drfindformat |
Please help by correcting and extending the Wiki pages.
The -sensitive qualifier also searches the definition strings.
The set of EDAM terms are then compared to entries in the Data Resource Catalogue, searching the 'efmt' EDAM format index.
% drfindformat fasta Find public databases by format Data resource output file [drfindformat.drcat]: |
Go to the output files for this example
Find public databases by format Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-query] string List of EDAM data keywords (Any string) [-outfile] outresource [*.drfindformat] Output data resource file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -sensitive boolean [N] By default, the query keywords are matched against the EDAM term names (and synonyms) only. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches. -[no]subclasses boolean [Y] Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type. Associated qualifiers: "-outfile" associated qualifiers -odirectory2 string Output directory -oformat2 string Data resource 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 |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-query] (Parameter 1) |
string | List of EDAM data keywords | Any string | |
[-outfile] (Parameter 2) |
outresource | Output data resource file name | Data resource entry | <*>.drfindformat |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-sensitive | boolean | By default, the query keywords are matched against the EDAM term names (and synonyms) only. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches. | Boolean value Yes/No | No |
-[no]subclasses | boolean | Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type. | Boolean value Yes/No | Yes |
Associated qualifiers | ||||
"-outfile" associated outresource qualifiers | ||||
-odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
-oformat2 -oformat_outfile |
string | Data resource output format | Any string | |
General qualifiers | ||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N |
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
-warning | boolean | Report warnings | Boolean value Yes/No | Y |
-error | boolean | Report errors | Boolean value Yes/No | Y |
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
-die | boolean | Report dying program messages | Boolean value Yes/No | Y |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
The output is a standard EMBOSS resource 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: drcat, basic, wsbasic, list.
See: http://emboss.sf.net/docs/themes/ResourceFormats.html for further information on resource formats.
ID UniProtKB_Swiss-Prot IDalt SwissProt Name Universal protein resource knowledge base / Swiss-Prot Desc Section of the UniProt knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature URL http://www.uniprot.org Taxon 1 | all EDAMtpc 0639 | Protein sequence analysis EDAMdat 2201 | Sequence record full EDAMid 3021 | UniProt accession EDAMfmt 1929 | FASTA format EDAMfmt 2376 | RDF EDAMfmt 2331 | HTML EDAMfmt 2332 | XML Xref EMBL_explicit | UniProt accession Query Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s Query Sequence record full | Text | 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.uniprot.org/uniprot/%s.fasta Example UniProt accession | P12345 ID UniProtKB_TrEMBL IDalt TrEMBL Name Universal protein resource knowledge base / Swiss-Prot Desc Section of the UniProt knowledgebase, containing computationally analysed records waiting for full manual annotation URL http://www.uniprot.org/ Taxon 1 | all EDAMtpc 0639 | Protein sequence analysis EDAMdat 2201 | Sequence record full EDAMid 3021 | UniProt accession EDAMfmt 1929 | FASTA format EDAMfmt 2376 | RDF EDAMfmt 2331 | HTML EDAMfmt 2332 | XML Xref SP_FT | None Query Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s Query Sequence record full | Text | 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.uniprot.org/uniprot/%s.fasta Example UniProt accession | Q00177 ID Ensembl Acc DB-0023 Name Ensembl eukaryotic genome annotation project Desc Genome databases for vertebrates and other eukaryotic species. URL http://www.ensembl.org/ Cat Genome annotation databases Taxon 33208 | Metazoa EDAMtpc 2818 | Eukaryotes [Part of this file has been deleted for brevity] 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.uniprot.org/uniprot/%s.fasta Example UniProt accession | P12345 ID dbEST Name dbEST database of EST sequences Desc dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. URL http://www.ncbi.nlm.nih.gov/dbEST/ Cat Not available Taxon 1 | all EDAMtpc 0655 | mRNA, EST or cDNA EDAMdat 0849 | Sequence record EDAMid 2314 | GI number EDAMid 1105 | dbEST accession EDAMfmt 2310 | FASTA-HTML EDAMfmt 2532 | GenBank-HTML EDAMfmt 2331 | HTML Xref SP_FT | None Query Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank Query Sequence record | HTML {est} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est Query Sequence record | HTML {docsum} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum Query Sequence record | FASTA-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta Query Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank Query Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank Query Sequence record | HTML {est} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est Query Sequence record | HTML {docsum} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum Query Sequence record | FASTA-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta Query Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank Example dbEST accession | f12345 Example GI number | 706694 ID REDIdb Name RNA editing database (REDIdb) Desc Sequences post-transcriptionally modified by RNA editing from primary databases and literature. All editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored. URL http://biologia.unical.it/py_script/overview.html Taxon 1 | all EDAMtpc 0114 | Gene structure and RNA splicing EDAMdat 2043 | Sequence record lite EDAMdat 1383 | Sequence alignment (nucleic acid) EDAMid 2781 | REDIdb ID EDAMfmt 2310 | FASTA-HTML EDAMfmt 2331 | HTML Query Sequence record lite {REDIdb entry} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/retrieve.py?query=%s Query Sequence record lite {REDIdb fasta} | FASTA-HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/fasta.py?query=%s Query Sequence alignment (nucleic acid) {REDIdb overview} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/display.py?query=%s Query Sequence alignment (nucleic acid) {REDIdb alignment} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/align.py?query=%s Example REDIdb ID | EDI_000000002 |
Program name | Description |
---|---|
drfinddata | Find public databases by data type |
drfindid | Find public databases by identifier |
drfindresource | Find public databases by resource |
drget | Get data resource entries |
drtext | Get data resource entries complete text |
edamdef | Find EDAM ontology terms by definition |
edamhasinput | Find EDAM ontology terms by has_input relation |
edamhasoutput | Find EDAM ontology terms by has_output relation |
edamisformat | Find EDAM ontology terms by is_format_of relation |
edamisid | Find EDAM ontology terms by is_identifier_of relation |
edamname | Find EDAM ontology terms by name |
wossdata | Find programs by EDAM data |
wossinput | Find programs by EDAM input data |
wossoperation | Find programs by EDAM operation |
wossoutput | Find programs by EDAM output data |
wossparam | Find programs by EDAM parameter |
wosstopic | Find programs by EDAM topic |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.