drtext 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 data resource entries complete text Description drtext reads one or more complete data resource entries from a database or a file and writes them to a text file. Optionally, the first data resourcefrom the input stream only can be retrieved. The complete entry, including heading annotation, is retrieved and written and the data is not altered or reformatted in any way. Usage Here is a sample session with drtext % drtext drcat:uniprot Get data resource entries complete text Full text output file [uniprot.drtext]: Go to the input files for this example Go to the output files for this example Command line arguments Get data resource entries complete text Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-resources] resource Data resource filename and optional format, or reference (input query) [-outfile] outfile [*.drtext] Full text output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-resources" associated qualifiers -iformat1 string Input resource format -idbname1 string User-provided database name "-outfile" associated qualifiers -odirectory2 string Output directory 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 resource query. The expected source of data resource information is the Data Resource Catalogue database "drcat" which is available as a standard database in all EMBOSS installations. Data can also be read from resource output in "drcat" format written by an EMBOSS application. Input files for usage example Database entry: drcat:uniprot ID UniProt IDalt UniProtKB Name Universal protein resource Desc A comprehensive, high-quality and freely accessible resource of protein sequence and functional information. URL http://www.uniprot.org/ Taxon 1 | all EDAMtpc 0000639 | Protein sequences EDAMdat 0002201 | Sequence record full EDAMid 0003021 | UniProt accession EDAMfmt 0001929 | FASTA format EDAMfmt 0002376 | RDF EDAMfmt 0002188 | uniprot EDAMfmt 0002331 | HTML EDAMfmt 0002332 | XML Xref SP_FT | None Query Sequence record full | HTML | UniProt accession | http://www.uniprot.or g/uniprot/%s Query Sequence record full | uniprot | UniProt accession | http://www.uniprot .org/uniprot/%s.txt Query Sequence record full | XML | UniProt accession | http://www.uniprot.org /uniprot/%s.xml Query Sequence record full | RDF | UniProt accession | http://www.uniprot.org /uniprot/%s.rdf Query Sequence record full | FASTA format | UniProt accession | http://www.un iprot.org/uniprot/%s.fasta Example UniProt accession | P12345 Output file format drtext reports the full text of the input resources. Output files for usage example File: uniprot.drtext ID UniProt IDalt UniProtKB Name Universal protein resource Desc A comprehensive, high-quality and freely accessible resource of protein sequence and functional information. URL http://www.uniprot.org/ Taxon 1 | all EDAMtpc 0000639 | Protein sequences EDAMdat 0002201 | Sequence record full EDAMid 0003021 | UniProt accession EDAMfmt 0001929 | FASTA format EDAMfmt 0002376 | RDF EDAMfmt 0002188 | uniprot EDAMfmt 0002331 | HTML EDAMfmt 0002332 | XML Xref SP_FT | None Query Sequence record full | HTML | UniProt accession | http://www.uniprot.org /uniprot/%s Query Sequence record full | uniprot | UniProt accession | http://www.uniprot. org/uniprot/%s.txt Query Sequence record full | XML | UniProt accession | http://www.uniprot.org/ uniprot/%s.xml Query Sequence record full | RDF | UniProt accession | http://www.uniprot.org/ uniprot/%s.rdf Query Sequence record full | FASTA format | UniProt accession | http://www.uni prot.org/uniprot/%s.fasta Example UniProt accession | P12345 Data files The Data Resource Catalogue is included in EMBOSS as local database drcat. 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 drfinddata Find public databases by data type drfindformat Find public databases by format drfindid Find public databases by identifier drfindresource Find public databases by resource drget Get data resource entries entret Retrieves sequence entries from flatfile databases and files ontotext Get ontology term(s) original full text textget Get text data entries textsearch Search the textual description of sequence(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