goat-cli 0.2.5

Query metadata for any species across the tree of life.
Documentation
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var searchIndex = JSON.parse('{\
"goat_cli":{"doc":"<code>goat-cli</code> is a command line interface to query the Genomes 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search index.","The current version of the GoaT API.","The current GoaT URL.","The base URL for GoaT.","The indexes we make searches over in GoaT.","tax_lineage() returns all of the nodes from a given taxon …","tax_name() returns only the taxon of interest.","The taxonomy that <code>goat-cli</code> uses.","The type of result to return in GoaT.","Taxon search index. The historical main functionality of …","tax_tree() returns a node and all of its descendants.","Upper limit for the number of entries in the file for CLI …","Upper limit for the CLI arg <code>--size</code>.","","","","","","","","","","","","","","","","","","","","","Query the GoaT count API.","","","","","","Implement <code>fmt::Display</code> for <code>IndexType</code> so we can use …","","Implement <code>fmt::Display</code> for <code>TaxType</code> so we can use …","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Query the GoaT lookup API.","A module to produce a progress bar.","Query the GoaT record API.","Query the GoaT search API.","","","","","","","","","","","","","","","","","","","","","","","Collection of utility functions used elsewhere.","","","","","","","<code>goat-cli count</code> presents an identical CLI to <code>goat-cli search</code>…","The inner structs used in lookup.","Main entry point for <code>goat-cli lookup</code>.","The assembly counterpart to the above function.","As the taxon and assembly return JSON’s are in different …","The assembly results.","Collect the results from concurrent <code>goat-cli taxon lookup</code> …","A wrapper so we can return the same from our request. …","The lookup struct","A vector of <code>Lookup</code> structs.","The taxon results.","Collect the results from concurrent <code>goat-cli taxon lookup</code> …","","","","","","","","","","","","","","","","","The entries in <code>Lookups</code>.","","","Took this out of <code>print_result</code> as","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","The identifiers, which is an enumeration of all of the …","The index type, currently taxon or assembly","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","From our lookup struct we can make an individual URL.","Make URLs calls <code>Lookup::make_url</code> on each element.","Constructor which takes the CLI args and returns <code>Self</code>.","Print the result from a collector struct. add an index, so …","Print the result from a collector struct. add an index, so …","the users search","User search value.","User search value.","The size for each search (default = 10)","The suggestions vector.","The suggestions vector.","The taxon id that we fetch. Can return multiple taxon id’…","The taxon id that we fetch. Can return multiple taxon id’…","A vector of optional taxon names.","The taxon rank.","","","","","","","","","","","","","","","","","","","","","","","","","","Adds a progress bar to large requests.","Fetch the corresponding report from the GoaT API.","Module providing parsing functionality for GoaT reports.","CLI entry point to get the Newick file from the GoaT API.","A histogram binned by category.","A histogram, which is a single variable binned.","A Newick text string.","The x or y options for a returned table.","The record struct to make URLs from.","The record type to return.","The scale types that are possible in GoaT reports (I …","A scatterplot, requiring two variables.","","","","","","","","The category. Required for CategoricalHistogram.","","","","","","Implement <code>fmt::Display</code> for <code>ReportType</code> so we can use …","","Implement <code>fmt::Display</code> for <code>Opts</code> so we can use <code>.to_string()</code> …","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","A function to construct the report URL for any kind of …","","","Constructor function for <code>Report</code>.","The rank of the return type. Default from CLI is species.","The type of the report; tree or table.","","A vector of taxon ID’s/names.","The size of the result to return","Taxon type: tax_tree or tax_name","","","","","","","","Try and parse a string of options into the CLI.","","","","","","","","","","The x value","x options. Always optional.","The y value. Required for Scatterplot.","The y options. Always optional.","Execute the <code>search</code> subcommand from <code>goat-cli</code>. Print a TSV.","Parse the command line arguments for <code>goat-cli search</code> and …","Parse an expression from the <code>-e</code> flag from the CLI.","Parse taxon ranks from the <code>--tax-ranks</code> from the CLI.","Generate the URLs from the CLI.","Utility functions used across <code>goat-cli</code>.","Stored data for each of the variables used in <code>goat-cli</code>. …","Parse variables on the CLI from the <code>-v</code> flag.","Take CLI arguments and parse them. Return a tuple of:","","The CLI expression which needs to be parsed.","","The column headers for <code>goat-cli search --print-expression</code>.","A date.","Kind of an option alias. Does a particular variable have a …","Half precision 16 bit float.","Signed 32 bit int.","A variable which itself is an enumeration.","Signed 64 bit int.","","None to catch parsing errors","Float with one decimal place.","Signed 16 bit int.","","Split a string and keep the delimiter. Thanks <code>BurntSushi</code>","","Float with two decimal places.","Serialize GoaT variables into their types.","","The GoaT variable of interest.","","","","","","","","","","","","","","","","Check the values input by a user, so <code>goat-cli</code> displays …","","","","","","","","","","","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","","","","","","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","","","","Constructor for <code>CLIexpression</code>.","","","The main function which parses a <code>CLIexpression</code>. A bit of a …","Print the table of GoaT variable data.","","The initial split on the keyword <code>AND</code>.","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","Taken from the NCBI taxdump on the date: 22.02.22.","The <code>TaxRanks</code> struct holds the NCBI taxon ranks defined in …","","","Format <code>TaxRanks</code> into a comma separated list.","Returns the argument unchanged.","Constructor for <code>TaxRanks</code>.","Calls <code>U::from(self)</code>.","Convert a <code>--tax-rank</code> CLI comma separated string into a URL …","","","","","","","Boolean struct containing all of the CLI flag information …","Assembly span and level.","BlobToolKit stats(?). No hit/target.","BUSCO completeness, lineage and string.","All the contig information.","GC content.","Gene and non-coding gene count.","Only chromosome count.","All scaffold information.","","","A function which formats all of the GoaT fields together …","","","Format an expression put into the <code>-e</code> flag on the CLI.","If names appears in <code>FieldBuilder</code>, then we add the GoaT URL …","Function to format the rank into a GoaT URL segment.","Returns the argument unchanged.","An implementation of exculding values returned if they are …","Calls <code>U::from(self)</code>.","The function which creats the GoaT API URLs which are then …","Add only assembly level/span GoaT fields.","Add bioproject GoaT field.","Add BUSCO completeness.","Add country list GoaT field.","Add C-value information GoaT field.","Add assembly &amp; EBP metric date GoaT fields.","Add GC percent GoaT field.","Add gene count GoaT field.","Add genome size GoaT fields.","Add karyotype GoaT fields; chromosome number and haploid …","Add return information for <code>isb_wildlife_act_1976</code>, …","Add mitochondrial assembly span and gc percent GoaT fields.","Add contig and scaffold n50 GoaT fields.","Add synonym, tolID, and common name GoaT fields.","Add plastid assembly span and gc percent GoaT fields.","Add ploidy GoaT field.","Add sex determination GoaT field.","Add sample tracking information GoaT field.","Add <code>long_list</code>, <code>other_priority</code>, and <code>family_representative</code> …","Render output in tidy format?","","A function to turn all of the fields into a small data …","","","","","Shamelessly poached from the Nushell core code. Suggest …","If multiple taxa are queried at once, headers will return …","Determine from the CLI matches how many URLs are needing …","Creates a vector of taxon ranks which will eventually form …","Compute the Levenshtein distance between two strings. …","Read NCBI taxon ID’s or binomial names of species, or …","Parse a comma separated string and return each of the …","Thanks to  <code>this</code> post on stack overflow. For error messages …","Thanks to this post on stack overflow. Make a string …","A function to replace certain combinations of characters …","Automatically generated GoaT variable data from a Bash …","Automatically generated GoaT variable data from a Bash …","","","","","","","Makes a static <code>BTreeMap</code> from the input of …","","","Returns the argument unchanged.","Returns the argument unchanged.","Calls <code>U::from(self)</code>.","Calls <code>U::from(self)</code>.","","","","","","","","","A struct to store the variables passed in the <code>-v</code> flag on …","","","Returns the argument unchanged.","Calls <code>U::from(self)</code>.","Constructor for <code>Variables</code>.","Simple parsing of a comma separated string, which will …","Parse a variable name into a string which will be entered …","Parse a single variable. Used in report until something …","","","","Variables which need to be 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