bioroebe 0.10.80 → 0.12.24
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- checksums.yaml +4 -4
- data/README.md +3946 -2817
- data/bin/bioroebe +13 -2
- data/bin/bioroebe_hash +7 -0
- data/bin/codon_to_aminoacid +6 -4
- data/bin/compacter +7 -0
- data/bin/plain_palindrome +7 -0
- data/bioroebe.gemspec +3 -3
- data/doc/README.gen +3918 -2793
- data/doc/quality_control/commandline_applications.md +3 -3
- data/doc/statistics/statistics.md +7 -7
- data/doc/todo/bioroebe_GUI_todo.md +19 -14
- data/doc/todo/bioroebe_java_todo.md +22 -0
- data/doc/todo/bioroebe_todo.md +2075 -2620
- data/lib/bioroebe/C++/DNA.cpp +69 -0
- data/lib/bioroebe/C++/RNA.cpp +58 -0
- data/lib/bioroebe/C++/sequence.cpp +35 -0
- data/lib/bioroebe/abstract/README.md +1 -0
- data/lib/bioroebe/abstract/features.rb +29 -0
- data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -9
- data/lib/bioroebe/aminoacids/codon_percentage.rb +1 -9
- data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +1 -9
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
- data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +1 -6
- data/lib/bioroebe/base/base_module/base_module.rb +36 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
- data/lib/bioroebe/base/commandline_application/commandline_application.rb +13 -9
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +24 -19
- data/lib/bioroebe/base/commandline_application/misc.rb +66 -49
- data/lib/bioroebe/base/commandline_application/opn.rb +8 -8
- data/lib/bioroebe/base/commandline_application/reset.rb +5 -3
- data/lib/bioroebe/base/internal_hash_module/internal_hash_module.rb +42 -0
- data/lib/bioroebe/base/misc.rb +35 -0
- data/lib/bioroebe/base/prototype/misc.rb +15 -9
- data/lib/bioroebe/base/prototype/reset.rb +10 -0
- data/lib/bioroebe/cleave_and_digest/digestion.rb +10 -2
- data/lib/bioroebe/cleave_and_digest/trypsin.rb +104 -50
- data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -10
- data/lib/bioroebe/codons/codons.rb +1 -1
- data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +208 -59
- data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +1 -9
- data/lib/bioroebe/codons/show_codon_tables.rb +8 -3
- data/lib/bioroebe/codons/show_codon_usage.rb +15 -4
- data/lib/bioroebe/colours/rev.rb +4 -1
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
- data/lib/bioroebe/constants/database_constants.rb +1 -1
- data/lib/bioroebe/constants/files_and_directories.rb +31 -4
- data/lib/bioroebe/constants/misc.rb +20 -0
- data/lib/bioroebe/constants/nucleotides.rb +7 -0
- data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +109 -39
- data/lib/bioroebe/count/count_amount_of_aminoacids.rb +3 -2
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
- data/lib/bioroebe/cpp +1 -0
- data/lib/bioroebe/crystal/README.md +2 -0
- data/lib/bioroebe/crystal/to_rna.cr +19 -0
- data/lib/bioroebe/data/README.md +11 -8
- data/lib/bioroebe/data/electron_microscopy/pos_example.pos +396 -0
- data/lib/bioroebe/data/electron_microscopy/test_particles.star +36 -0
- data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_alpha_HBB_mRNA.fasta +9 -0
- data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_beta_HBB_mRNA.fasta +8 -0
- data/lib/bioroebe/data/fasta/human/README.md +2 -0
- data/lib/bioroebe/dotplots/advanced_dotplot.rb +1 -1
- data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +15 -18
- data/lib/bioroebe/{fasta_and_fastq/parse_fasta/run.rb → electron_microscopy/electron_microscopy_module.rb} +16 -8
- data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +1 -9
- data/lib/bioroebe/electron_microscopy/flipy.rb +83 -0
- data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +2 -10
- data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +1 -9
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +4 -9
- data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +10 -3
- data/lib/bioroebe/enzymes/restriction_enzyme.rb +23 -1
- data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +65 -0
- data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +1 -9
- data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +7 -9
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -5
- data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +81 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +1518 -7
- data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +11 -2
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +27 -12
- data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -5
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +0 -5
- data/lib/bioroebe/genome/README.md +4 -0
- data/lib/bioroebe/genome/genome.rb +130 -0
- data/lib/bioroebe/genomes/genome_pattern.rb +3 -9
- data/lib/bioroebe/gui/gtk +1 -0
- data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +106 -137
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb +27 -61
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb +1 -1
- data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +1 -2
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +1 -2
- data/lib/bioroebe/gui/gtk3/controller/controller.rb +46 -29
- data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +77 -52
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +1 -2
- data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +100 -23
- data/lib/bioroebe/gui/gtk3/format_converter/format_converter.rb +1 -2
- data/lib/bioroebe/gui/gtk3/gene/gene.rb +1 -2
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +43 -30
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +1 -2
- data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +120 -73
- data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb +1 -2
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +19 -20
- data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +20 -13
- data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb +1 -2
- data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb +97 -22
- data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +3 -73
- data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +1 -2
- data/lib/bioroebe/gui/gtk3/sizeseq/sizeseq.rb +1 -2
- data/lib/bioroebe/gui/gtk3/three_to_one/three_to_one.rb +1 -2
- data/lib/bioroebe/gui/gtk3/www_finder/www_finder.rb +1 -2
- data/lib/bioroebe/gui/javafx/bioroebe/Bioroebe.class +0 -0
- data/lib/bioroebe/gui/javafx/bioroebe/Bioroebe.java +104 -0
- data/lib/bioroebe/gui/javafx/bioroebe.jar +0 -0
- data/lib/bioroebe/gui/javafx/bioroebe.mf +1 -0
- data/lib/bioroebe/gui/javafx/module-info.class +0 -0
- data/lib/bioroebe/gui/javafx/module-info.java +5 -0
- data/lib/bioroebe/gui/jruby/alignment/alignment.rb +165 -0
- data/lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb +166 -0
- data/lib/bioroebe/gui/libui/alignment/alignment.rb +3 -1
- data/lib/bioroebe/gui/libui/controller/controller.rb +116 -0
- data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +18 -2
- data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +2 -0
- data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +8 -6
- data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +102 -0
- data/lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb +94 -0
- data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +18 -16
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
- data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$1.class +0 -0
- data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$CloseListener.class +0 -0
- data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.class +0 -0
- data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java +141 -0
- data/lib/bioroebe/images/FORWARD_PRIMER.png +0 -0
- data/lib/bioroebe/images/REVERSE_PRIMER.png +0 -0
- data/lib/bioroebe/images/images.html +29845 -0
- data/lib/bioroebe/java/README.md +5 -0
- data/lib/bioroebe/java/bioroebe/AllInOne.java +1 -0
- data/lib/bioroebe/java/bioroebe/Base.class +0 -0
- data/lib/bioroebe/java/bioroebe/Base.java +39 -5
- data/lib/bioroebe/java/bioroebe/IsPalindrome.java +23 -5
- data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.java +0 -0
- data/lib/bioroebe/java/bioroebe/Sequence.java +28 -3
- data/lib/bioroebe/java/bioroebe/ToCamelcase.class +0 -0
- data/lib/bioroebe/java/bioroebe/ToCamelcase.java +16 -4
- data/lib/bioroebe/java/bioroebe/ToRNA.java +43 -0
- data/lib/bioroebe/java/bioroebe/ToplevelMethods.java +6 -0
- data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.class → src/BisulfiteTreatment.class} +0 -0
- data/lib/bioroebe/java/bioroebe/{Codons.class → src/Codons.class} +0 -0
- data/lib/bioroebe/java/bioroebe/src/Codons.java +35 -0
- data/lib/bioroebe/java/bioroebe/src/Commandline.class +0 -0
- data/lib/bioroebe/java/bioroebe/src/Commandline.java +101 -0
- data/lib/bioroebe/java/bioroebe/{Esystem.class → src/Esystem.class} +0 -0
- data/lib/bioroebe/java/bioroebe/{Esystem.java → src/Esystem.java} +6 -1
- data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.class → src/GenerateRandomDnaSequence.class} +0 -0
- data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.java → src/GenerateRandomDnaSequence.java} +8 -2
- data/lib/bioroebe/java/bioroebe/src/PartnerNucleotide.class +0 -0
- data/lib/bioroebe/java/bioroebe/src/PartnerNucleotide.java +56 -0
- data/lib/bioroebe/java/bioroebe/{RemoveFile.java → src/RemoveFile.java} +10 -4
- data/lib/bioroebe/java/bioroebe/{RemoveNumbers.class → src/RemoveNumbers.class} +0 -0
- data/lib/bioroebe/java/bioroebe/{RemoveNumbers.java → src/RemoveNumbers.java} +1 -0
- data/lib/bioroebe/java/bioroebe/src/toplevel_methods/BaseComposition.class +0 -0
- data/lib/bioroebe/java/bioroebe/src/toplevel_methods/BaseComposition.java +75 -0
- data/lib/bioroebe/misc/ruler.rb +11 -2
- data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +1 -9
- data/lib/bioroebe/nucleotides/sanitize_nucleotide_sequence.rb +59 -18
- data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +7 -7
- data/lib/bioroebe/parsers/genbank_parser.rb +347 -26
- data/lib/bioroebe/parsers/gff.rb +1 -9
- data/lib/bioroebe/patterns/scan_for_repeat.rb +1 -5
- data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb +1 -9
- data/lib/bioroebe/pdb/parse_mmCIF_file.rb +1 -9
- data/lib/bioroebe/pdb/parse_pdb_file.rb +4 -10
- data/lib/bioroebe/project/project.rb +1 -1
- data/lib/bioroebe/python/README.md +1 -0
- data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
- data/lib/bioroebe/python/gui/gtk3/all_in_one.css +4 -0
- data/lib/bioroebe/python/gui/gtk3/all_in_one.py +59 -0
- data/lib/bioroebe/python/gui/gtk3/widget1.py +20 -0
- data/lib/bioroebe/python/gui/tkinter/all_in_one.py +91 -0
- data/lib/bioroebe/python/mymodule.py +8 -0
- data/lib/bioroebe/python/protein_to_dna.py +33 -0
- data/lib/bioroebe/python/shell/shell.py +19 -0
- data/lib/bioroebe/python/to_rna.py +14 -0
- data/lib/bioroebe/python/toplevel_methods/convert_dna_to_aminoacid_sequence.py +137 -0
- data/lib/bioroebe/python/toplevel_methods/esystem.py +12 -0
- data/lib/bioroebe/python/toplevel_methods/open_in_browser.py +20 -0
- data/lib/bioroebe/python/toplevel_methods/palindromes.py +52 -0
- data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
- data/lib/bioroebe/python/toplevel_methods/shuffleseq.py +23 -0
- data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +37 -0
- data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
- data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +21 -0
- data/lib/bioroebe/requires/require_cleave_and_digest.rb +3 -1
- data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
- data/lib/bioroebe/sequence/alignment.rb +14 -4
- data/lib/bioroebe/sequence/dna.rb +1 -0
- data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
- data/lib/bioroebe/sequence/protein.rb +105 -3
- data/lib/bioroebe/sequence/rna.rb +220 -0
- data/lib/bioroebe/sequence/sequence.rb +128 -40
- data/lib/bioroebe/shell/menu.rb +3815 -3696
- data/lib/bioroebe/shell/misc.rb +9019 -3133
- data/lib/bioroebe/shell/readline/readline.rb +1 -1
- data/lib/bioroebe/shell/shell.rb +1137 -28
- data/lib/bioroebe/siRNA/siRNA.rb +81 -1
- data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
- data/lib/bioroebe/string_matching/hamming_distance.rb +1 -9
- data/lib/bioroebe/taxonomy/class_methods.rb +3 -8
- data/lib/bioroebe/taxonomy/constants.rb +4 -3
- data/lib/bioroebe/taxonomy/edit.rb +2 -1
- data/lib/bioroebe/taxonomy/help/help.rb +10 -10
- data/lib/bioroebe/taxonomy/help/helpline.rb +2 -2
- data/lib/bioroebe/taxonomy/info/check_available.rb +15 -9
- data/lib/bioroebe/taxonomy/info/info.rb +18 -11
- data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
- data/lib/bioroebe/taxonomy/interactive.rb +140 -104
- data/lib/bioroebe/taxonomy/menu.rb +27 -18
- data/lib/bioroebe/taxonomy/parse_fasta.rb +3 -1
- data/lib/bioroebe/taxonomy/shared.rb +1 -0
- data/lib/bioroebe/taxonomy/taxonomy.rb +1 -0
- data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
- data/lib/bioroebe/toplevel_methods/colourize_related_methods.rb +164 -0
- data/lib/bioroebe/toplevel_methods/databases.rb +1 -1
- data/lib/bioroebe/toplevel_methods/digest.rb +18 -8
- data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +107 -63
- data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +14 -2
- data/lib/bioroebe/toplevel_methods/frequencies.rb +8 -1
- data/lib/bioroebe/toplevel_methods/misc.rb +175 -11
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +118 -46
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
- data/lib/bioroebe/toplevel_methods/palindromes.rb +75 -47
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +3 -3
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
- data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +1 -9
- data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +1 -9
- data/lib/bioroebe/utility_scripts/compacter/compacter.rb +251 -0
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
- data/lib/bioroebe/utility_scripts/consensus_sequence.rb +6 -6
- data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +1 -9
- data/lib/bioroebe/utility_scripts/dot_alignment.rb +1 -9
- data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +1 -4
- data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +2 -2
- data/lib/bioroebe/utility_scripts/permutations.rb +36 -9
- data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -5
- data/lib/bioroebe/utility_scripts/showorf/reset.rb +1 -4
- data/lib/bioroebe/version/version.rb +2 -2
- data/lib/bioroebe/www/embeddable_interface.rb +121 -58
- data/lib/bioroebe/www/sinatra/sinatra.rb +186 -71
- data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
- data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +17 -17
- data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
- 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/genomes/README.md +3 -4
- data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +5 -0
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +57 -57
- data/spec/README.md +6 -0
- data/spec/project_wide_specification/classes.md +5 -0
- metadata +107 -70
- data/doc/setup.rb +0 -1655
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +0 -50
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +0 -86
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +0 -117
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +0 -981
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +0 -156
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +0 -128
- data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
- data/lib/bioroebe/java/bioroebe/AllInOne.class +0 -0
- data/lib/bioroebe/java/bioroebe/Cat.class +0 -0
- data/lib/bioroebe/java/bioroebe/Codons.java +0 -22
- data/lib/bioroebe/java/bioroebe/IsPalindrome.class +0 -0
- data/lib/bioroebe/java/bioroebe/PartnerNucleotide.class +0 -0
- data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java +0 -19
- data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.class +0 -0
- data/lib/bioroebe/java/bioroebe/ToplevelMethods.class +0 -0
- data/lib/bioroebe/java/bioroebe.jar +0 -0
- data/lib/bioroebe/shell/add.rb +0 -108
- data/lib/bioroebe/shell/assign.rb +0 -360
- data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
- data/lib/bioroebe/shell/constants.rb +0 -166
- data/lib/bioroebe/shell/download.rb +0 -335
- data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
- data/lib/bioroebe/shell/enzymes.rb +0 -310
- data/lib/bioroebe/shell/fasta.rb +0 -345
- data/lib/bioroebe/shell/gtk.rb +0 -76
- data/lib/bioroebe/shell/history.rb +0 -132
- data/lib/bioroebe/shell/initialize.rb +0 -217
- data/lib/bioroebe/shell/loop.rb +0 -74
- data/lib/bioroebe/shell/prompt.rb +0 -107
- data/lib/bioroebe/shell/random.rb +0 -289
- data/lib/bioroebe/shell/reset.rb +0 -335
- data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
- data/lib/bioroebe/shell/search.rb +0 -337
- data/lib/bioroebe/shell/sequences.rb +0 -200
- data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
- data/lib/bioroebe/shell/startup.rb +0 -127
- data/lib/bioroebe/shell/taxonomy.rb +0 -14
- data/lib/bioroebe/shell/tk.rb +0 -23
- data/lib/bioroebe/shell/user_input.rb +0 -88
- data/lib/bioroebe/shell/xorg.rb +0 -45
- data/lib/bioroebe/utility_scripts/compacter.rb +0 -131
- /data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.java → src/BisulfiteTreatment.java} +0 -0
- /data/lib/bioroebe/java/bioroebe/{RemoveFile.class → src/RemoveFile.class} +0 -0
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@@ -0,0 +1,164 @@
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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::Colourize
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#
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# This file can be used to colourize a string representing DNA (in fasta
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# format), for use (or display) on a website. HTML colour code and CSS
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# rules will be used.
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#
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# The colour to use can be passed via the second method to four of the
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# module-level methods in this file.
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# =========================================================================== #
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module Bioroebe
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module Colourize # === Bioroebe::Colourize
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require 'bioroebe/colours/colours.rb'
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require 'bioroebe/toplevel_methods/e.rb'
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require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
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# ========================================================================= #
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# === Bioroebe::Colourize.generate_HTML_page_via_this_input
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#
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# This method will generate a .html page, using the default colourization
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# rules defined in this file here.
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# ========================================================================= #
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def self.generate_HTML_page_via_this_input(i)
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if i.is_a? Array
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i = i.join(' ').strip
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end
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what = "<!DOCTYPE html>\n<html lang=\"en\"><head>"\
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"<title>Colourized FASTA Sequence</title><style>\n".dup
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what << "#{return_default_CSS_rules_to_use}\n\n"
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what << "</style>\n</head>\n<body>\n"
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result = colourize_this_FASTA_sequence(i)
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what << "#{result}</body></html>\n"
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# ======================================================================= #
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# The name of the generated file is determined by the input
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# argument given.
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# ======================================================================= #
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into = File.basename(i).delete_suffix(File.extname(i))+
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'.html'
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if File.exist? into
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e 'Can not store into an already existing file.'
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else
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e 'Storing into the file '+::Bioroebe.sfile(into)+' next.'
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::Bioroebe.write_what_into(what, into)
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end
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end
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# ========================================================================= #
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# === Bioroebe::Colourize.return_default_CSS_rules_to_use
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# ========================================================================= #
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def self.return_default_CSS_rules_to_use
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return '.lightgreen {
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color: lightgreen;
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}
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.lightblue {
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color: lightblue;
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}
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.mediumslateblue {
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color: lightblue;
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}
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.olivedrab {
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color: olivedrab;
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}
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body {
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background-color: black;
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color: white;
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font-family: monospace;
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font-size: 2em;
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}'
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end
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# ========================================================================= #
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# === Bioroebe::Colourize.colourize_this_FASTA_sequence
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# ========================================================================= #
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def self.colourize_this_FASTA_sequence(
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i = ARGV
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)
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if i.is_a? Array
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i = i.join(' ').strip
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end
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if i and File.file?(i)
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# unless Bioroebe.const_defined?(:ParseFasta)
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# require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
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# end
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# i = Bioroebe::ParseFasta.new(i) { :be_quiet }.sequence?
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i = File.readlines(i).reject {|line|
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line.start_with?('#','>')
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}.join("\n")
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end
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result = colourize_TUG_start_codon(i)
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result = colourize_TAG_stop_codon(result)
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result = colourize_TAA_stop_codon(result)
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result = colourize_TGA_stop_codon(result)
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return result
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end
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# ========================================================================= #
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# === Bioroebe::Colourize.colourize_TAG_stop_codon
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# ========================================================================= #
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def self.colourize_TAG_stop_codon(
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i = '',
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use_this_colour = :lightblue
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)
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return i.gsub(
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/(TA\n?G)/,
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'<span class="'+use_this_colour.to_s+'">\1</span>'
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)
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end
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# ========================================================================= #
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# === Bioroebe::Colourize.colourize_TAA_stop_codon
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# ========================================================================= #
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def self.colourize_TAA_stop_codon(
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i = '',
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use_this_colour = :lightgreen
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)
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return i.gsub(
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/(TA\n?A)/,
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'<span class="'+use_this_colour.to_s+'">\1</span>'
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)
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end
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# ========================================================================= #
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# === Bioroebe::Colourize.colourize_TGA_stop_codon
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# ========================================================================= #
|
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134
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+
def self.colourize_TGA_stop_codon(
|
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135
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i = '',
|
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136
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use_this_colour = :olivedrab
|
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)
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return i.gsub(
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/(TG\n?A)/,
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'<span class="'+use_this_colour.to_s+'">\1</span>'
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)
|
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+
end
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+
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144
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# ========================================================================= #
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145
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# === Bioroebe::Colourize.colourize_TUG_start_codon
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146
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# ========================================================================= #
|
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147
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+
def self.colourize_TUG_start_codon(
|
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148
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i = '',
|
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149
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use_this_colour = :mediumslateblue
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)
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return i.gsub(
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/(TU\n?G)/,
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'<span class="'+use_this_colour.to_s+'">\1</span>'
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)
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end
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+
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end; end
|
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+
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159
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+
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160
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if __FILE__ == $PROGRAM_NAME
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161
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alias e puts
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162
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# e Bioroebe::Colourize.colourize_this_FASTA_sequence(ARGV)
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163
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Bioroebe::Colourize.generate_HTML_page_via_this_input(ARGV)
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164
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end # colourizerelatedmethods alu_elements.fasta
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@@ -15,7 +15,7 @@ module Bioroebe
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15
15
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# can pass the password for the postgreSQL database.
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16
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# ========================================================================= #
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17
17
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def self.set_pgpassword(
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-
new_password = POSTGRE_PASSWORD
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18
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+
new_password = Bioroebe::Postgresql::POSTGRE_PASSWORD
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19
19
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)
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20
20
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ENV['PGPASSWORD'] = new_password
|
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21
21
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end; self.instance_eval { alias set_password set_pgpassword } # === Bioroebe.set_password
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@@ -11,15 +11,17 @@ module Bioroebe
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11
11
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#
|
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12
12
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# Usage examples:
|
|
13
13
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#
|
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14
|
-
# Bioroebe.digest_this_dna(:lambda_genome, with: :EcoRI)
|
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15
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-
# Bioroebe.digest_this_dna("/root/Bioroebe/fasta/NC_001416.1_Enterobacteria_phage_lambda_complete_genome.fasta", with: :EcoRI)
|
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14
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# x = Bioroebe.digest_this_dna(:lambda_genome, with: :EcoRI)
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15
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# x = Bioroebe.digest_this_dna("/root/Bioroebe/fasta/NC_001416.1_Enterobacteria_phage_lambda_complete_genome.fasta", with: :EcoRI)
|
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16
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# x = Bioroebe.digest_this_dna("/Depot/j/foobar.fasta", with: :PvuII)
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16
17
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#
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17
18
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# ========================================================================= #
|
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18
19
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def self.digest_this_dna(
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19
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-
this_DNA_sequence,
|
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20
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this_DNA_sequence,
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hash = {}
|
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20
22
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)
|
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21
|
-
require 'bioroebe/toplevel_methods/e.rb'
|
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22
23
|
require 'bioroebe/constants/files_and_directories.rb'
|
|
24
|
+
require 'bioroebe/toplevel_methods/e.rb'
|
|
23
25
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require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
|
|
24
26
|
restriction_enzymes = Bioroebe.load_and_return_the_restriction_enzymes
|
|
25
27
|
this_restriction_enzyme = nil
|
|
@@ -46,16 +48,24 @@ module Bioroebe
|
|
|
46
48
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target_sequence.chop!
|
|
47
49
|
target_sequence.strip!
|
|
48
50
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end
|
|
49
|
-
if nucleotide_sequence
|
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50
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-
|
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51
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+
if nucleotide_sequence and
|
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52
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+
nucleotide_sequence.include?(target_sequence)
|
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53
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+
print rev+'Yes, the restriction-sequence '+
|
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54
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+
lightblue(target_sequence)+
|
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55
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rev+
|
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56
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+
' is found in the given sequence. '
|
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51
57
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scanned = nucleotide_sequence.scan(
|
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52
58
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/#{target_sequence}/
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53
59
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)
|
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54
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-
|
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60
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erev "It can be found #{steelblue(scanned.size.to_s)}#{rev} "\
|
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61
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"times, at these positions:"
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62
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+
e
|
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55
63
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sub_sequences = nucleotide_sequence.split(/#{target_sequence}/)
|
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56
64
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sub_sequences.sort_by {|entry| entry.size }.reverse.each {|sequence|
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|
57
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-
|
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65
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erev " #{sequence.size}"
|
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58
66
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}
|
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67
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e
|
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68
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return sub_sequences
|
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59
69
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else
|
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60
70
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e 'Nothing found.'
|
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61
71
|
end
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@@ -49,68 +49,6 @@ module Bioroebe
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|
49
49
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end
|
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50
50
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end
|
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51
51
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|
52
|
-
# ========================================================================= #
|
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53
|
-
# === Bioroebe.colourize_this_fasta_dna_sequence
|
|
54
|
-
#
|
|
55
|
-
# This toplevel method can be used to colourize a FASTA (DNA)
|
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56
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# sequence, e. g. "ATGCGCGTATTA" and so forth.
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57
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#
|
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58
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-
# Note that this is intended for the commandline, that is to be
|
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59
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-
# displayed on e. g. a KDE Konsole terminal.
|
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60
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-
#
|
|
61
|
-
# Usage example:
|
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62
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-
#
|
|
63
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-
# puts Bioroebe.colourize_this_fasta_dna_sequence('ATGCGCATGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA')
|
|
64
|
-
#
|
|
65
|
-
# ========================================================================= #
|
|
66
|
-
def self.colourize_this_fasta_dna_sequence(
|
|
67
|
-
i = nil
|
|
68
|
-
)
|
|
69
|
-
if i.nil?
|
|
70
|
-
e 'Please provide a valid FASTA sequence as input to '\
|
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71
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-
'Bioroebe.colourize_this_fasta_dna_sequence()'
|
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72
|
-
return
|
|
73
|
-
end
|
|
74
|
-
if i.is_a? Array
|
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75
|
-
# ===================================================================== #
|
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76
|
-
# Arrays will be joined together.
|
|
77
|
-
# ===================================================================== #
|
|
78
|
-
i = i.join(' ').strip
|
|
79
|
-
end
|
|
80
|
-
if i.is_a? String
|
|
81
|
-
# ===================================================================== #
|
|
82
|
-
# The colours are either defined in a file called
|
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83
|
-
# 'colourize_fasta_sequences.yml' or they are simply hardcoded.
|
|
84
|
-
#
|
|
85
|
-
# The preferred (and thus default) way is to simply make use
|
|
86
|
-
# of that .yml file. That works on my home system, so it
|
|
87
|
-
# should work for other people as well.
|
|
88
|
-
# ===================================================================== #
|
|
89
|
-
if use_colours?
|
|
90
|
-
i = i.dup if i.frozen?
|
|
91
|
-
this_file = FILE_COLOURIZE_FASTA_SEQUENCES
|
|
92
|
-
if File.exist? this_file
|
|
93
|
-
dataset_for_the_colours = YAML.load_file(this_file)
|
|
94
|
-
dataset_for_the_colours.each_pair {|this_nucleotide, this_colour_to_be_used|
|
|
95
|
-
i.gsub!(
|
|
96
|
-
/#{this_nucleotide}/,
|
|
97
|
-
send(this_colour_to_be_used, this_nucleotide)+
|
|
98
|
-
rev
|
|
99
|
-
)
|
|
100
|
-
}
|
|
101
|
-
else
|
|
102
|
-
i.gsub!(/A/, "#{teal('A')}#{rev}")
|
|
103
|
-
i.gsub!(/C/, "#{slateblue('C')}#{rev}")
|
|
104
|
-
i.gsub!(/G/, "#{royalblue('G')}#{rev}")
|
|
105
|
-
i.gsub!(/T/, "#{steelblue('T')}#{rev}")
|
|
106
|
-
i.gsub!(/U/, "#{steelblue('U')}#{rev}") # Uracil is just the same as Thymine.
|
|
107
|
-
end
|
|
108
|
-
end
|
|
109
|
-
end
|
|
110
|
-
i
|
|
111
|
-
end; self.instance_eval { alias colourize_this_fasta_sequence colourize_this_fasta_dna_sequence } # === Bioroebe.colourize_this_fasta_sequence
|
|
112
|
-
self.instance_eval { alias colourized_parse_fasta colourize_this_fasta_dna_sequence } # === Bioroebe.colourized_parse_fasta
|
|
113
|
-
|
|
114
52
|
# ========================================================================= #
|
|
115
53
|
# === Bioroebe.calculate_weight_of_the_aminoacids_in_this_fasta_file
|
|
116
54
|
#
|
|
@@ -317,13 +255,119 @@ module Bioroebe
|
|
|
317
255
|
end
|
|
318
256
|
end
|
|
319
257
|
|
|
258
|
+
# ========================================================================= #
|
|
259
|
+
# === Bioroebe.colourize_this_fasta_dna_sequence
|
|
260
|
+
#
|
|
261
|
+
# This toplevel method can be used to colourize a FASTA (DNA)
|
|
262
|
+
# sequence, e. g. "ATGCGCGTATTA" and so forth.
|
|
263
|
+
#
|
|
264
|
+
# Note that this is intended for the commandline, that is to be
|
|
265
|
+
# displayed on e. g. a KDE Konsole terminal.
|
|
266
|
+
#
|
|
267
|
+
# Usage examples:
|
|
268
|
+
#
|
|
269
|
+
# puts Bioroebe.colourize_this_fasta_dna_sequence('ATGCGCATGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA')
|
|
270
|
+
# puts Bioroebe.colourize_this_fasta_dna_sequence('ATGCGCATGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA') { :with_ruler }
|
|
271
|
+
# puts Bioroebe.colourize_this_fasta_dna_sequence('TGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA') { :with_ruler_steelblue_colour }
|
|
272
|
+
#
|
|
273
|
+
# ========================================================================= #
|
|
274
|
+
def self.colourize_this_fasta_dna_sequence(
|
|
275
|
+
i = nil,
|
|
276
|
+
&block
|
|
277
|
+
)
|
|
278
|
+
unless ::Bioroebe.respond_to?(:ruler_return_as_string_without_colours)
|
|
279
|
+
require 'bioroebe/misc/ruler.rb'
|
|
280
|
+
end
|
|
281
|
+
if i.nil?
|
|
282
|
+
e 'Please provide a valid FASTA sequence as input to '\
|
|
283
|
+
'Bioroebe.colourize_this_fasta_dna_sequence()'
|
|
284
|
+
return
|
|
285
|
+
end
|
|
286
|
+
if i.is_a? Array
|
|
287
|
+
# ===================================================================== #
|
|
288
|
+
# Arrays will be joined together.
|
|
289
|
+
# ===================================================================== #
|
|
290
|
+
i = i.join(' ').strip
|
|
291
|
+
end
|
|
292
|
+
# ======================================================================= #
|
|
293
|
+
# Check for existing files next:
|
|
294
|
+
# ======================================================================= #
|
|
295
|
+
if i and File.file?(i)
|
|
296
|
+
i = File.read(i)
|
|
297
|
+
end
|
|
298
|
+
original_input = i.dup
|
|
299
|
+
i = i.dup # Always dup it here.
|
|
300
|
+
if i.is_a? String
|
|
301
|
+
# ===================================================================== #
|
|
302
|
+
# The colours are either defined in a file called
|
|
303
|
+
# 'colourize_fasta_sequences.yml' or they are simply hardcoded.
|
|
304
|
+
#
|
|
305
|
+
# The preferred (and thus default) way is to simply make use
|
|
306
|
+
# of that .yml file. That works on my home system, so it
|
|
307
|
+
# should work for other people as well.
|
|
308
|
+
# ===================================================================== #
|
|
309
|
+
if use_colours?
|
|
310
|
+
this_file = FILE_COLOURIZE_FASTA_SEQUENCES
|
|
311
|
+
if File.exist? this_file
|
|
312
|
+
dataset_for_the_colours = YAML.load_file(this_file)
|
|
313
|
+
dataset_for_the_colours.each_pair {|this_nucleotide, this_colour_to_be_used|
|
|
314
|
+
i.gsub!(
|
|
315
|
+
/#{this_nucleotide}/,
|
|
316
|
+
Colours.send(this_colour_to_be_used, this_nucleotide)+
|
|
317
|
+
rev
|
|
318
|
+
)
|
|
319
|
+
}
|
|
320
|
+
else
|
|
321
|
+
i.gsub!(/A/, "#{teal('A')}#{rev}")
|
|
322
|
+
i.gsub!(/C/, "#{slateblue('C')}#{rev}")
|
|
323
|
+
i.gsub!(/G/, "#{royalblue('G')}#{rev}")
|
|
324
|
+
i.gsub!(/T/, "#{steelblue('T')}#{rev}")
|
|
325
|
+
i.gsub!(/U/, "#{steelblue('U')}#{rev}") # Uracil is just the same as Thymine.
|
|
326
|
+
end
|
|
327
|
+
end
|
|
328
|
+
end
|
|
329
|
+
# ======================================================================= #
|
|
330
|
+
# === Handle blocks next
|
|
331
|
+
# ======================================================================= #
|
|
332
|
+
if block_given?
|
|
333
|
+
yielded = yield
|
|
334
|
+
case yielded
|
|
335
|
+
# ===================================================================== #
|
|
336
|
+
# === with_ruler
|
|
337
|
+
# ===================================================================== #
|
|
338
|
+
when :with_ruler,
|
|
339
|
+
:add_ruler,
|
|
340
|
+
:ruler
|
|
341
|
+
i.prepend(
|
|
342
|
+
::Bioroebe.ruler_return_as_string_without_colours(original_input)+
|
|
343
|
+
"\n"
|
|
344
|
+
)
|
|
345
|
+
else # Assume something like:
|
|
346
|
+
# :with_ruler_steelblue_colour
|
|
347
|
+
if yielded.to_s.include? 'colo' # This assumes "colour" or "color".
|
|
348
|
+
use_this_colour = yielded.to_s.sub(/_colou?r/,'').
|
|
349
|
+
sub(/with_ruler_/,'')
|
|
350
|
+
this_string = send(use_this_colour,
|
|
351
|
+
::Bioroebe.ruler_return_as_string_without_colours(original_input)+
|
|
352
|
+
"\n"
|
|
353
|
+
)
|
|
354
|
+
i.prepend(this_string)
|
|
355
|
+
end
|
|
356
|
+
end
|
|
357
|
+
end
|
|
358
|
+
return i
|
|
359
|
+
end; self.instance_eval { alias colourize_this_fasta_sequence colourize_this_fasta_dna_sequence } # === Bioroebe.colourize_this_fasta_sequence
|
|
360
|
+
self.instance_eval { alias colourized_parse_fasta colourize_this_fasta_dna_sequence } # === Bioroebe.colourized_parse_fasta
|
|
361
|
+
|
|
320
362
|
# ========================================================================= #
|
|
321
363
|
# === Bioroebe.show_fasta_header
|
|
322
364
|
#
|
|
323
365
|
# This ad-hoc method can be used to quickly show the first line of an
|
|
324
366
|
# assumed .fasta file.
|
|
325
367
|
# ========================================================================= #
|
|
326
|
-
def self.show_fasta_header(
|
|
368
|
+
def self.show_fasta_header(
|
|
369
|
+
of_this_file
|
|
370
|
+
)
|
|
327
371
|
if of_this_file.is_a? Array
|
|
328
372
|
of_this_file = of_this_file.first
|
|
329
373
|
end
|
|
@@ -13,6 +13,13 @@ module Bioroebe
|
|
|
13
13
|
require 'bioroebe/colours/sfile.rb'
|
|
14
14
|
require 'bioroebe/colours/sdir.rb'
|
|
15
15
|
|
|
16
|
+
# ========================================================================= #
|
|
17
|
+
# === Bioroebe.move_file
|
|
18
|
+
# ========================================================================= #
|
|
19
|
+
def self.move_file(a, b)
|
|
20
|
+
FileUtils.mv(a, b)
|
|
21
|
+
end
|
|
22
|
+
|
|
16
23
|
# ========================================================================= #
|
|
17
24
|
# === Bioroebe.pwd (pwd tag)
|
|
18
25
|
#
|
|
@@ -134,6 +141,9 @@ module Bioroebe
|
|
|
134
141
|
be_verbose = false
|
|
135
142
|
)
|
|
136
143
|
case be_verbose
|
|
144
|
+
# ======================================================================= #
|
|
145
|
+
# === :do_report_current_directory
|
|
146
|
+
# ======================================================================= #
|
|
137
147
|
when :do_report_current_directory,
|
|
138
148
|
:be_verbose
|
|
139
149
|
be_verbose = true
|
|
@@ -160,12 +170,14 @@ module Bioroebe
|
|
|
160
170
|
# Bioroebe.save_dir? is defined in bioroebe/toplevel_methods/store_here.rb.
|
|
161
171
|
# ======================================================================= #
|
|
162
172
|
when 'base',
|
|
163
|
-
'logdir'
|
|
173
|
+
'logdir',
|
|
174
|
+
:bioroebe_log_directory
|
|
164
175
|
# ===================================================================== #
|
|
165
176
|
# Enter the main log dir, unless a file exists with the same name.
|
|
166
177
|
# ===================================================================== #
|
|
167
|
-
i = save_dir? unless File.exist?
|
|
178
|
+
i = save_dir? unless File.exist?(i.to_s) # .to_s to avoid Symbols here.
|
|
168
179
|
end
|
|
180
|
+
i = i.dup if i.is_a?(String) and i.frozen?
|
|
169
181
|
i << '/' unless i.end_with? '/'
|
|
170
182
|
if File.directory? i
|
|
171
183
|
e sdir(i) if be_verbose # Also colourize the directory and output it.
|
|
@@ -10,6 +10,7 @@ module Bioroebe
|
|
|
10
10
|
require 'bioroebe/project/project.rb'
|
|
11
11
|
require 'bioroebe/toplevel_methods/e.rb'
|
|
12
12
|
require 'bioroebe/colours/colours.rb'
|
|
13
|
+
require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
|
|
13
14
|
|
|
14
15
|
# ========================================================================= #
|
|
15
16
|
# === Bioroebe.calculate_the_frequencies_of_this_species
|
|
@@ -34,7 +35,7 @@ module Bioroebe
|
|
|
34
35
|
when :homo_sapiens,
|
|
35
36
|
:homo,
|
|
36
37
|
:human
|
|
37
|
-
i = "#{
|
|
38
|
+
i = "#{project_base_directory?}"\
|
|
38
39
|
"codon_tables/frequencies/9606_Homo_sapiens.yml"
|
|
39
40
|
end
|
|
40
41
|
hash = YAML.load_file(i)
|
|
@@ -87,6 +88,12 @@ module Bioroebe
|
|
|
87
88
|
end
|
|
88
89
|
|
|
89
90
|
if __FILE__ == $PROGRAM_NAME
|
|
91
|
+
alias e puts
|
|
92
|
+
e
|
|
90
93
|
Bioroebe.calculate_the_frequencies_of_this_species(ARGV)
|
|
94
|
+
e
|
|
95
|
+
e 'Aminoacid frequency:'
|
|
96
|
+
e; print ' '
|
|
91
97
|
pp Bioroebe.aminoacid_frequency('MVTDEGAIYFTKDAARNWKAAVEETVSATLNRTVSSGITGASYYTGTFST')
|
|
98
|
+
e
|
|
92
99
|
end # calculatethefrequenciesofthisspecies
|