Parses the NCBI genetic code table with a multiline Regex, generating hash maps of each species' name, start codons, stop codons and codon table. The output can be easily customized and used to update the respective constants of BioRuby's CodonTable class whenever the original data changes.
$ gem install codon_table_parser
Without any parameters, the genetic code file is downloaded directly from the NCBI web site
parser = CodonTableParser.new
Alternatively, the genetic code file can be loaded from a path
file = 'path/to/genetic_code.txt'
parser = CodonTableParser.new(file)
The first line of the file is read to determine if the content is correct. If not, an exception is thrown:
wrong_content = 'path/to/wrong_content.txt'
parser = CodonTableParser.new(wrong_content)
# Exception: This is not the NCBI genetic code table
The following instance methods are available:
Every intance method can take a :range option that specifies the ids of the species to be considered in the output. A range is specified as an array of integers, Ranges or both. Example:
:range => [(1..3), 5, 9] # converted internally to [1, 2, 3, 5, 9]
ids not present in the originial data are ignored. Besides the :range option, several methods also take other options as demonstrated below.
parser = CodonTableParser.new
# Return default hash map of names
definitions = parser.definitions
definitions
# {1=>"Standard",
# 2=>"Vertebrate Mitochondrial",
# 3=>"Yeast Mitochondrial",
# 4=>"Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma",
# 5=>"Invertebrate Mitochondrial",
# 6=>"Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear",
# 9=>"Echinoderm Mitochondrial; Flatworm Mitochondrial",
# 10=>"Euplotid Nuclear",
# 11=>"Bacterial and Plant Plastid",
# 12=>"Alternative Yeast Nuclear",
# 13=>"Ascidian Mitochondrial",
# 14=>"Alternative Flatworm Mitochondrial",
# 15=>"Blepharisma Macronuclear",
# 16=>"Chlorophycean Mitochondrial",
# 21=>"Trematode Mitochondrial",
# 22=>"Scenedesmus obliquus Mitochondrial",
# 23=>"Thraustochytrium Mitochondrial"}
# Return the names names for the ids specified in :range
definitions = parser.definitions :range => [(1..3), 5, 9]
# Return default hash map with custom names for the ids 1 and 3
definitions = parser.definitions :names => {1 => "Standard (Eukaryote)",
3 => "Yeast Mitochondorial"}
definitions[1]
# "Standard (Eukaryote)"
definitions[3]
# "Yeast Mitochondorial"
# Return the names for the ids specified in :range, with custom names for the ids 1 and 3
parser.definitions :range => [(1..3), 5, 9],
:names => {1 => "Standard (Eukaryote)",
3 => "Yeast Mitochondorial"}
parser = CodonTableParser.new
# Return default hash map of start codons
start_codons = parser.starts
start_codons
# {1=>["ttg", "ctg", "atg"],
# 2=>["att", "atc", "ata", "atg", "gtg"],
# 3=>["ata", "atg"],
# 4=>["tta", "ttg", "ctg", "att", "atc", "ata", "atg", "gtg"],
# 5=>["ttg", "att", "atc", "ata", "atg", "gtg"],
# 6=>["atg"],
# 9=>["atg", "gtg"],
# 10=>["atg"],
# 11=>["ttg", "ctg", "att", "atc", "ata", "atg", "gtg"],
# 12=>["ctg", "atg"],
# 13=>["ttg", "ata", "atg", "gtg"],
# 14=>["atg"],
# 15=>["atg"],
# 16=>["atg"],
# 21=>["atg", "gtg"],
# 22=>["atg"],
# 23=>["att", "atg", "gtg"]}
# Return the start codons for the ids specified in :range
start_codons = parser.starts :range => [(1..3), 5, 9]
# Add or remove start codons as necessary
start_codons = parser.starts 1 => {:add => ['gtg']},
13 => {:remove => ['ttg', 'ata', 'gtg']}
start_codons[1]
# ["ttg", "ctg", "atg", "gtg"]
start_codons[13]
# ["atg"]
# Alternative syntax, normally only used in the bundle method described below
start_codons = parser.starts :starts => {1 => {:add => ['gtg']},
13 => {:remove => ['ttg', 'ata', 'gtg']}}
# Return the start codons for the ids specified with :range, add or remove codons from specific ids
start_codons = parser.starts :range => [(1..3), 13],
1 => {:add => ['gtg']},
13 => {:remove => ['ttg', 'ata', 'gtg']}
parser = CodonTableParser.new
# Return the default hash map of stop codons
stop_codons = parser.stops
stops
# {1=>["taa", "tag", "tga"],
# 2=>["taa", "tag", "aga", "agg"],
# 3=>["taa", "tag"],
# 4=>["taa", "tag"],
# 5=>["taa", "tag"],
# 6=>["tga"],
# 9=>["taa", "tag"],
# 10=>["taa", "tag"],
# 11=>["taa", "tag", "tga"],
# 12=>["taa", "tag", "tga"],
# 13=>["taa", "tag"],
# 14=>["tag"],
# 15=>["taa", "tga"],
# 16=>["taa", "tga"],
# 21=>["taa", "tag"],
# 22=>["tca", "taa", "tga"],
# 23=>["tta", "taa", "tag", "tga"]}
# Return the stop codons for the ids specified with :range
stop_codons = parser.stops :range => [(1..3), 5, 9]
# Add or remove stop codons as necessary
stop_codons = parser.stops 1 => {:add => ['gtg'], :remove => ['taa']},
13 => {:add => ['gcc'], :remove => ['taa', 'tag']}
stop_codons[1]
# ["tag", "tga", "gtg"]
stop_codons[13]
# ["gcc"]
# Alternative syntax, normally only used in the bundle method described below
stop_codons = parser.stops :stops => {1 => {:add => ['gtg'], :remove => ['taa']},
13 => {:add => ['gcc'], :remove => ['taa', 'tag']}}
# Return the stop codons for the ids specified with :range, add or remove codons from specific ids
stop_codons = parser.stops :range => [(1..3), 5, 13],
1 => {:add => ['gtg'], :remove => ['taa']},
13 => {:add => ['gcc'], :remove => ['taa', 'tag']}
parser = CodonTableParser.new
# Return codon tables of all species
codon_tables = parser.tables
tables
# {
# 1 => {
# 'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
# 'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
# 'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
# 'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
#
# 'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
# 'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
# 'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
# 'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
#
# 'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
# 'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
# 'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
# 'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
#
# 'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
# 'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
# 'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
# 'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
# },
# 2 => { ... },
# 3 => { ... },
# ...
# 23 => { ... }
# }
# Return the codon tables for the ids specified with :range
codon_tables = parser.tables :range => [(1..3), 5, 9, 23]
parser = CodonTableParser.new
# Return the definitions, codon table, start and stop codons for all species as a hash map
bundle = parser.bundle
bundle
# {:definitions => {return value of the 'definitions' method}
# :starts => {return value of the 'starts' method}
# :stops => {return value of the 'stops' method}
# :tables => {return value of the 'tables' method}
# }
The bundle method accepts all options from the methods described above, that is:
To return the same values as are assigned to the constants DEFINITIONS, STARTS, STOPS, and TABLES of BioRuby's CodonTable class, calling bundle with the following options will do:
bundle = parser.bundle :names => {1 => "Standard (Eukaryote)",
4 => "Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma",
3 => "Yeast Mitochondorial",
6 => "Ciliate Macronuclear and Dasycladacean",
9 => "Echinoderm Mitochondrial",
11 => "Bacteria",
14 => "Flatworm Mitochondrial",
22 => "Scenedesmus obliquus mitochondrial"},
:starts => {1 => {:add => ['gtg']},
13 => {:remove => ['ttg', 'ata', 'gtg']}}
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We found that codon_table_parser demonstrated a not healthy version release cadence and project activity because the last version was released a year ago. It has 1 open source maintainer collaborating on the project.
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