bioroebe 0.12.24 → 0.13.32
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- checksums.yaml +4 -4
- data/LICENSE.md +7 -8
- data/README.md +566 -354
- data/bin/all_positions_of_this_nucleotide +1 -1
- data/bin/aminoacid_frequencies +1 -1
- data/bin/automatically_rename_this_fasta_file +1 -1
- data/bin/base_composition +1 -1
- data/bin/batch_create_windows_executables +1 -1
- data/bin/bioroebe +12 -1
- data/bin/bioroebe_cat +7 -0
- data/bin/calculate_exponential_growth +7 -0
- data/bin/calculate_n50_value +1 -1
- data/bin/calculate_the_frequencies_of_this_species +7 -0
- data/bin/chunked_display +1 -1
- data/bin/codon_frequency +1 -1
- data/bin/codon_to_aminoacid +1 -1
- data/bin/colourize_this_fasta_sequence +1 -1
- data/bin/complementary_dna_strand +1 -1
- data/bin/complementary_rna_strand +1 -1
- data/bin/consensus_sequence +1 -1
- data/bin/dna_to_rna +1 -1
- data/bin/downcase_chunked_display +1 -1
- data/bin/download_this_pdb +1 -1
- data/bin/fasta_index +1 -1
- data/bin/fetch_data_from_uniprot +1 -1
- data/bin/filter_away_invalid_nucleotides +1 -1
- data/bin/find_substring +1 -1
- data/bin/input_as_dna +1 -1
- data/bin/is_palindrome +1 -1
- data/bin/leading_five_prime +1 -1
- data/bin/longest_ORF +1 -1
- data/bin/longest_substring +1 -1
- data/bin/open_reading_frames +1 -1
- data/bin/partner_nucleotide +1 -1
- data/bin/plain_palindrome +1 -1
- data/bin/random_dna_sequence +1 -1
- data/bin/random_sequence +1 -1
- data/bin/raw_hamming_distance +1 -1
- data/bin/return_longest_substring_via_LCS_algorithm +1 -1
- data/bin/reverse_sequence +1 -1
- data/bin/short_aminoacid_letter_from_long_aminoacid_name +1 -1
- data/bin/show_atomic_composition +1 -1
- data/bin/show_fasta_header +1 -1
- data/bin/show_nucleotide_sequence +1 -1
- data/bin/show_this_dna_sequence +1 -1
- data/bin/show_time_now +7 -0
- data/bin/sort_aminoacid_based_on_its_hydrophobicity +1 -1
- data/bin/strict_filter_away_invalid_aminoacids +1 -1
- data/{lib/bioroebe/base/reset.rb → bin/three_delimiter} +9 -6
- data/bin/three_to_one +1 -1
- data/bin/to_rna +1 -1
- data/bin/trailing_three_prime +1 -1
- data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +1 -1
- data/bioroebe.gemspec +6 -7
- data/doc/README.gen +534 -322
- data/doc/blosum/blosum.md +4 -0
- data/doc/compatibility/BIO_PHP.md +20 -18
- data/doc/compatibility/README.md +2 -3
- data/doc/compatibility/emboss.md +5 -3
- data/doc/{extensive_usage_example.md → extensive_usage_example/extensive_usage_example.md} +4 -2
- data/doc/{instructions_for_the_taxonomy_subproject.md → instructions_for_the_taxonomy_subproject/instructions_for_the_taxonomy_subproject.md} +36 -33
- data/doc/{legacy_paths.md → legacy_paths/legacy_paths.md} +3 -3
- data/doc/statistics/statistics.md +12 -10
- data/doc/todo/bioroebe_GUI_todo.md +6 -1
- data/doc/todo/bioroebe_java_todo.md +3 -2
- data/doc/todo/bioroebe_todo.md +352 -310
- data/doc/{using_biomart.md → using_biomart/using_biomart.md} +7 -3
- data/lib/bioroebe/abstract/features.rb +0 -0
- data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -1
- data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +3 -1
- data/lib/bioroebe/aminoacids/codon_percentage.rb +18 -10
- data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +5 -2
- data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +90 -64
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -3
- data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +2 -2
- data/lib/bioroebe/annotations/create_annotation_format.rb +2 -2
- data/lib/bioroebe/base/base.rb +101 -6
- data/lib/bioroebe/base/base_module/base_module.rb +9 -1
- data/lib/bioroebe/base/colours.rb +3 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +80 -44
- data/lib/bioroebe/base/commandline_application/README.md +1 -1
- data/lib/bioroebe/base/commandline_application/commandline_application.rb +663 -22
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +2 -1
- data/lib/bioroebe/base/infer_the_namespace_module/infer_the_namespace_module.rb +37 -0
- data/lib/bioroebe/base/internal_hash_module/internal_hash_module.rb +1 -6
- data/lib/bioroebe/base/prototype/prototype.rb +155 -14
- data/lib/bioroebe/biomart/attribute.rb +1 -1
- data/lib/bioroebe/biomart/biomart.rb +8 -9
- data/lib/bioroebe/biomart/server.rb +1 -1
- data/lib/bioroebe/blosum/blosum.rb +2 -2
- data/lib/bioroebe/calculate/calculate_blosum_score.rb +5 -3
- data/lib/bioroebe/calculate/calculate_gc_content.rb +1 -1
- data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +5 -3
- data/lib/bioroebe/calculate/calculate_melting_temperature.rb +2 -10
- data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +6 -15
- data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +4 -2
- data/lib/bioroebe/cell/cell.rb +3 -2
- data/lib/bioroebe/cell/specialized_cells/B_cell.rb +60 -0
- data/lib/bioroebe/cell/specialized_cells/Macrophage.rb +60 -0
- data/lib/bioroebe/cell/specialized_cells/README.md +5 -0
- data/lib/bioroebe/cell/specialized_cells/T_cell.rb +60 -0
- data/lib/bioroebe/cleave_and_digest/cleave.rb +3 -1
- data/lib/bioroebe/cleave_and_digest/digestion.rb +1 -1
- data/lib/bioroebe/codon_tables/frequencies/10090_Mus_musculus.yml +93 -0
- data/lib/bioroebe/codon_tables/frequencies/107243_Thlaspi_caerulescens.yml +72 -0
- data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -2
- data/lib/bioroebe/codons/codon_table.rb +10 -2
- data/lib/bioroebe/codons/codons.rb +3 -3
- data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +18 -15
- data/lib/bioroebe/codons/determine_optimal_codons.rb +1 -1
- data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +4 -2
- data/lib/bioroebe/codons/show_codon_tables.rb +1 -1
- data/lib/bioroebe/codons/show_codon_usage.rb +1 -2
- data/lib/bioroebe/codons/show_this_codon_table.rb +2 -2
- data/lib/bioroebe/codons/start_codons.rb +7 -3
- data/lib/bioroebe/colours/colour_schemes/README.md +1 -1
- data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +3 -3
- data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +3 -3
- data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +4 -3
- data/lib/bioroebe/colours/colour_schemes/helix.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/score.rb +13 -2
- data/lib/bioroebe/colours/colour_schemes/strand.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/turn.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/zappo.rb +1 -1
- data/lib/bioroebe/{toplevel_methods/colourize_related_methods.rb → colours/colourize_related_code.rb} +1 -3
- data/lib/bioroebe/colours/colourize_sequence.rb +3 -1
- data/lib/bioroebe/colours/colours.rb +172 -15
- data/lib/bioroebe/configuration/configuration.rb +1 -1
- data/lib/bioroebe/constants/GUIs.rb +2 -2
- data/lib/bioroebe/constants/constants.rb +1349 -0
- data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +8 -13
- data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +62 -16
- data/lib/bioroebe/count/count_amount_of_aminoacids.rb +11 -10
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +1 -1
- data/lib/bioroebe/count/count_at.rb +2 -1
- data/lib/bioroebe/databases/download_taxonomy_database.rb +1 -1
- data/lib/bioroebe/dotplots/advanced_dotplot.rb +2 -2
- data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +2 -2
- data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +2 -2
- data/lib/bioroebe/electron_microscopy/flipy.rb +2 -2
- data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +3 -11
- data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +15 -15
- data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +6 -6
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +2 -2
- data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +1 -1
- data/lib/bioroebe/enzymes/restriction_enzyme.rb +1 -1
- data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +4 -3
- data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +1 -1
- data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +4 -3
- data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +3 -3
- data/lib/bioroebe/ext/main.cpp +0 -1
- data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +3 -3
- data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +11 -17
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +37 -11
- data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +2 -2
- data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +5 -13
- data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +3 -6
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +3 -3
- data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +20 -11
- data/lib/bioroebe/genome/genome.rb +1 -1
- data/lib/bioroebe/genomes/genome_pattern.rb +17 -16
- data/lib/bioroebe/genomes/genome_retriever.rb +4 -2
- data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +10 -13
- data/lib/bioroebe/gui/universal_widgets/alignment/alignment.rb +557 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/aminoacid_composition.rb +498 -198
- data/lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb +665 -0
- data/lib/bioroebe/gui/universal_widgets/blosum_matrix_viewer/blosum_matrix_viewer.rb +329 -0
- data/lib/bioroebe/gui/universal_widgets/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +423 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/controller/controller.rb +170 -118
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +277 -215
- data/lib/bioroebe/gui/{shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb → universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb} +297 -107
- data/lib/bioroebe/gui/universal_widgets/fasta_table_widget/fasta_table_widget.rb +643 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/format_converter/format_converter.rb +236 -164
- data/lib/bioroebe/gui/universal_widgets/gene/gene.rb +278 -0
- data/lib/bioroebe/gui/universal_widgets/hamming_distance/hamming_distance.rb +646 -0
- data/lib/bioroebe/gui/{shared_code/levensthein_distance/levensthein_distance_module.rb → universal_widgets/levensthein_distance/levensthein_distance.rb} +313 -88
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/nucleotide_analyser/nucleotide_analyser.rb +281 -189
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/parse_pdb_file/parse_pdb_file.rb +265 -149
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/primer_design_widget/primer_design_widget.rb +337 -263
- data/lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb +408 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/random_sequence/random_sequence.rb +245 -187
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.rb +207 -137
- data/lib/bioroebe/gui/universal_widgets/shell/shell.rb +288 -0
- data/lib/bioroebe/gui/{gtk3/show_codon_table/misc.rb → universal_widgets/show_codon_table/show_codon_table.rb} +290 -110
- data/lib/bioroebe/gui/{shared_code/show_codon_usage/show_codon_usage_module.rb → universal_widgets/show_codon_usage/show_codon_usage.rb} +228 -47
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/sizeseq/sizeseq.rb +151 -69
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/three_to_one/three_to_one.rb +190 -127
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.rb +211 -152
- data/lib/bioroebe/images/images.html +953 -1170
- data/lib/bioroebe/images/misc/README.md +6 -0
- data/lib/bioroebe/images/misc/activation.avif +0 -0
- data/lib/bioroebe/images/misc/inhibition.avif +0 -0
- data/lib/bioroebe/images/misc/small_virus_logo.avif +0 -0
- data/lib/bioroebe/{constants/base_directory.rb → log_directory/log_directory.rb} +79 -59
- data/lib/bioroebe/matplotlib/matplotlib_generator.rb +1 -1
- data/lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb +1 -1
- data/lib/bioroebe/misc/ruler.rb +5 -5
- data/lib/bioroebe/misc/useful_formulas.rb +3 -3
- data/lib/bioroebe/ncbi/efetch.rb +3 -4
- data/lib/bioroebe/ngs/phred_quality_score_table.rb +3 -3
- data/lib/bioroebe/nucleotides/complementary_dna_strand.rb +3 -6
- data/lib/bioroebe/nucleotides/molecular_weight_of_nucleotides.rb +3 -3
- data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +6 -10
- data/lib/bioroebe/nucleotides/{show_nucleotide_sequence.rb → show_nucleotide_sequence/show_nucleotide_sequence.rb} +377 -255
- data/lib/bioroebe/palindromes/palindrome_2D_structure.rb +1 -1
- data/lib/bioroebe/palindromes/palindrome_finder.rb +1 -1
- data/lib/bioroebe/palindromes/palindrome_generator.rb +2 -10
- data/lib/bioroebe/parsers/biolang_parser.rb +1 -1
- data/lib/bioroebe/parsers/blosum_parser.rb +14 -19
- data/lib/bioroebe/parsers/genbank_parser.rb +2 -6
- data/lib/bioroebe/parsers/gff.rb +9 -9
- data/lib/bioroebe/parsers/parse_embl.rb +2 -6
- data/lib/bioroebe/parsers/stride_parser.rb +4 -12
- data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +2 -2
- data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +6 -3
- data/lib/bioroebe/patterns/profile_pattern.rb +2 -2
- data/lib/bioroebe/patterns/rgg_scanner.rb +4 -2
- data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/alpha_helix.rb +2 -2
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/download_this_pdb.rb +2 -3
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/fetch_fasta_sequence_from_pdb.rb +4 -4
- data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/helical_wheel.rb +2 -2
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_mmCIF_file.rb +1 -1
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_pdb_file.rb +3 -3
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/report_secondary_structures_from_this_pdb_file.rb +3 -3
- data/lib/bioroebe/project/project.rb +3 -1
- data/lib/bioroebe/raw_sequence/README.md +8 -8
- data/lib/bioroebe/raw_sequence/raw_sequence.rb +11 -2
- data/lib/bioroebe/regexes/regexes.rb +1 -2
- data/lib/bioroebe/requires/commandline_application.rb +3 -1
- data/lib/bioroebe/requires/require_all_pdb_files.rb +1 -1
- data/lib/bioroebe/requires/require_all_taxonomy_files.rb +1 -1
- data/lib/bioroebe/requires/require_all_utility_scripts_files.rb +10 -0
- data/lib/bioroebe/requires/require_colours.rb +1 -1
- data/lib/bioroebe/requires/require_the_bioroebe_project.rb +5 -7
- data/lib/bioroebe/requires/require_the_bioroebe_sinatra_components.rb +1 -1
- data/lib/bioroebe/requires/require_the_constants.rb +2 -14
- data/lib/bioroebe/requires/require_yaml.rb +7 -5
- data/lib/bioroebe/sequence/alignment.rb +1 -1
- data/lib/bioroebe/sequence/dna.rb +4 -2
- data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +22 -8
- data/lib/bioroebe/sequence/protein.rb +2 -2
- data/lib/bioroebe/sequence/reverse_complement.rb +3 -3
- data/lib/bioroebe/sequence/rna.rb +9 -8
- data/lib/bioroebe/sequence/sequence.rb +3 -3
- data/lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml +0 -0
- data/lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml +0 -0
- data/lib/bioroebe/shell/configuration/upcase_nucleotides.yml +0 -0
- data/lib/bioroebe/shell/configuration/use_silent_startup.yml +1 -1
- data/lib/bioroebe/shell/help/class.rb +68 -19
- data/lib/bioroebe/shell/menu.rb +5244 -5322
- data/lib/bioroebe/shell/{readline/readline.rb → readline.rb} +1 -3
- data/lib/bioroebe/shell/shell.rb +11240 -453
- data/lib/bioroebe/siRNA/siRNA.rb +3 -3
- data/lib/bioroebe/{gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb → sinatra/sinatra_interface.rb} +28 -19
- data/lib/bioroebe/{www/sinatra/sinatra.rb → sinatra/sinatra_wrapper.rb} +731 -754
- data/lib/bioroebe/string_matching/find_longest_substring.rb +2 -10
- data/lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb +4 -14
- data/lib/bioroebe/string_matching/hamming_distance.rb +17 -16
- data/lib/bioroebe/string_matching/levensthein.rb +5 -17
- data/lib/bioroebe/string_matching/simple_string_comparer.rb +48 -4
- data/lib/bioroebe/string_matching/smith_waterman.rb +11 -6
- data/lib/bioroebe/svg/glyph.rb +4 -1
- data/lib/bioroebe/svg/mini_feature.rb +1 -1
- data/lib/bioroebe/svg/page.rb +18 -7
- data/lib/bioroebe/svg/svgee.rb +22 -13
- data/lib/bioroebe/svg/track.rb +20 -4
- data/lib/bioroebe/taxonomy/chart.rb +2 -2
- data/lib/bioroebe/taxonomy/class_methods.rb +5 -6
- data/lib/bioroebe/taxonomy/constants.rb +1 -1
- data/lib/bioroebe/taxonomy/info/info.rb +1 -1
- data/lib/bioroebe/taxonomy/info/is_dna.rb +1 -1
- data/lib/bioroebe/taxonomy/interactive.rb +5 -4
- data/lib/bioroebe/taxonomy/menu.rb +1 -1
- data/lib/bioroebe/taxonomy/node.rb +1 -1
- data/lib/bioroebe/taxonomy/parse_fasta.rb +4 -2
- data/lib/bioroebe/taxonomy/shared.rb +5 -4
- data/lib/bioroebe/taxonomy/taxonomy.rb +2 -4
- data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +3 -45
- data/lib/bioroebe/toplevel_methods/{is_on_roebe.rb → roebe.rb} +1 -11
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +6 -12
- data/lib/bioroebe/toplevel_methods/toplevel_methods.rb +5607 -0
- data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +4 -3
- data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +2 -2
- data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +16 -9
- data/lib/bioroebe/utility_scripts/compacter/compacter.rb +4 -2
- data/lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb +119 -0
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +11 -9
- data/lib/bioroebe/utility_scripts/{consensus_sequence.rb → consensus_sequence/consensus_sequence.rb} +13 -4
- data/lib/bioroebe/utility_scripts/{create_batch_entrez_file.rb → create_batch_entrez_file/create_batch_entrez_file.rb} +5 -5
- data/lib/bioroebe/utility_scripts/{determine_antigenic_areas.rb → determine_antigenic_areas/determine_antigenic_areas.rb} +5 -5
- data/lib/bioroebe/utility_scripts/{determine_missing_nucleotides_percentage.rb → determine_missing_nucleotides_percentage/determine_missing_nucleotides_percentage.rb} +16 -15
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +7 -7
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +1 -1
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +2 -0
- data/lib/bioroebe/utility_scripts/{dot_alignment.rb → dot_alignment/dot_alignment.rb} +3 -3
- data/lib/bioroebe/utility_scripts/{download_files_from_rebase.rb → download_files_from_rebase/download_files_from_rebase.rb} +5 -5
- data/lib/bioroebe/utility_scripts/fetch_data_from_uniprot/fetch_data_from_uniprot.rb +269 -0
- data/lib/bioroebe/utility_scripts/find_gene.rb +4 -2
- data/lib/bioroebe/utility_scripts/{mirror_repeat.rb → mirror_repeat/mirror_repeat.rb} +5 -5
- data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +3 -3
- data/lib/bioroebe/utility_scripts/{parse_taxonomy.rb → parse_taxonomy/parse_taxonomy.rb} +15 -6
- data/lib/bioroebe/utility_scripts/{pathways.rb → pathways/pathways.rb} +4 -3
- data/lib/bioroebe/utility_scripts/{permutations.rb → permutations/permutations.rb} +3 -3
- data/lib/bioroebe/utility_scripts/punnet/punnet.rb +4 -2
- data/lib/bioroebe/utility_scripts/{show_this_dna_sequence.rb → show_this_dna_sequence/show_this_dna_sequence.rb} +1 -1
- data/lib/bioroebe/utility_scripts/showorf/showorf.rb +406 -10
- data/lib/bioroebe/version/version.rb +2 -2
- data/lib/bioroebe/viennarna/rnafold_wrapper.rb +5 -13
- data/lib/bioroebe/virus/individual_viruses/README.md +15 -0
- data/lib/bioroebe/virus/individual_viruses/tobacco_mosaic_virus.rb +40 -0
- data/lib/bioroebe/virus/virus.rb +76 -0
- data/lib/bioroebe/www/bioroebe.cgi +4 -3
- data/lib/bioroebe/www/embeddable_interface.rb +85 -49
- data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +6 -6
- data/lib/bioroebe/yaml/antisense/antisense.yml +2 -0
- data/lib/bioroebe/yaml/blosum/blosum50.yml +6 -0
- data/lib/bioroebe/yaml/blosum/blosum90.yml +2 -1
- data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +2 -2
- data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -1
- data/lib/bioroebe/yaml/consensus_sequences/consensus_sequences.yml +1 -0
- data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +7 -6
- data/lib/bioroebe/yaml/humans/human_chromosomes.yml +3 -3
- data/lib/bioroebe/yaml/mRNA/mRNA.yml +1 -5
- data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +1 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +2 -1
- data/lib/bioroebe/yaml/promoters/35S.yml +3 -1
- data/lib/bioroebe/yaml/proteases/proteases.yml +3 -1
- data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -1
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +7 -7
- data/spec/testing_toplevel_method_editor.rb +1 -1
- data/spec/testing_toplevel_method_verbose.rb +1 -1
- data/test/testing_dna_to_rna_conversion.rb +1 -1
- metadata +127 -235
- data/doc/blosum.md +0 -5
- data/lib/bioroebe/base/commandline_application/aminoacids.rb +0 -33
- data/lib/bioroebe/base/commandline_application/directory.rb +0 -33
- data/lib/bioroebe/base/commandline_application/extract.rb +0 -22
- data/lib/bioroebe/base/commandline_application/misc.rb +0 -502
- data/lib/bioroebe/base/commandline_application/opn.rb +0 -47
- data/lib/bioroebe/base/commandline_application/reset.rb +0 -42
- data/lib/bioroebe/base/commandline_application/warnings.rb +0 -36
- data/lib/bioroebe/base/commandline_application/write_what_into.rb +0 -29
- data/lib/bioroebe/base/initialize.rb +0 -18
- data/lib/bioroebe/base/misc.rb +0 -129
- data/lib/bioroebe/base/namespace.rb +0 -16
- data/lib/bioroebe/base/prototype/e_and_ee.rb +0 -24
- data/lib/bioroebe/base/prototype/misc.rb +0 -114
- data/lib/bioroebe/base/prototype/mkdir.rb +0 -20
- data/lib/bioroebe/base/prototype/reset.rb +0 -36
- data/lib/bioroebe/colours/misc_colours.rb +0 -80
- data/lib/bioroebe/colours/rev.rb +0 -44
- data/lib/bioroebe/colours/sdir.rb +0 -21
- data/lib/bioroebe/colours/sfancy.rb +0 -21
- data/lib/bioroebe/colours/sfile.rb +0 -21
- data/lib/bioroebe/colours/simp.rb +0 -21
- data/lib/bioroebe/colours/swarn.rb +0 -29
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +0 -147
- data/lib/bioroebe/constants/carriage_return.rb +0 -14
- data/lib/bioroebe/constants/codon_tables.rb +0 -77
- data/lib/bioroebe/constants/database_constants.rb +0 -107
- data/lib/bioroebe/constants/files_and_directories.rb +0 -606
- data/lib/bioroebe/constants/misc.rb +0 -209
- data/lib/bioroebe/constants/newline.rb +0 -14
- data/lib/bioroebe/constants/nucleotides.rb +0 -121
- data/lib/bioroebe/constants/regex.rb +0 -28
- data/lib/bioroebe/constants/roebe.rb +0 -38
- data/lib/bioroebe/constants/row_terminator.rb +0 -16
- data/lib/bioroebe/constants/tabulator.rb +0 -14
- data/lib/bioroebe/constants/unicode.rb +0 -12
- data/lib/bioroebe/constants/urls.rb +0 -50
- data/lib/bioroebe/gui/gtk +0 -1
- data/lib/bioroebe/gui/gtk3/README.md +0 -2
- data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +0 -306
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +0 -29
- data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -195
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -105
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -188
- data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +0 -322
- data/lib/bioroebe/gui/gtk3/gene/gene.rb +0 -181
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +0 -383
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +0 -174
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +0 -181
- data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +0 -101
- data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +0 -145
- data/lib/bioroebe/gui/gtk3/three_to_one/title.rb +0 -23
- data/lib/bioroebe/gui/jruby/alignment/alignment.rb +0 -165
- data/lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb +0 -166
- data/lib/bioroebe/gui/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -82
- data/lib/bioroebe/gui/libui/README.md +0 -4
- data/lib/bioroebe/gui/libui/alignment/alignment.rb +0 -116
- data/lib/bioroebe/gui/libui/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -112
- data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -60
- data/lib/bioroebe/gui/libui/controller/controller.rb +0 -116
- data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +0 -161
- data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -76
- data/lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb +0 -135
- data/lib/bioroebe/gui/libui/levensthein_distance/levensthein_distance.rb +0 -118
- data/lib/bioroebe/gui/libui/protein_to_DNA/protein_to_DNA.rb +0 -115
- data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +0 -190
- data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +0 -134
- data/lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb +0 -89
- data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +0 -113
- data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +0 -102
- data/lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb +0 -94
- data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +0 -216
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +0 -192
- data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +0 -72
- data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +0 -206
- data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -140
- data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +0 -262
- data/lib/bioroebe/gui/tk/levensthein_distance/levensthein_distance.rb +0 -243
- data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +0 -199
- data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +0 -519
- data/lib/bioroebe/shell/colours/colours.rb +0 -235
- data/lib/bioroebe/shell/help/help.rb +0 -25
- data/lib/bioroebe/shell/misc.rb +0 -10227
- data/lib/bioroebe/toplevel_methods/ad_hoc_task.rb +0 -56
- data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +0 -722
- data/lib/bioroebe/toplevel_methods/atomic_composition.rb +0 -198
- data/lib/bioroebe/toplevel_methods/base_composition.rb +0 -121
- data/lib/bioroebe/toplevel_methods/blast.rb +0 -153
- data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +0 -57
- data/lib/bioroebe/toplevel_methods/cat.rb +0 -71
- data/lib/bioroebe/toplevel_methods/chunked_display.rb +0 -92
- data/lib/bioroebe/toplevel_methods/cliner.rb +0 -81
- data/lib/bioroebe/toplevel_methods/complement.rb +0 -58
- data/lib/bioroebe/toplevel_methods/convert_global_env.rb +0 -39
- data/lib/bioroebe/toplevel_methods/databases.rb +0 -73
- data/lib/bioroebe/toplevel_methods/delimiter.rb +0 -19
- data/lib/bioroebe/toplevel_methods/digest.rb +0 -81
- data/lib/bioroebe/toplevel_methods/download_and_fetch_data.rb +0 -146
- data/lib/bioroebe/toplevel_methods/e.rb +0 -20
- data/lib/bioroebe/toplevel_methods/editor.rb +0 -21
- data/lib/bioroebe/toplevel_methods/esystem.rb +0 -22
- data/lib/bioroebe/toplevel_methods/exponential_growth.rb +0 -74
- data/lib/bioroebe/toplevel_methods/extract.rb +0 -56
- data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +0 -269
- data/lib/bioroebe/toplevel_methods/frequencies.rb +0 -99
- data/lib/bioroebe/toplevel_methods/hamming_distance.rb +0 -60
- data/lib/bioroebe/toplevel_methods/infer.rb +0 -66
- data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +0 -101
- data/lib/bioroebe/toplevel_methods/levensthein.rb +0 -63
- data/lib/bioroebe/toplevel_methods/log_directory.rb +0 -109
- data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +0 -55
- data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +0 -88
- data/lib/bioroebe/toplevel_methods/matches.rb +0 -259
- data/lib/bioroebe/toplevel_methods/misc.rb +0 -596
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +0 -787
- data/lib/bioroebe/toplevel_methods/number_of_clones.rb +0 -63
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +0 -79
- data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +0 -236
- data/lib/bioroebe/toplevel_methods/opn.rb +0 -34
- data/lib/bioroebe/toplevel_methods/palindromes.rb +0 -155
- data/lib/bioroebe/toplevel_methods/parse.rb +0 -59
- data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +0 -68
- data/lib/bioroebe/toplevel_methods/rds.rb +0 -24
- data/lib/bioroebe/toplevel_methods/remove.rb +0 -86
- data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +0 -35
- data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +0 -68
- data/lib/bioroebe/toplevel_methods/rna_splicing.rb +0 -73
- data/lib/bioroebe/toplevel_methods/rnalfold.rb +0 -69
- data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +0 -116
- data/lib/bioroebe/toplevel_methods/shuffleseq.rb +0 -37
- data/lib/bioroebe/toplevel_methods/statistics.rb +0 -53
- data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +0 -62
- data/lib/bioroebe/toplevel_methods/three_delimiter.rb +0 -34
- data/lib/bioroebe/toplevel_methods/time_and_date.rb +0 -53
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +0 -31
- data/lib/bioroebe/toplevel_methods/truncate.rb +0 -48
- data/lib/bioroebe/toplevel_methods/url.rb +0 -36
- data/lib/bioroebe/toplevel_methods/verbose.rb +0 -59
- data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -31
- data/lib/bioroebe/utility_scripts/showorf/help.rb +0 -33
- data/lib/bioroebe/utility_scripts/showorf/initialize.rb +0 -52
- data/lib/bioroebe/utility_scripts/showorf/menu.rb +0 -68
- data/lib/bioroebe/utility_scripts/showorf/reset.rb +0 -36
- data/lib/bioroebe/utility_scripts/showorf/run.rb +0 -152
- data/lib/bioroebe/utility_scripts/showorf/show.rb +0 -97
- /data/doc/{german_names_for_the_aminoacids.md → german_names_for_the_aminoacids/german_names_for_the_aminoacids.md} +0 -0
- /data/doc/{pdb_ATOM_entry.md → pdb_ATOM_entry/pdb_ATOM_entry.md} +0 -0
- /data/doc/{resources.md → resources/resources.md} +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/customized_dialog.rb +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/anti_sense_strand/anti_sense_strand.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/hamming_distance/hamming_distance.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/levensthein_distance/levensthein_distance.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/protein_to_DNA/protein_to_DNA.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.config +0 -0
- /data/lib/bioroebe/yaml/{base_composition_of_dna.yml → base_composition_of_dna/base_composition_of_dna.yml} +0 -0
- /data/lib/bioroebe/yaml/{nuclear_localization_sequences.yml → nuclear_localization_sequences/nuclear_localization_sequences.yml} +0 -0
- /data/lib/bioroebe/yaml/{talens.yml → talens/talens.yml} +0 -0
@@ -15,11 +15,11 @@
|
|
15
15
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# require 'bioroebe/enzymes/show_restriction_enzymes.rb'
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# Bioroebe::ShowRestrictionEnzymes.new
|
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17
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# =========================================================================== #
|
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-
require 'bioroebe/
|
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+
require 'bioroebe/requires/commandline_application.rb'
|
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module Bioroebe
|
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21
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-
class ShowRestrictionEnzymes <
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class ShowRestrictionEnzymes < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowRestrictionEnzymes
|
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23
|
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24
24
|
require 'bioroebe/enzymes/restriction_enzymes_file.rb'
|
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25
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@@ -97,7 +97,7 @@ class ShowRestrictionEnzymes < Base # === Bioroebe::ShowRestrictionEnzymes
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97
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# ========================================================================= #
|
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98
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# === Bioroebe::ShowRestrictionEnzymes[]
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99
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# ========================================================================= #
|
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-
def self.[](i =
|
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def self.[](i = ARGV)
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101
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new(i)
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end
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103
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data/lib/bioroebe/ext/main.cpp
CHANGED
@@ -15,7 +15,7 @@
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15
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# =========================================================================== #
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# require 'bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb'
|
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# =========================================================================== #
|
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require 'bioroebe/
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require 'bioroebe/requires/commandline_application.rb'
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19
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20
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module Bioroebe
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@@ -58,7 +58,7 @@ class AutocorrectTheNameOfThisFastaFile < CommandlineApplication # === Bioroebe:
|
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58
58
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new_name = new_name.split(' ').first
|
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59
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end
|
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60
|
new_name = new_name.tr('|','_')+'.fasta'
|
61
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-
|
61
|
+
opnerev 'Now renaming from `'+sfile(original_filename)+
|
62
62
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rev+'` to `'+sfile(new_name)+'`.'
|
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63
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rename(original_filename, new_name)
|
64
64
|
else
|
@@ -69,7 +69,7 @@ class AutocorrectTheNameOfThisFastaFile < CommandlineApplication # === Bioroebe:
|
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69
69
|
# ========================================================================= #
|
70
70
|
# === Bioroebe::AutocorrectTheNameOfThisFastaFile[]
|
71
71
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# ========================================================================= #
|
72
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-
def self.[](i =
|
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+
def self.[](i = ARGV)
|
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73
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new(i)
|
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74
|
end
|
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75
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|
@@ -14,7 +14,7 @@
|
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14
14
|
# require 'bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb'
|
15
15
|
# Bioroebe::CompactFastaFile.new(ARGV)
|
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16
|
# =========================================================================== #
|
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-
require 'bioroebe/
|
17
|
+
require 'bioroebe/requires/commandline_application.rb'
|
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module Bioroebe
|
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20
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@@ -14,7 +14,7 @@
|
|
14
14
|
# =========================================================================== #
|
15
15
|
# require 'bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb'
|
16
16
|
# =========================================================================== #
|
17
|
-
require 'bioroebe/
|
17
|
+
require 'bioroebe/requires/commandline_application.rb'
|
18
18
|
|
19
19
|
module Bioroebe
|
20
20
|
|
@@ -15,7 +15,7 @@
|
|
15
15
|
# =========================================================================== #
|
16
16
|
# require 'bioroebe/fasta_and_fastq/download_fasta.rb'
|
17
17
|
# =========================================================================== #
|
18
|
-
require 'bioroebe/
|
18
|
+
require 'bioroebe/requires/commandline_application.rb'
|
19
19
|
|
20
20
|
module Bioroebe
|
21
21
|
|
@@ -23,11 +23,6 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
|
|
23
23
|
|
24
24
|
require 'bioroebe/ncbi/efetch.rb'
|
25
25
|
|
26
|
-
# ========================================================================= #
|
27
|
-
# === NAMESPACE
|
28
|
-
# ========================================================================= #
|
29
|
-
NAMESPACE = inspect
|
30
|
-
|
31
26
|
# ========================================================================= #
|
32
27
|
# === BASE_URL
|
33
28
|
# ========================================================================= #
|
@@ -61,20 +56,19 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
|
|
61
56
|
# ========================================================================= #
|
62
57
|
def reset
|
63
58
|
super()
|
64
|
-
|
65
|
-
# === @namespace
|
66
|
-
# ======================================================================= #
|
67
|
-
@namespace = NAMESPACE
|
59
|
+
infer_the_namespace
|
68
60
|
end
|
69
61
|
|
70
62
|
# ========================================================================= #
|
71
63
|
# === enter_log_directory
|
72
64
|
# ========================================================================= #
|
73
|
-
def enter_log_directory(
|
65
|
+
def enter_log_directory(
|
66
|
+
be_verbose = true
|
67
|
+
)
|
74
68
|
_ = log_dir?
|
75
69
|
if !(return_pwd == _)
|
76
70
|
if be_verbose
|
77
|
-
|
71
|
+
opne "#{rev}Now changing directory to `#{sdir(_)}#{rev}`."
|
78
72
|
end
|
79
73
|
unless File.exist? _
|
80
74
|
mkdir(_)
|
@@ -90,7 +84,7 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
|
|
90
84
|
i = @file_is_stored_here
|
91
85
|
)
|
92
86
|
if i and File.exist?(i)
|
93
|
-
|
87
|
+
opnerev "The file is now stored at `#{sfile(i)}#{rev}`."
|
94
88
|
end
|
95
89
|
end
|
96
90
|
|
@@ -106,7 +100,7 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
|
|
106
100
|
# ========================================================================= #
|
107
101
|
def rename_to_fasta(i)
|
108
102
|
@file = rds(File.dirname(i)+'/'+File.basename(i)+'.fa')
|
109
|
-
|
103
|
+
opnerev "Next renaming `#{sfile(i)}` to `#{sfile(@file)}`."
|
110
104
|
mv(i, @file)
|
111
105
|
end
|
112
106
|
|
@@ -140,7 +134,7 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
|
|
140
134
|
url.include?('&id=WP_')
|
141
135
|
match = url
|
142
136
|
else
|
143
|
-
|
137
|
+
opne "#{rev}We will use the URL `#{simp(url)}#{rev}`"
|
144
138
|
remote_file_content = ''.dup # Our variable.
|
145
139
|
# =================================================================== #
|
146
140
|
# We store the content of the remote page in the variable called
|
@@ -170,7 +164,7 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
|
|
170
164
|
end
|
171
165
|
end
|
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166
|
rescue Errno::ENOENT => error
|
173
|
-
|
167
|
+
opne tomato('We encountered an error, which we will feedback next.')
|
174
168
|
pp error
|
175
169
|
match = url
|
176
170
|
end
|
@@ -215,7 +209,7 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
|
|
215
209
|
if File.exist? this_file # This here is mostly done for testing-purposes.
|
216
210
|
this_file = File.readlines(this_file).reject {|entry| entry.strip.empty? }
|
217
211
|
unless this_file.first.include? '/'
|
218
|
-
|
212
|
+
opnerev 'Now working on '+this_file.size.to_s+' entries.'
|
219
213
|
this_file.map! {|entry|
|
220
214
|
entry = entry.dup if entry.frozen?
|
221
215
|
entry.delete!("\n")
|
@@ -17,7 +17,7 @@
|
|
17
17
|
# =========================================================================== #
|
18
18
|
# require 'bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb'
|
19
19
|
# =========================================================================== #
|
20
|
-
require 'bioroebe/
|
20
|
+
require 'bioroebe/requires/commandline_application.rb'
|
21
21
|
|
22
22
|
module Bioroebe
|
23
23
|
|
@@ -14,7 +14,7 @@
|
|
14
14
|
# =========================================================================== #
|
15
15
|
# require 'bioroebe/fasta/fasta_to_yaml/fasta_to_yaml.rb'
|
16
16
|
# =========================================================================== #
|
17
|
-
require 'bioroebe/
|
17
|
+
require 'bioroebe/requires/commandline_application.rb'
|
18
18
|
|
19
19
|
module Bioroebe
|
20
20
|
|
@@ -26,7 +26,7 @@
|
|
26
26
|
# =========================================================================== #
|
27
27
|
# require 'bioroebe/fastq_and_fastq/fastq_format_explainer.rb'
|
28
28
|
# =========================================================================== #
|
29
|
-
require 'bioroebe/
|
29
|
+
require 'bioroebe/requires/commandline_application.rb'
|
30
30
|
|
31
31
|
module Bioroebe
|
32
32
|
|
@@ -15,7 +15,7 @@
|
|
15
15
|
# require 'bioroebe/fasta_and_fastq/length_modifier/simplify_fasta_header.rb'
|
16
16
|
# Bioroebe::LengthModifier.new(ARGV)
|
17
17
|
# =========================================================================== #
|
18
|
-
require 'bioroebe/
|
18
|
+
require 'bioroebe/requires/commandline_application.rb'
|
19
19
|
|
20
20
|
module Bioroebe
|
21
21
|
|
@@ -20,7 +20,7 @@
|
|
20
20
|
# Bioroebe.parse_fasta
|
21
21
|
# Bioroebe.sizeseq
|
22
22
|
# =========================================================================== #
|
23
|
-
require 'bioroebe/
|
23
|
+
require 'bioroebe/requires/commandline_application.rb'
|
24
24
|
|
25
25
|
module Bioroebe
|
26
26
|
|
@@ -834,7 +834,7 @@ TGGGAACCTGCGGGCAGTAGGTGGAAT'
|
|
834
834
|
i = [i].flatten.compact.first.to_s.dup
|
835
835
|
if File.exist? i.to_s # First try to read in from a file.
|
836
836
|
if be_verbose?
|
837
|
-
|
837
|
+
opnerev "Will read from the file `#{sfile(i)}#{rev}`."
|
838
838
|
end
|
839
839
|
i = File.readlines(i)
|
840
840
|
if @is_a_genbank_file
|
@@ -849,8 +849,8 @@ TGGGAACCTGCGGGCAGTAGGTGGAAT'
|
|
849
849
|
end
|
850
850
|
if i.nil? or i.empty?
|
851
851
|
i = DEFAULT_FASTA
|
852
|
-
|
853
|
-
|
852
|
+
opnerev 'No input was provided. Thus a default FASTA '\
|
853
|
+
'sequence will be used instead.'
|
854
854
|
end
|
855
855
|
i = sanitize_data(i)
|
856
856
|
i = i.split(N) if i.is_a? String
|
@@ -979,17 +979,17 @@ TGGGAACCTGCGGGCAGTAGGTGGAAT'
|
|
979
979
|
result < 'FASTA '
|
980
980
|
end
|
981
981
|
result << 'file was found in this directory ('+sfile(file)+').'
|
982
|
-
|
983
|
-
|
982
|
+
opnerev result
|
983
|
+
opnerev 'We will use it.'
|
984
984
|
end
|
985
985
|
i = file
|
986
986
|
end
|
987
987
|
unless Dir['*.{fa,fasta}'].empty?
|
988
988
|
file = Dir['*.{fa,fasta}'].first
|
989
989
|
if be_verbose?
|
990
|
-
|
991
|
-
|
992
|
-
|
990
|
+
opnerev "We have found a file in this "\
|
991
|
+
"directory (#{sfile(file)}#{rev})."
|
992
|
+
opnerev 'We will use it.'
|
993
993
|
end
|
994
994
|
i = file
|
995
995
|
end
|
@@ -1072,7 +1072,7 @@ TGGGAACCTGCGGGCAGTAGGTGGAAT'
|
|
1072
1072
|
write_what_into(what, into)
|
1073
1073
|
return File.absolute_path(into) # And return the file we saved into.
|
1074
1074
|
else
|
1075
|
-
|
1075
|
+
opnerev 'No @data variable exists.'
|
1076
1076
|
end
|
1077
1077
|
end; alias do_save_the_file save_into_a_fasta_file # === do_save_the_file
|
1078
1078
|
|
@@ -1451,7 +1451,7 @@ end
|
|
1451
1451
|
#
|
1452
1452
|
# Invocation example:
|
1453
1453
|
#
|
1454
|
-
# Bioroebe.genbank_to_fasta('/home/x/
|
1454
|
+
# Bioroebe.genbank_to_fasta('/home/x/programming/ruby/src/bioroebe/lib/bioroebe/data/genbank/sample_file.genbank')
|
1455
1455
|
#
|
1456
1456
|
# =========================================================================== #
|
1457
1457
|
def self.genbank_to_fasta(
|
@@ -1521,6 +1521,32 @@ def self.parse_fasta(
|
|
1521
1521
|
::Bioroebe::ParseFasta.new(i) { use_this_hash }
|
1522
1522
|
end; self.instance_eval { alias fasta parse_fasta } # === Bioroebe.fasta
|
1523
1523
|
|
1524
|
+
# =========================================================================== #
|
1525
|
+
# === Bioroebe.sanitize_this_fasta_file
|
1526
|
+
#
|
1527
|
+
# This method will modify a .fasta file's sequence header, by appending
|
1528
|
+
# the number of aminoacids to this header.
|
1529
|
+
#
|
1530
|
+
# Usage example:
|
1531
|
+
#
|
1532
|
+
# Bioroebe.sanitize_this_fasta_file('/root/Bioroebe/fasta/IFNB1-P01574.fasta')
|
1533
|
+
#
|
1534
|
+
# =========================================================================== #
|
1535
|
+
def self.sanitize_this_fasta_file(i)
|
1536
|
+
if File.exist? i
|
1537
|
+
dataset = File.readlines(i).map(&:strip)
|
1538
|
+
header = dataset.first.dup
|
1539
|
+
aminoacid_sequence = Bioroebe::ParseFasta.new(i) { :be_silent }.return_n_aminoacids
|
1540
|
+
header << ", #{aminoacid_sequence} aminoacids"
|
1541
|
+
dataset[0] = header
|
1542
|
+
# ===================================================================== #
|
1543
|
+
# Now we can save it again.
|
1544
|
+
# ===================================================================== #
|
1545
|
+
e 'Storing the modified data into '+sfile(i)+'.'
|
1546
|
+
write_what_into(dataset.join(N), i)
|
1547
|
+
end
|
1548
|
+
end
|
1549
|
+
|
1524
1550
|
end
|
1525
1551
|
|
1526
1552
|
if __FILE__ == $PROGRAM_NAME
|
@@ -13,7 +13,7 @@
|
|
13
13
|
# =========================================================================== #
|
14
14
|
# require 'biroebe/fastq/parse_fastq.rb'
|
15
15
|
# =========================================================================== #
|
16
|
-
require 'bioroebe/
|
16
|
+
require 'bioroebe/requires/commandline_application.rb'
|
17
17
|
|
18
18
|
module Bioroebe
|
19
19
|
|
@@ -72,7 +72,7 @@ e 'The .fastq file is valid.'
|
|
72
72
|
# ========================================================================= #
|
73
73
|
# === Bioroebe::ParseFastq[]
|
74
74
|
# ========================================================================= #
|
75
|
-
def self.[](i =
|
75
|
+
def self.[](i = ARGV)
|
76
76
|
new(i)
|
77
77
|
end
|
78
78
|
|
@@ -7,7 +7,7 @@
|
|
7
7
|
# =========================================================================== #
|
8
8
|
module Bioroebe
|
9
9
|
|
10
|
-
require 'bioroebe/toplevel_methods/
|
10
|
+
require 'bioroebe/toplevel_methods/toplevel_methods.rb'
|
11
11
|
|
12
12
|
# ========================================================================= #
|
13
13
|
# === Bioroebe.return_fasta_subsection_of_this_file
|
@@ -13,17 +13,12 @@
|
|
13
13
|
# =========================================================================== #
|
14
14
|
# require 'bioroebe/fasta_and_fastq/show_fasta_headers.rb'
|
15
15
|
# =========================================================================== #
|
16
|
-
require 'bioroebe/
|
16
|
+
require 'bioroebe/requires/commandline_application.rb'
|
17
17
|
|
18
18
|
module Bioroebe
|
19
19
|
|
20
20
|
class ShowFastaHeaders < Bioroebe::CommandlineApplication # === Biroebe::ShowFastaHeaders
|
21
21
|
|
22
|
-
# ========================================================================= #
|
23
|
-
# === NAMESPACE
|
24
|
-
# ========================================================================= #
|
25
|
-
NAMESPACE = inspect
|
26
|
-
|
27
22
|
# ========================================================================= #
|
28
23
|
# === BASE_DIR
|
29
24
|
#
|
@@ -49,14 +44,11 @@ class ShowFastaHeaders < Bioroebe::CommandlineApplication # === Biroebe::ShowFas
|
|
49
44
|
# ========================================================================= #
|
50
45
|
def reset
|
51
46
|
super()
|
47
|
+
infer_the_namespace
|
52
48
|
# ======================================================================= #
|
53
|
-
# ===
|
54
|
-
# ======================================================================= #
|
55
|
-
@be_verbose = true
|
56
|
-
# ======================================================================= #
|
57
|
-
# === @namespace
|
49
|
+
# === :be_verbose
|
58
50
|
# ======================================================================= #
|
59
|
-
|
51
|
+
set_be_verbose
|
60
52
|
end
|
61
53
|
|
62
54
|
# ========================================================================= #
|
@@ -109,7 +101,7 @@ class ShowFastaHeaders < Bioroebe::CommandlineApplication # === Biroebe::ShowFas
|
|
109
101
|
# === report_this_header_from_that_file
|
110
102
|
# ========================================================================= #
|
111
103
|
def report_this_header_from_that_file(header, file)
|
112
|
-
if
|
104
|
+
if be_verbose?
|
113
105
|
erev "The file at #{sfile(file)}#{rev} has the following FASTA header:"
|
114
106
|
e
|
115
107
|
end
|
@@ -14,7 +14,7 @@
|
|
14
14
|
# =========================================================================== #
|
15
15
|
# require 'bioroebe/fasta_and_fastq/show_fasta_statistics.rb'
|
16
16
|
# =========================================================================== #
|
17
|
-
require 'bioroebe/
|
17
|
+
require 'bioroebe/requires/commandline_application.rb'
|
18
18
|
|
19
19
|
module Bioroebe
|
20
20
|
|
@@ -21,7 +21,7 @@
|
|
21
21
|
# Bioroebe.overwrite_fasta_header(ARGV)
|
22
22
|
# Bioroebe::SimplifyFastaHeader.new(ARGV)
|
23
23
|
# =========================================================================== #
|
24
|
-
require 'bioroebe/
|
24
|
+
require 'bioroebe/requires/commandline_application.rb'
|
25
25
|
|
26
26
|
module Bioroebe
|
27
27
|
|
@@ -13,14 +13,11 @@ class SplitThisFastaFileIntoChromosomes < ::Bioroebe::CommandlineApplication # =
|
|
13
13
|
# ========================================================================= #
|
14
14
|
def reset
|
15
15
|
super()
|
16
|
+
infer_the_namespace
|
16
17
|
# ======================================================================= #
|
17
|
-
# ===
|
18
|
+
# === :be_verbose
|
18
19
|
# ======================================================================= #
|
19
|
-
|
20
|
-
# ======================================================================= #
|
21
|
-
# === @be_verbose
|
22
|
-
# ======================================================================= #
|
23
|
-
@be_verbose = false
|
20
|
+
set_be_quiet
|
24
21
|
# ======================================================================= #
|
25
22
|
# === @this_file
|
26
23
|
#
|
@@ -16,7 +16,7 @@
|
|
16
16
|
# require 'bioroebe/fasta/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb'
|
17
17
|
# Bioroebe::SplitThisFastaFileIntoChromosomes.new
|
18
18
|
# =========================================================================== #
|
19
|
-
require 'bioroebe/
|
19
|
+
require 'bioroebe/requires/commandline_application.rb'
|
20
20
|
|
21
21
|
module Bioroebe
|
22
22
|
|
@@ -252,8 +252,8 @@ class SplitThisFastaFileIntoChromosomes < ::Bioroebe::CommandlineApplication # =
|
|
252
252
|
# Here we have found a match, so we can simply store this
|
253
253
|
# into the file in that event.
|
254
254
|
# =============================================================== #
|
255
|
-
if
|
256
|
-
|
255
|
+
if be_verbose?
|
256
|
+
opnerev "The following line belongs to chromosome "\
|
257
257
|
"number `#{sfancy(match)}#{rev}`."
|
258
258
|
e crimson(fasta_header_string)
|
259
259
|
end
|
@@ -17,7 +17,7 @@
|
|
17
17
|
# =========================================================================== #
|
18
18
|
# require 'bioroebe/genbank/genbank_flat_file_format_generator.rb'
|
19
19
|
# =========================================================================== #
|
20
|
-
require 'bioroebe/
|
20
|
+
require 'bioroebe/requires/commandline_application.rb'
|
21
21
|
|
22
22
|
module Bioroebe
|
23
23
|
|
@@ -78,20 +78,27 @@ class GenbankFlatFileFormatGenerator < ::Bioroebe::CommandlineApplication # ===
|
|
78
78
|
def reset
|
79
79
|
super()
|
80
80
|
# ======================================================================= #
|
81
|
-
# ===
|
81
|
+
# === :be_verbose
|
82
82
|
# ======================================================================= #
|
83
|
-
|
83
|
+
set_be_verbose
|
84
84
|
# ======================================================================= #
|
85
85
|
# === @shall_we_downcase
|
86
86
|
# ======================================================================= #
|
87
87
|
@shall_we_downcase = true
|
88
88
|
# ======================================================================= #
|
89
|
-
# === @string
|
89
|
+
# === @internal_hash[:string]
|
90
90
|
# ======================================================================= #
|
91
|
-
@string = ''.dup # This is the one that will be output.
|
91
|
+
@internal_hash[:string] = ''.dup # This is the one that will be output.
|
92
92
|
set_name_of_the_locus
|
93
93
|
end
|
94
94
|
|
95
|
+
# ========================================================================= #
|
96
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# === shall_we_downcase?
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# ========================================================================= #
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def shall_we_downcase?
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@shall_we_downcase
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+
end
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+
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# ========================================================================= #
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# === n_nucleotides?
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# ========================================================================= #
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@@ -104,7 +111,7 @@ class GenbankFlatFileFormatGenerator < ::Bioroebe::CommandlineApplication # ===
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# ========================================================================= #
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def set_input(
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i = '',
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-
shall_we_downcase =
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+
shall_we_downcase = shall_we_downcase?
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)
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i = i.first if i.is_a? Array
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i = i.to_s.dup.strip
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@@ -151,7 +158,7 @@ class GenbankFlatFileFormatGenerator < ::Bioroebe::CommandlineApplication # ===
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# === add
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# ========================================================================= #
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def add(i)
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-
@string << i
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+
@internal_hash[:string] << i
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end
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# ========================================================================= #
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@@ -176,15 +183,17 @@ class GenbankFlatFileFormatGenerator < ::Bioroebe::CommandlineApplication # ===
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# ========================================================================= #
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# === show_main_string
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# ========================================================================= #
|
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-
def show_main_string
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-
|
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+
def show_main_string(
|
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+
be_verbose = be_verbose?
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+
)
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+
e string? if be_verbose
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end
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191
|
|
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|
# ========================================================================= #
|
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193
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# === string?
|
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194
|
# ========================================================================= #
|
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195
|
def string?
|
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-
@string
|
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+
@internal_hash[:string]
|
188
197
|
end
|
189
198
|
|
190
199
|
# ========================================================================= #
|
@@ -264,7 +273,7 @@ return_chunked_numbered_and_properly_spaced_sequence+
|
|
264
273
|
# ========================================================================= #
|
265
274
|
# === Bioroebe::GenbankFlatFileFormatGenerator[]
|
266
275
|
# ========================================================================= #
|
267
|
-
def self.[](i =
|
276
|
+
def self.[](i = ARGV)
|
268
277
|
new(i)
|
269
278
|
end
|
270
279
|
|
@@ -13,7 +13,7 @@
|
|
13
13
|
# =========================================================================== #
|
14
14
|
# require 'bioroebe/genome/genome.rb'
|
15
15
|
# =========================================================================== #
|
16
|
-
require 'bioroebe/
|
16
|
+
require 'bioroebe/requires/commandline_application.rb'
|
17
17
|
|
18
18
|
module Bioroebe
|
19
19
|
|
@@ -20,7 +20,7 @@
|
|
20
20
|
# =========================================================================== #
|
21
21
|
# require 'bioroebe/genomes/genome_pattern.rb'
|
22
22
|
# =========================================================================== #
|
23
|
-
require 'bioroebe/
|
23
|
+
require 'bioroebe/requires/commandline_application.rb'
|
24
24
|
|
25
25
|
module Bioroebe
|
26
26
|
|
@@ -50,17 +50,14 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
|
|
50
50
|
# === @hash
|
51
51
|
# ======================================================================= #
|
52
52
|
@hash = {}
|
53
|
+
# ======================================================================= #
|
53
54
|
# === :array_genes
|
55
|
+
# ======================================================================= #
|
54
56
|
@hash[:array_genes] = []
|
57
|
+
# ======================================================================= #
|
55
58
|
# === :be_verbose
|
56
|
-
|
57
|
-
|
58
|
-
|
59
|
-
# ========================================================================= #
|
60
|
-
# === be_verbose?
|
61
|
-
# ========================================================================= #
|
62
|
-
def be_verbose?
|
63
|
-
@hash[:be_verbose]
|
59
|
+
# ======================================================================= #
|
60
|
+
set_be_verbose
|
64
61
|
end
|
65
62
|
|
66
63
|
# ========================================================================= #
|
@@ -88,11 +85,13 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
|
|
88
85
|
# ========================================================================= #
|
89
86
|
# === add_gene
|
90
87
|
# ========================================================================= #
|
91
|
-
def add_gene(
|
88
|
+
def add_gene(
|
89
|
+
i = :foo
|
90
|
+
)
|
92
91
|
_ = array_genes?
|
93
92
|
unless _.include? i
|
94
93
|
if be_verbose?
|
95
|
-
|
94
|
+
opnerev "Now adding the gene `#{sfancy(i.to_s)}#{rev}`."
|
96
95
|
end
|
97
96
|
_ << i
|
98
97
|
end
|
@@ -113,11 +112,11 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
|
|
113
112
|
# ========================================================================= #
|
114
113
|
def report
|
115
114
|
if genome?.empty?
|
116
|
-
|
115
|
+
opnerev 'We have no genes stored.'
|
117
116
|
else
|
118
|
-
|
117
|
+
opnerev 'We have these genes:'
|
119
118
|
genes?.each {|entry|
|
120
|
-
|
119
|
+
opnerev " #{sfancy(entry.to_s)}"
|
121
120
|
}
|
122
121
|
end
|
123
122
|
end
|
@@ -127,7 +126,9 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
|
|
127
126
|
#
|
128
127
|
# Use this method to remove a Gene again.
|
129
128
|
# ========================================================================= #
|
130
|
-
def remove_gene(
|
129
|
+
def remove_gene(
|
130
|
+
i = :foo, be_verbose = be_verbose?
|
131
|
+
)
|
131
132
|
case be_verbose
|
132
133
|
when :be_verbose
|
133
134
|
be_verbose = true
|
@@ -135,7 +136,7 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
|
|
135
136
|
_ = array_genes?
|
136
137
|
if _.include? i
|
137
138
|
if be_verbose
|
138
|
-
|
139
|
+
opnerev "Now removing the gene `#{sfancy(i.to_s)}#{rev}`."
|
139
140
|
end
|
140
141
|
_.delete i
|
141
142
|
end
|
@@ -11,7 +11,7 @@
|
|
11
11
|
# =========================================================================== #
|
12
12
|
# require 'bioroebe/genomes/genome_retriever.rb'
|
13
13
|
# =========================================================================== #
|
14
|
-
require 'bioroebe/
|
14
|
+
require 'bioroebe/requires/commandline_application.rb'
|
15
15
|
|
16
16
|
module Bioroebe
|
17
17
|
|
@@ -46,6 +46,7 @@ class GenomeRetriever < ::Bioroebe::CommandlineApplication # === Bioroebe::Genom
|
|
46
46
|
# ========================================================================= #
|
47
47
|
def fetch(what)
|
48
48
|
case what.to_sym
|
49
|
+
# === :human
|
49
50
|
when :human,
|
50
51
|
:humans
|
51
52
|
open_via_the_browser 'https://www.genome.jp/dbget-bin/www_bget?hsa+20+21+22'
|
@@ -56,7 +57,8 @@ class GenomeRetriever < ::Bioroebe::CommandlineApplication # === Bioroebe::Genom
|
|
56
57
|
# === open_via_the_browser
|
57
58
|
# ========================================================================= #
|
58
59
|
def open_via_the_browser(
|
59
|
-
url,
|
60
|
+
url,
|
61
|
+
use_this_browser = :firefox
|
60
62
|
)
|
61
63
|
system_cmd "#{use_this_browser} --new-tab #{url}"
|
62
64
|
end
|