #
|
153
|
+
# === red
|
154
|
+
# ========================================================================= #
|
155
|
+
def red(i)
|
156
|
+
Colours.red(i)
|
157
|
+
end
|
158
|
+
|
159
|
+
# ========================================================================= #
|
160
|
+
# === show_info_output
|
161
|
+
#
|
162
|
+
# Show (all) relevant info here.
|
163
|
+
# ========================================================================= #
|
164
|
+
def show_info_output
|
165
|
+
e red('@location')+' is at: '+
|
166
|
+
sfancy(@location.to_s)
|
167
|
+
e red('@taxonomy_id')+' is at: '+
|
168
|
+
sfancy(@taxonomy_id.to_s) if @taxonomy_id
|
169
|
+
e red('@genbank_common_name')+' at: '+
|
170
|
+
sfancy(@genbank_common_name.to_s) if @genbank_common_name
|
171
|
+
e red('@data')+' (the full content of the file) is: '+
|
172
|
+
simp(@data.to_s)
|
173
|
+
end
|
174
|
+
|
175
|
+
# ========================================================================= #
|
176
|
+
# === Info.parse
|
177
|
+
# ========================================================================= #
|
178
|
+
def self.parse(
|
179
|
+
i = DEFAULT_TARGET
|
180
|
+
)
|
181
|
+
_ = Info.new(i)
|
182
|
+
_.try_to_report_the_taxonomy_id
|
183
|
+
return _
|
184
|
+
end
|
185
|
+
|
186
|
+
# ========================================================================= #
|
187
|
+
# === show_likely_fasta_file_if_it_can_be_found
|
188
|
+
#
|
189
|
+
# We will show likely fasta file, if it can be found.
|
190
|
+
# ========================================================================= #
|
191
|
+
def show_likely_fasta_file_if_it_can_be_found
|
192
|
+
entries = try_to_find_likely_fasta_file
|
193
|
+
if @corresponding_datafile
|
194
|
+
e "We found #{entries.size} match(es) of potential .fa files. "\
|
195
|
+
"Now showing all of them."
|
196
|
+
entries.map {|entry| e ' '+sfile(entry) } # Display via padding.
|
197
|
+
e '(This can be parsed through class ParseFasta, which is '\
|
198
|
+
'aliased to "pfasta"'
|
199
|
+
e 'in the interactive shell; or simply paste the file path '\
|
200
|
+
'into the shell.)'
|
201
|
+
else
|
202
|
+
e 'We could not find a corresponding local fasta file.'
|
203
|
+
end
|
204
|
+
end
|
205
|
+
|
206
|
+
# ========================================================================= #
|
207
|
+
# === check_for_genbank_common_name
|
208
|
+
# ========================================================================= #
|
209
|
+
def check_for_genbank_common_name
|
210
|
+
if @data.include? 'Genbank common name' # Ok, we have a Taxonomy ID.
|
211
|
+
@data =~ /Genbank common name: (.+)/
|
212
|
+
@genbank_common_name = $1.dup if $1
|
213
|
+
else
|
214
|
+
e 'The file '+sfile(filename)+' has no Genbank common name.' if @be_verbose
|
215
|
+
end if @data
|
216
|
+
end
|
217
|
+
|
218
|
+
# ========================================================================= #
|
219
|
+
# === check_for_taxonomy_id
|
220
|
+
#
|
221
|
+
# This method attempts to fetch the Taxonomy ID from the .INFO file.
|
222
|
+
# Some .INFO files may not have a Taxonomy ID.
|
223
|
+
# ========================================================================= #
|
224
|
+
def check_for_taxonomy_id
|
225
|
+
if @data.include? 'Taxonomy ID' # Ok, we have a Taxonomy ID.
|
226
|
+
@data =~ /Taxonomy ID: (\d+)/ #n
|
227
|
+
@taxonomy_id = $1.dup if $1
|
228
|
+
else
|
229
|
+
# First check whether the file has an entry with only numbers.
|
230
|
+
# We could use this entry, but this may give us false positives,
|
231
|
+
# such as in the file /data/curated/sequences/INFO/Micromonas_pusilla.INFO
|
232
|
+
# scan = @data.scan(/^\d+$/)
|
233
|
+
# unless scan.empty?
|
234
|
+
# @taxonomy_id = scan[0]
|
235
|
+
# @taxonomy_id
|
236
|
+
# else
|
237
|
+
e 'The file '+sfile(filename)+' has no Taxonomy ID.' if @be_verbose
|
238
|
+
# end
|
239
|
+
end if @data
|
240
|
+
end
|
241
|
+
|
242
|
+
# ========================================================================= #
|
243
|
+
# === Info.status
|
244
|
+
#
|
245
|
+
# This method will display some status information.
|
246
|
+
# ========================================================================= #
|
247
|
+
def self.status(
|
248
|
+
from_this_base_dir = INFO_DIR
|
249
|
+
)
|
250
|
+
total_entries = Dir[from_this_base_dir+'*'].reject {|entry|
|
251
|
+
File.directory?(entry) # Reject directories.
|
252
|
+
}.size
|
253
|
+
n_entries = Dir[from_this_base_dir+'*.INFO'].size
|
254
|
+
e 'The directory at '+sdir(from_this_base_dir)+' has '+simp(n_entries)+
|
255
|
+
' entries for .INFO available.' if n_entries > 0
|
256
|
+
if (total_entries - n_entries) > 0
|
257
|
+
e 'That means that there are some entries that are not .INFO '+
|
258
|
+
'files in that directory.'
|
259
|
+
e '(The total number of files in that directory '+
|
260
|
+
'is '+sfancy(total_entries)+')'
|
261
|
+
end
|
262
|
+
end
|
263
|
+
|
264
|
+
# ========================================================================= #
|
265
|
+
# === try_to_find_likely_fasta_file
|
266
|
+
#
|
267
|
+
# We attempt to find a likely fasta file. The current directory has
|
268
|
+
# priority over the AA_DIR.
|
269
|
+
# ========================================================================= #
|
270
|
+
def try_to_find_likely_fasta_file(i = @location)
|
271
|
+
_ = without_extname(File.basename(i))+'*.fa' # This will be a Filename glob, such as: "Nematostella_vectensis_pep*.fa"
|
272
|
+
if Dir[return_pwd+_].size > 0
|
273
|
+
entries = Dir[return_pwd+_]
|
274
|
+
else
|
275
|
+
where = AA_DIR+_
|
276
|
+
entries = Dir[where]
|
277
|
+
end
|
278
|
+
@corresponding_datafile = entries.first
|
279
|
+
return entries
|
280
|
+
end; alias find_fasta try_to_find_likely_fasta_file # === find_fasta
|
281
|
+
|
282
|
+
# ========================================================================= #
|
283
|
+
# === fasta?
|
284
|
+
# ========================================================================= #
|
285
|
+
def fasta?
|
286
|
+
if @corresponding_datafile.nil?
|
287
|
+
try_to_find_likely_fasta_file
|
288
|
+
end
|
289
|
+
@corresponding_datafile # This should be fine now as the above method tried to determine this.
|
290
|
+
end
|
291
|
+
|
292
|
+
# ========================================================================= #
|
293
|
+
# === taxid
|
294
|
+
#
|
295
|
+
# The alias hax_taxonomy_id? will feedback whether we have a taxonomy
|
296
|
+
# id or not.
|
297
|
+
# ========================================================================= #
|
298
|
+
def taxid
|
299
|
+
@taxonomy_id
|
300
|
+
end; alias tax_id taxid # === tax_id
|
301
|
+
alias taxid? taxid # === taxid?
|
302
|
+
alias has_taxonomy_id? taxid # === has_taxonomy_id?
|
303
|
+
|
304
|
+
# ========================================================================= #
|
305
|
+
# === try_to_report_the_taxonomy_id
|
306
|
+
#
|
307
|
+
# Report about the ID but only if it is known.
|
308
|
+
# ========================================================================= #
|
309
|
+
def try_to_report_the_taxonomy_id
|
310
|
+
if @taxonomy_id
|
311
|
+
opnn; e 'The taxonomy_id that we could find is: '+
|
312
|
+
sfancy(@taxonomy_id)
|
313
|
+
end
|
314
|
+
end; alias report_id try_to_report_the_taxonomy_id # === report_Id
|
315
|
+
|
316
|
+
# ========================================================================= #
|
317
|
+
# === data?
|
318
|
+
# ========================================================================= #
|
319
|
+
def data?
|
320
|
+
@data
|
321
|
+
end
|
322
|
+
|
323
|
+
# ========================================================================= #
|
324
|
+
# === run
|
325
|
+
#
|
326
|
+
# Bundle together the various methods that check the file.
|
327
|
+
# ========================================================================= #
|
328
|
+
def run
|
329
|
+
check_for_taxonomy_id # Determine @taxonomy_id here.
|
330
|
+
check_for_genbank_common_name
|
331
|
+
end
|
332
|
+
|
333
|
+
end; end; end
|
334
|
+
|
335
|
+
if __FILE__ == $PROGRAM_NAME
|
336
|
+
Bioroebe::Taxonomy::Info.parse(ARGV.first)
|
337
|
+
end # infoparseex
|
@@ -0,0 +1,150 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::Taxonomy:IsDNA
|
6
|
+
#
|
7
|
+
# This class will try to find out whether we have a DNA file or a
|
8
|
+
# protein file.
|
9
|
+
#
|
10
|
+
# The input to it should be a string such as 'ATTATTCCGTTT',
|
11
|
+
# which, obviously, would correspond to a DNA dataset.
|
12
|
+
# =========================================================================== #
|
13
|
+
# require 'taxonomy/info/is_dna.rb'
|
14
|
+
# =========================================================================== #
|
15
|
+
require 'bioroebe/taxonomy/shared.rb' # Also pulls in module Colours.
|
16
|
+
|
17
|
+
module Bioroebe
|
18
|
+
|
19
|
+
module Taxonomy # Taxonomy::IsDNA
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class IsDNA # === Bioroebe::Taxonomy::IsDNA['ATTAAA']
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require 'bioroebe/taxonomy/parse_fasta.rb'
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include Taxonomy::Shared
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# - Prozente
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# - min-Zeichen
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attr_reader :n_entries # How many characters we will process in total.
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attr_reader :total_characters
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# ========================================================================= #
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# === initialize
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# ========================================================================= #
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def initialize(
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i = 'MGMGMGMMM',
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run_already = true
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)
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reset
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set_input(i)
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run if run_already
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end
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# ========================================================================= #
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# === reset (reset tag)
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# ========================================================================= #
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def reset
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# ======================================================================= #
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# === @be_verbose
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# ======================================================================= #
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@be_verbose = false
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@n_entries = 0
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end
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# ========================================================================= #
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# === set_input
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# ========================================================================= #
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def set_input(i)
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if File.exist? i
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if Object.const_defined? Taxonomy::ParseFasta
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i = Taxonomy::ParseFasta.new(i)
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end
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end if i.is_a? String
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i = [i].flatten
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@input = i
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determine_how_many_characters_we_have
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end
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# ========================================================================= #
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# === determine_how_many_characters_we_have
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# ========================================================================= #
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def determine_how_many_characters_we_have
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@total_characters = @input.join('').size
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end
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# ========================================================================= #
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# === IsDNA['ABC']
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#
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# Class method for a more convenient output.
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# ========================================================================= #
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def self.[](i)
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return IsDNA.new(i).result
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end
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# ========================================================================= #
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# === run
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# ========================================================================= #
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def run
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result = true
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# @input is an array.
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@input.each {|entry|
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splitted = entry.chars
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splitted.each {|inner_entry|
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@n_entries += 1
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if ARRAY_VALID_DNA_SEQUENCES.include? inner_entry
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else # else it can not be DNA.
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if @be_verbose
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e 'Nope, '+sfancy(inner_entry)+' is not DNA.'
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pp splitted
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end
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result = false
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break
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end
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}
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}
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@result = result
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return result
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end
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# ========================================================================= #
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# === is_dna?
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#
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# Query method to determine whether this is DNA or whether it is not.
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# @result is a boolean value.
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# ========================================================================= #
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def is_dna?
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@result
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end
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# ========================================================================= #
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# === report
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#
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# Do a verbose report here.
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# ========================================================================= #
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def report
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is_or_is_not_dna = ''
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if is_dna?
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else
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is_or_is_not_dna << steelblue('not ')
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end
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erev 'The dataset is '+is_or_is_not_dna+rev+'DNA.'
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end
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# ========================================================================= #
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# === result?
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# ========================================================================= #
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def result?
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@result
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end; alias result result? # === result
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end; end; end
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if __FILE__ == $PROGRAM_NAME
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include Bioroebe::Taxonomy
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puts IsDNA.new('ATTTAAA').result
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puts IsDNA.new().result
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puts IsDNA.new('TGGGGTACTACTTTGATGAGTACTGTCAGGTGAACGCCACGACACGAAGCATTTCTTCTGTTGCATCCTTCATTGACTTTGATGTATTTGGCTTTGTCAATGAGATTTGCAGTGACTCATTTGAGACATACGAAGCAGTATACAACGCTTCTTACAGTTGCACCACTAACGGCGGTGCTTATCTTGAATCGGATGATAGTGGGTACGATAATTCTGGAGACCAAGGCAAAGATGGAAACAACGAAGAAAGGCACGAGCGCGAAGATAACAGAGAAGAGGAAGATAGGAACTCAAGAGACAGCCAGGAGTTTGAGATGTCAGGAGAGGACGTATGTTTTGCAGTTTACACAGCTGAACATTTTCAATCTATAAGAAACAAGGAGATCGCAGTGCACTACCTCAAGACACTGGTGC').result
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puts IsDNA['ABC']
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end # rb is_dna.rb
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