taxgetup Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Get parents of taxon(s) Description taxgetup reads in one or more taxons, and reports the parent taxon. The taxon input may be a literal sequence or read from a database, file, file of taxon names, or even the command-line or the output of another programs. The taxon output can be written to screen, to file, or passed to another program. A wide range of standard taxon formats may be specified for input and output. Algorithm The NCBI taxonomy records the parent of each taxon, up to a known top level 1. Usage Here is a sample session with taxgetup % taxgetup ttax:9606 -oformat excel Get parents of taxon(s) Taxon output file [9606.excel]: Go to the input files for this example Go to the output files for this example Example 2 % taxgetup ttax:9606 -hidden -oformat excel Get parents of taxon(s) Taxon output file [9606.excel]: Go to the output files for this example Command line arguments Get parents of taxon(s) Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-taxons] taxon Taxon filename and optional format, or reference (input query) [-outfile] outtaxon (no help text) outtaxon value Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -hidden boolean [N] Show taxons hidden in GenBank Associated qualifiers: "-taxons" associated qualifiers -iformat1 string Input taxonomy format -idbname1 string User-provided database name "-outfile" associated qualifiers -odirectory2 string Output directory -oformat2 string Taxonomy output format General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format The input is a standard EMBOSS taxonomy query. The expected source of taxonomy information is the NCBI Taxonomy database "taxon" which is available as a standard database in all EMBOSS installations. Data can also be read from taxonomy output in "ncbi" format written by an EMBOSS application. See: http://emboss.sf.net/docs/themes/TaxonFormats.html for further information on taxon formats. Input files for usage example 'ttax:9606' is a sequence entry in the example taxonomy database 'ttax' Database entry: ttax:9606 id: 9606 parent: 9605 rank: species emblprefix: HS division: 5 divflag: 1 gencode: 1 gcflag: 1 mitocode: 2 mgcflag 1 hidden: 1 nosequence: 1 scientific name: Homo sapiens authority: Homo sapiens Linnaeus, 1758 genbank common name: human common name: man Output file format The output is a standard EMBOSS taxon file. The results can be output in one of several styles by using the command-line qualifier -oformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: ncbi, ebi, tax, excel. See: http://emboss.sf.net/docs/themes/TaxonFormats.html for further information on taxon formats. Output files for usage example File: 9606.excel 9605 207598 genus N Homo 9604 314295 family N Hominidae 9526 314293 parvorder N Catarrhini 376913 9443 suborder N Haplorrhini 9443 314146 order N Primates 314146 9347 superorder N Euarchontoglires 9347 32525 no rank N Eutheria 40674 32524 class N Mammalia 117571 117570 no rank N Euteleostomi 7742 89593 no rank N Vertebrata 89593 7711 subphylum N Craniata 7711 33511 phylum N Chordata 33208 33154 kingdom N Metazoa 2759 131567 superkingdom N Eukaryota Output files for usage example 2 File: 9606.excel 9605 207598 genus N Homo 207598 9604 subfamily Y Homininae 9604 314295 family N Hominidae 314295 9526 superfamily Y Hominoidea 9526 314293 parvorder N Catarrhini 314293 376913 infraorder Y Simiiformes 376913 9443 suborder N Haplorrhini 9443 314146 order N Primates 314146 9347 superorder N Euarchontoglires 9347 32525 no rank N Eutheria 32525 40674 no rank Y Theria 40674 32524 class N Mammalia 32524 32523 no rank Y Amniota 32523 8287 no rank Y Tetrapoda 8287 117571 no rank Y Sarcopterygii 117571 117570 no rank N Euteleostomi 117570 7776 no rank Y Teleostomi 7776 7742 superclass Y Gnathostomata 7742 89593 no rank N Vertebrata 89593 7711 subphylum N Craniata 7711 33511 phylum N Chordata 33511 33316 no rank Y Deuterostomia 33316 33213 no rank Y Coelomata 33213 6072 no rank Y Bilateria 6072 33208 no rank Y Eumetazoa 33208 33154 kingdom N Metazoa 33154 2759 no rank Y Fungi/Metazoa group 2759 131567 superkingdom N Eukaryota 131567 1 no rank Y cellular organisms Data files The NCBI Taxonomy Ontology is included in EMBOSS as local database taxon. Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description taxget Get taxon(s) taxgetdown Get descendants of taxon(s) taxgetrank Get parents of taxon(s) taxgetspecies Get all species under taxon(s) Author(s) Peter Rice European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None