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showdb |
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Function
Displays information on configured databasesDescription
showdb displays a table with the names, contents and access methods of the sequence databases configured for your EMBOSS installation.
Usage
Here is a sample session with showdbDisplay information on the currently available databases:
% showdb Displays information on configured databases # Name Type ID Qry All Comment # =============== ========== == === === ======= qapblast Protein OK OK OK BLAST swissnew qapblastall Protein OK OK OK BLAST swissnew, all fields indexed qapblastsplit Protein OK OK OK BLAST swissnew split in 5 files qapblastsplitexc Protein OK OK OK BLAST swissnew split in 5 files, not file 02 qapblastsplitinc Protein OK OK OK BLAST swissnew split in 5 files, only file 02 qapfasta Protein OK OK OK FASTA file swissnew entries qapflat Protein OK OK OK SpTrEmbl flatfile qapflatall Protein OK OK OK SpTrEmbl flatfiles, all fields indexed qapir Protein OK OK OK PIR qapirall Protein OK OK OK PIR qapirinc Protein OK OK OK PIR qapxfasta Protein OK OK OK FASTA file swissnew entries qapxflat Protein OK OK OK Swissnew flatfiles qaxpir Protein OK OK OK PIR qaxpirall Protein OK OK OK PIR qaxpirinc Protein OK OK OK PIR tpir Protein OK OK OK PIR using NBRF access for 4 files tsw Protein OK OK OK Swissprot native format with EMBL CD-ROM index tswnew Protein OK OK OK SpTrEmbl as 3 files in native format with EMBL CD-ROM index qanfasta Nucleotide OK OK OK FASTA file EMBL rodents qanfastaall Nucleotide OK OK OK FASTA file EMBL rodents, all fields indexed qanflat Nucleotide OK OK OK EMBL flatfiles qanflatall Nucleotide OK OK OK EMBL flatfiles qanflatexc Nucleotide OK OK OK EMBL flatfiles, no rodent file qanflatinc Nucleotide OK OK OK EMBL flatfiles, only rodent file qangcg Nucleotide OK OK OK GCG format EMBL qangcgall Nucleotide OK OK OK GCG format EMBL qangcgexc Nucleotide OK OK OK GCG format EMBL without prokaryotes qangcginc Nucleotide OK OK OK GCG format EMBL only prokaryotes qanxfasta Nucleotide OK OK OK FASTA file EMBL rodents qanxfastaall Nucleotide OK OK OK FASTA file EMBL rodents, all fields indexed qanxflat Nucleotide OK OK OK EMBL flatfiles qanxflatall Nucleotide OK OK OK EMBL flatfiles, all fields indexed qanxflatexc Nucleotide OK OK OK EMBL flatfiles, no rodent file qanxflatinc Nucleotide OK OK OK EMBL flatfiles, only rodent file qanxgcg Nucleotide OK OK OK GCG format EMBL qanxgcgall Nucleotide OK OK OK GCG format EMBL qanxgcgexc Nucleotide OK OK OK GCG format EMBL without prokaryotes qanxgcginc Nucleotide OK OK OK GCG format EMBL only prokaryotes qapirexc Nucleotide OK OK OK PIR qasrswww Nucleotide OK OK OK Remote SRS web server qawfasta Nucleotide OK OK OK FASTA file wormpep entries qawxfasta Nucleotide OK OK OK FASTA file wormpep entries qaxpirexc Nucleotide OK OK OK PIR tembl Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index temblall Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index temblrest Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index temblvrt Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index tensembldasgrch37 Nucleotide OK - - Homo_sapiens Reference server based on GRCh37 assembly testdb Nucleotide OK OK OK test sequence data tgb Nucleotide OK OK OK Genbank IDs tgenbank Nucleotide OK OK OK GenBank in native format with EMBL CD-ROM index tgenedashuman Nucleotide OK - - The Ensembl human Gene_ID reference source tflybase Features OK - - tgenedb Features OK - - ttax Taxonomy OK OK OK taxon Taxonomy OK OK OK drcat Resource OK OK OK tedam Obo OK OK OK EDAM using dbxedam test indexes tobo Obo OK OK OK EDAM using dbxobo test indexes eco Obo OK OK OK edam Obo OK OK OK go Obo OK OK OK pw Obo OK OK OK ro Obo OK OK OK so Obo OK OK OK |
Example 2
Write the results to a file:
% showdb -outfile showdb.out Displays information on configured databases |
Go to the output files for this example
Example 3
Display information on one explicit database:
% showdb -database tsw Displays information on configured databases # Name Type ID Qry All Comment # ============ ======= == === === ======= tsw Protein OK OK OK Swissprot native format with EMBL CD-ROM index |
Go to the input files for this example
Example 4
Display information on the databases formatted in HTML:
% showdb -html Displays information on configured databases
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Example 5
Display protein databases only:
% showdb -nonucleic Displays information on configured databases # Name Type ID Qry All Comment # =============== ========== == === === ======= qapblast Protein OK OK OK BLAST swissnew qapblastall Protein OK OK OK BLAST swissnew, all fields indexed qapblastsplit Protein OK OK OK BLAST swissnew split in 5 files qapblastsplitexc Protein OK OK OK BLAST swissnew split in 5 files, not file 02 qapblastsplitinc Protein OK OK OK BLAST swissnew split in 5 files, only file 02 qapfasta Protein OK OK OK FASTA file swissnew entries qapflat Protein OK OK OK SpTrEmbl flatfile qapflatall Protein OK OK OK SpTrEmbl flatfiles, all fields indexed qapir Protein OK OK OK PIR qapirall Protein OK OK OK PIR qapirinc Protein OK OK OK PIR qapxfasta Protein OK OK OK FASTA file swissnew entries qapxflat Protein OK OK OK Swissnew flatfiles qaxpir Protein OK OK OK PIR qaxpirall Protein OK OK OK PIR qaxpirinc Protein OK OK OK PIR tpir Protein OK OK OK PIR using NBRF access for 4 files tsw Protein OK OK OK Swissprot native format with EMBL CD-ROM index tswnew Protein OK OK OK SpTrEmbl as 3 files in native format with EMBL CD-ROM index tflybase Features OK - - tgenedb Features OK - - ttax Taxonomy OK OK OK taxon Taxonomy OK OK OK drcat Resource OK OK OK tedam Obo OK OK OK EDAM using dbxedam test indexes tobo Obo OK OK OK EDAM using dbxobo test indexes eco Obo OK OK OK edam Obo OK OK OK go Obo OK OK OK pw Obo OK OK OK ro Obo OK OK OK so Obo OK OK OK |
Example 6
Display the information with no headings:
% showdb -noheading Displays information on configured databases qapblast Protein OK OK OK BLAST swissnew qapblastall Protein OK OK OK BLAST swissnew, all fields indexed qapblastsplit Protein OK OK OK BLAST swissnew split in 5 files qapblastsplitexc Protein OK OK OK BLAST swissnew split in 5 files, not file 02 qapblastsplitinc Protein OK OK OK BLAST swissnew split in 5 files, only file 02 qapfasta Protein OK OK OK FASTA file swissnew entries qapflat Protein OK OK OK SpTrEmbl flatfile qapflatall Protein OK OK OK SpTrEmbl flatfiles, all fields indexed qapir Protein OK OK OK PIR qapirall Protein OK OK OK PIR qapirinc Protein OK OK OK PIR qapxfasta Protein OK OK OK FASTA file swissnew entries qapxflat Protein OK OK OK Swissnew flatfiles qaxpir Protein OK OK OK PIR qaxpirall Protein OK OK OK PIR qaxpirinc Protein OK OK OK PIR tpir Protein OK OK OK PIR using NBRF access for 4 files tsw Protein OK OK OK Swissprot native format with EMBL CD-ROM index tswnew Protein OK OK OK SpTrEmbl as 3 files in native format with EMBL CD-ROM index qanfasta Nucleotide OK OK OK FASTA file EMBL rodents qanfastaall Nucleotide OK OK OK FASTA file EMBL rodents, all fields indexed qanflat Nucleotide OK OK OK EMBL flatfiles qanflatall Nucleotide OK OK OK EMBL flatfiles qanflatexc Nucleotide OK OK OK EMBL flatfiles, no rodent file qanflatinc Nucleotide OK OK OK EMBL flatfiles, only rodent file qangcg Nucleotide OK OK OK GCG format EMBL qangcgall Nucleotide OK OK OK GCG format EMBL qangcgexc Nucleotide OK OK OK GCG format EMBL without prokaryotes qangcginc Nucleotide OK OK OK GCG format EMBL only prokaryotes qanxfasta Nucleotide OK OK OK FASTA file EMBL rodents qanxfastaall Nucleotide OK OK OK FASTA file EMBL rodents, all fields indexed qanxflat Nucleotide OK OK OK EMBL flatfiles qanxflatall Nucleotide OK OK OK EMBL flatfiles, all fields indexed qanxflatexc Nucleotide OK OK OK EMBL flatfiles, no rodent file qanxflatinc Nucleotide OK OK OK EMBL flatfiles, only rodent file qanxgcg Nucleotide OK OK OK GCG format EMBL qanxgcgall Nucleotide OK OK OK GCG format EMBL qanxgcgexc Nucleotide OK OK OK GCG format EMBL without prokaryotes qanxgcginc Nucleotide OK OK OK GCG format EMBL only prokaryotes qapirexc Nucleotide OK OK OK PIR qasrswww Nucleotide OK OK OK Remote SRS web server qawfasta Nucleotide OK OK OK FASTA file wormpep entries qawxfasta Nucleotide OK OK OK FASTA file wormpep entries qaxpirexc Nucleotide OK OK OK PIR tembl Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index temblall Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index temblrest Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index temblvrt Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index tensembldasgrch37 Nucleotide OK - - Homo_sapiens Reference server based on GRCh37 assembly testdb Nucleotide OK OK OK test sequence data tgb Nucleotide OK OK OK Genbank IDs tgenbank Nucleotide OK OK OK GenBank in native format with EMBL CD-ROM index tgenedashuman Nucleotide OK - - The Ensembl human Gene_ID reference source tflybase Features OK - - tgenedb Features OK - - ttax Taxonomy OK OK OK taxon Taxonomy OK OK OK drcat Resource OK OK OK tedam Obo OK OK OK EDAM using dbxedam test indexes tobo Obo OK OK OK EDAM using dbxobo test indexes eco Obo OK OK OK edam Obo OK OK OK go Obo OK OK OK pw Obo OK OK OK ro Obo OK OK OK so Obo OK OK OK |
Example 7
Display just a list of the available database names:
% showdb -noheading -notype -noid -noquery -noall -nocomment -auto qapblast qapblastall qapblastsplit qapblastsplitexc qapblastsplitinc qapfasta qapflat qapflatall qapir qapirall qapirinc qapxfasta qapxflat qaxpir qaxpirall qaxpirinc tpir tsw tswnew qanfasta qanfastaall qanflat qanflatall qanflatexc qanflatinc qangcg qangcgall qangcgexc qangcginc qanxfasta qanxfastaall qanxflat qanxflatall qanxflatexc qanxflatinc qanxgcg qanxgcgall qanxgcgexc qanxgcginc qapirexc qasrswww qawfasta qawxfasta qaxpirexc tembl temblall temblrest temblvrt tensembldasgrch37 testdb tgb tgenbank tgenedashuman tflybase tgenedb ttax taxon drcat tedam tobo eco edam go pw ro so |
Example 8
Display only the names and types:
% showdb -only -type Displays information on configured databases qapblast Protein qapblastall Protein qapblastsplit Protein qapblastsplitexc Protein qapblastsplitinc Protein qapfasta Protein qapflat Protein qapflatall Protein qapir Protein qapirall Protein qapirinc Protein qapxfasta Protein qapxflat Protein qaxpir Protein qaxpirall Protein qaxpirinc Protein tpir Protein tsw Protein tswnew Protein qanfasta Nucleotide qanfastaall Nucleotide qanflat Nucleotide qanflatall Nucleotide qanflatexc Nucleotide qanflatinc Nucleotide qangcg Nucleotide qangcgall Nucleotide qangcgexc Nucleotide qangcginc Nucleotide qanxfasta Nucleotide qanxfastaall Nucleotide qanxflat Nucleotide qanxflatall Nucleotide qanxflatexc Nucleotide qanxflatinc Nucleotide qanxgcg Nucleotide qanxgcgall Nucleotide qanxgcgexc Nucleotide qanxgcginc Nucleotide qapirexc Nucleotide qasrswww Nucleotide qawfasta Nucleotide qawxfasta Nucleotide qaxpirexc Nucleotide tembl Nucleotide temblall Nucleotide temblrest Nucleotide temblvrt Nucleotide tensembldasgrch37 Nucleotide testdb Nucleotide tgb Nucleotide tgenbank Nucleotide tgenedashuman Nucleotide tflybase Features tgenedb Features ttax Taxonomy taxon Taxonomy drcat Resource tedam Obo tobo Obo eco Obo edam Obo go Obo pw Obo ro Obo so Obo |
Example 9
Display everything
% showdb -full Displays information on configured databases # Name Type ID Qry All Method Fields Defined Release Comment # =============== ========== == === === ========= ============================================================================================== ======== ======= ======= qapblast Protein OK OK OK blast - special BLAST swissnew qapblastall Protein OK OK OK blast sv,des special BLAST swissnew, all fields indexed qapblastsplit Protein OK OK OK blast - special BLAST swissnew split in 5 files qapblastsplitexc Protein OK OK OK blast - special BLAST swissnew split in 5 files, not file 02 qapblastsplitinc Protein OK OK OK blast - special BLAST swissnew split in 5 files, only file 02 qapfasta Protein OK OK OK emblcd - special FASTA file swissnew entries qapflat Protein OK OK OK emblcd - special SpTrEmbl flatfile qapflatall Protein OK OK OK emblcd sv,des,org,key special SpTrEmbl flatfiles, all fields indexed qapir Protein OK OK OK gcg - special PIR qapirall Protein OK OK OK gcg des,org,key special PIR qapirinc Protein OK OK OK gcg - special PIR qapxfasta Protein OK OK OK emboss - special FASTA file swissnew entries qapxflat Protein OK OK OK emboss - special Swissnew flatfiles qaxpir Protein OK OK OK embossgcg - special PIR qaxpirall Protein OK OK OK embossgcg des,org,key special PIR qaxpirinc Protein OK OK OK embossgcg - special PIR tpir Protein OK OK OK gcg des,org,key special PIR using NBRF access for 4 files tsw Protein OK OK OK emblcd id,acc,sv,des,org,key special 36 Swissprot native format with EMBL CD-ROM index tswnew Protein OK OK OK emblcd sv,des,org,key special 37 SpTrEmbl as 3 files in native format with EMBL CD-ROM index qanfasta Nucleotide OK OK OK emblcd - special FASTA file EMBL rodents qanfastaall Nucleotide OK OK OK emblcd sv,des special FASTA file EMBL rodents, all fields indexed qanflat Nucleotide OK OK OK emblcd - special EMBL flatfiles qanflatall Nucleotide OK OK OK emblcd - special EMBL flatfiles qanflatexc Nucleotide OK OK OK emblcd - special EMBL flatfiles, no rodent file qanflatinc Nucleotide OK OK OK emblcd - special EMBL flatfiles, only rodent file qangcg Nucleotide OK OK OK gcg - special GCG format EMBL qangcgall Nucleotide OK OK OK gcg sv,des,org,key special GCG format EMBL qangcgexc Nucleotide OK OK OK gcg - special GCG format EMBL without prokaryotes qangcginc Nucleotide OK OK OK gcg - special GCG format EMBL only prokaryotes qanxfasta Nucleotide OK OK OK emboss - special FASTA file EMBL rodents qanxfastaall Nucleotide OK OK OK emboss sv,des special FASTA file EMBL rodents, all fields indexed qanxflat Nucleotide OK OK OK emboss - special EMBL flatfiles qanxflatall Nucleotide OK OK OK emboss des,org,key special EMBL flatfiles, all fields indexed qanxflatexc Nucleotide OK OK OK emboss - special EMBL flatfiles, no rodent file qanxflatinc Nucleotide OK OK OK emboss - special EMBL flatfiles, only rodent file qanxgcg Nucleotide OK OK OK embossgcg - special GCG format EMBL qanxgcgall Nucleotide OK OK OK embossgcg sv,des,org,key special GCG format EMBL qanxgcgexc Nucleotide OK OK OK embossgcg - special GCG format EMBL without prokaryotes qanxgcginc Nucleotide OK OK OK embossgcg - special GCG format EMBL only prokaryotes qapirexc Nucleotide OK OK OK gcg - special PIR qasrswww Nucleotide OK OK OK srswww sv,des,org,key special Remote SRS web server qawfasta Nucleotide OK OK OK emblcd - special FASTA file wormpep entries qawxfasta Nucleotide OK OK OK emboss - special FASTA file wormpep entries qaxpirexc Nucleotide OK OK OK embossgcg - special PIR tembl Nucleotide OK OK OK emblcd sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM index temblall Nucleotide OK OK OK direct sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM index temblrest Nucleotide OK OK OK direct sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM index temblvrt Nucleotide OK OK OK direct sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM index tensembldasgrch37 Nucleotide OK - - das - special Homo_sapiens Reference server based on GRCh37 assembly testdb Nucleotide OK OK OK emblcd des special 01 test sequence data tgb Nucleotide OK OK OK srswww sv,des,org,key special Genbank IDs tgenbank Nucleotide OK OK OK emblcd sv,des,org,key special 01 GenBank in native format with EMBL CD-ROM index tgenedashuman Nucleotide OK - - das - special The Ensembl human Gene_ID reference source tflybase Features OK - - chado(id) uniquename special tgenedb Features OK - - chado(id) uniquename special ttax Taxonomy OK OK OK embosstax id,acc,nam,rnk,up,gc,mgc special taxon Taxonomy OK OK OK embosstax id,acc,tax,rnk,up,gc,mgc standard drcat Resource OK OK OK emboss id,acc,nam,des,url,cat,edat,efmt,eid,etpc,xref,qout,qfmt,qin,qurl,cc,rest,soap,stat,xref,taxid standard tedam Obo OK OK OK emboss id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc special beta11 EDAM using dbxedam test indexes tobo Obo OK OK OK emboss id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc special beta11 EDAM using dbxobo test indexes eco Obo OK OK OK emboss id,acc,nam,isa,des standard edam Obo OK OK OK emboss id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc standard go Obo OK OK OK emboss id,acc,nam,isa,des,ns standard pw Obo OK OK OK emboss id,acc,nam,isa,des standard ro Obo OK OK OK emboss id,acc,nam,isa,des standard so Obo OK OK OK emboss id,acc,nam,isa,des standard |
Command line arguments
Displays information on configured databases
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers: (none)
Additional (Optional) qualifiers:
-database string Name of a single database to give
information on (Any string)
-html boolean [N] Format output as an HTML table
-[no]protein boolean [Y] Display protein databases
-[no]nucleic boolean [Y] Display nucleotide databases
-[no]sequence boolean [Y] Display general sequence databases
-[no]feature boolean [Y] Display feature annotation databases
-[no]text boolean [Y] Display text databases
-[no]taxonomy boolean [Y] Display taxonomy databases
-[no]resource boolean [Y] Display resource databases
-[no]assembly boolean [Y] Display sequence assembly databases
-[no]obo boolean [Y] Display obo bio-ontology databases
-full boolean [N] Display all columns
-methods boolean [$(full)] This displays the access methods
that can be used on this database, for all,
query or ID access
-fields boolean [$(full)] This displays the search fields
that can be used on this database, other
than the standard 'id' or 'acc' fields.
-defined boolean [$(full)] This displays a short name for the
file containing the database definition
-release boolean [$(full)] Display 'release' column
-outfile outfile [stdout] Output file name
Advanced (Unprompted) qualifiers:
-only toggle [N] This is a way of shortening the command
line if you only want a few standard columns
to be displayed. Instead of specifying:
'-nohead -notype -noid -noquery -noall'
to get only the comment output, you can
specify
'-only -comment'
-heading boolean [@(!$(only))] Display column headings
-type boolean [@(!$(only))] Display 'type' column
-id boolean [@(!$(only))] Display 'id' column
-query boolean [@(!$(only))] Display 'qry' column
-all boolean [@(!$(only))] Display 'all' column
-comment boolean [@(!$(only))] Display 'comment' column
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory 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
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| (none) | ||||
| Additional (Optional) qualifiers | ||||
| -database | string | Name of a single database to give information on | Any string | |
| -html | boolean | Format output as an HTML table | Boolean value Yes/No | No |
| -[no]protein | boolean | Display protein databases | Boolean value Yes/No | Yes |
| -[no]nucleic | boolean | Display nucleotide databases | Boolean value Yes/No | Yes |
| -[no]sequence | boolean | Display general sequence databases | Boolean value Yes/No | Yes |
| -[no]feature | boolean | Display feature annotation databases | Boolean value Yes/No | Yes |
| -[no]text | boolean | Display text databases | Boolean value Yes/No | Yes |
| -[no]taxonomy | boolean | Display taxonomy databases | Boolean value Yes/No | Yes |
| -[no]resource | boolean | Display resource databases | Boolean value Yes/No | Yes |
| -[no]assembly | boolean | Display sequence assembly databases | Boolean value Yes/No | Yes |
| -[no]obo | boolean | Display obo bio-ontology databases | Boolean value Yes/No | Yes |
| -full | boolean | Display all columns | Boolean value Yes/No | No |
| -methods | boolean | This displays the access methods that can be used on this database, for all, query or ID access | Boolean value Yes/No | $(full) |
| -fields | boolean | This displays the search fields that can be used on this database, other than the standard 'id' or 'acc' fields. | Boolean value Yes/No | $(full) |
| -defined | boolean | This displays a short name for the file containing the database definition | Boolean value Yes/No | $(full) |
| -release | boolean | Display 'release' column | Boolean value Yes/No | $(full) |
| -outfile | outfile | Output file name | Output file | stdout |
| Advanced (Unprompted) qualifiers | ||||
| -only | toggle | This is a way of shortening the command line if you only want a few standard columns to be displayed. Instead of specifying: '-nohead -notype -noid -noquery -noall' to get only the comment output, you can specify '-only -comment' | Toggle value Yes/No | No |
| -heading | boolean | Display column headings | Boolean value Yes/No | @(!$(only)) |
| -type | boolean | Display 'type' column | Boolean value Yes/No | @(!$(only)) |
| -id | boolean | Display 'id' column | Boolean value Yes/No | @(!$(only)) |
| -query | boolean | Display 'qry' column | Boolean value Yes/No | @(!$(only)) |
| -all | boolean | Display 'all' column | Boolean value Yes/No | @(!$(only)) |
| -comment | boolean | Display 'comment' column | Boolean value Yes/No | @(!$(only)) |
| Associated qualifiers | ||||
| "-outfile" associated outfile qualifiers | ||||
| -odirectory | string | Output directory | 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 |
Input file format
showdb examines the databases defined for this EMBOSS installation and for the current user.Input files for usage example 3
'tsw' is a sequence entry in the example protein database 'tsw'
Output file format
Output files for usage example 2
File: showdb.out
# Name Type ID Qry All Comment # =============== ========== == === === ======= qapblast Protein OK OK OK BLAST swissnew qapblastall Protein OK OK OK BLAST swissnew, all fields indexed qapblastsplit Protein OK OK OK BLAST swissnew split in 5 files qapblastsplitexc Protein OK OK OK BLAST swissnew split in 5 files, not file 02 qapblastsplitinc Protein OK OK OK BLAST swissnew split in 5 files, only file 02 qapfasta Protein OK OK OK FASTA file swissnew entries qapflat Protein OK OK OK SpTrEmbl flatfile qapflatall Protein OK OK OK SpTrEmbl flatfiles, all fields indexed qapir Protein OK OK OK PIR qapirall Protein OK OK OK PIR qapirinc Protein OK OK OK PIR qapxfasta Protein OK OK OK FASTA file swissnew entries qapxflat Protein OK OK OK Swissnew flatfiles qaxpir Protein OK OK OK PIR qaxpirall Protein OK OK OK PIR qaxpirinc Protein OK OK OK PIR tpir Protein OK OK OK PIR using NBRF access for 4 files tsw Protein OK OK OK Swissprot native format with EMBL CD-ROM index tswnew Protein OK OK OK SpTrEmbl as 3 files in native format with EMBL CD-ROM index qanfasta Nucleotide OK OK OK FASTA file EMBL rodents qanfastaall Nucleotide OK OK OK FASTA file EMBL rodents, all fields indexed qanflat Nucleotide OK OK OK EMBL flatfiles qanflatall Nucleotide OK OK OK EMBL flatfiles qanflatexc Nucleotide OK OK OK EMBL flatfiles, no rodent file qanflatinc Nucleotide OK OK OK EMBL flatfiles, only rodent file qangcg Nucleotide OK OK OK GCG format EMBL qangcgall Nucleotide OK OK OK GCG format EMBL qangcgexc Nucleotide OK OK OK GCG format EMBL without prokaryotes qangcginc Nucleotide OK OK OK GCG format EMBL only prokaryotes qanxfasta Nucleotide OK OK OK FASTA file EMBL rodents qanxfastaall Nucleotide OK OK OK FASTA file EMBL rodents, all fields indexed qanxflat Nucleotide OK OK OK EMBL flatfiles qanxflatall Nucleotide OK OK OK EMBL flatfiles, all fields indexed qanxflatexc Nucleotide OK OK OK EMBL flatfiles, no rodent file qanxflatinc Nucleotide OK OK OK EMBL flatfiles, only rodent file qanxgcg Nucleotide OK OK OK GCG format EMBL qanxgcgall Nucleotide OK OK OK GCG format EMBL qanxgcgexc Nucleotide OK OK OK GCG format EMBL without prokaryotes qanxgcginc Nucleotide OK OK OK GCG format EMBL only prokaryotes qapirexc Nucleotide OK OK OK PIR qasrswww Nucleotide OK OK OK Remote SRS web server qawfasta Nucleotide OK OK OK FASTA file wormpep entries qawxfasta Nucleotide OK OK OK FASTA file wormpep entries qaxpirexc Nucleotide OK OK OK PIR tembl Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index temblall Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index temblrest Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index temblvrt Nucleotide OK OK OK EMBL in native format with EMBL CD-ROM index tensembldasgrch37 Nucleotide OK - - Homo_sapiens Reference server based on GRCh37 assembly testdb Nucleotide OK OK OK test sequence data tgb Nucleotide OK OK OK Genbank IDs tgenbank Nucleotide OK OK OK GenBank in native format with EMBL CD-ROM index tgenedashuman Nucleotide OK - - The Ensembl human Gene_ID reference source tflybase Features OK - - tgenedb Features OK - - ttax Taxonomy OK OK OK taxon Taxonomy OK OK OK drcat Resource OK OK OK tedam Obo OK OK OK EDAM using dbxedam test indexes tobo Obo OK OK OK EDAM using dbxobo test indexes eco Obo OK OK OK edam Obo OK OK OK go Obo OK OK OK pw Obo OK OK OK ro Obo OK OK OK so Obo OK OK OK |
The output is a simple text table.
Type 'P' indicates that this is a Protein database.
Type 'N' indicates that this is a Nucleic database.
'OK' under ID, Qry or All indicates that that access method can be used on this database. A '-' indicates that you cannot access this database in that way.
Note that 'OK' does not mean that the database is working correctly. It simply means that showdb has read the database definition correctly and that this method of access to the database should be possible.
If you are setting up a new database, then you should check that it works correctly by extracting entries from it using seqret.
When the -html qualifier is specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as <HTML>, <BODY>, </BODY> and </HTML> are not output by this program as the table of databases is expected to form only part of the contents of a web page - the rest of the web page must be supplied by the user.
Data files
The databases are specified in the files "emboss.defaults" for site wide definitions, and "~/.embossrc" for the user's own settings.Notes
EMBOSS provides excellent database support. All the common sequence formats you are likely to come across are supported. There are three basic levels of database query with different ways to search for and retrieve entries: entry A single entry specified by database ID or accession number is retrieved. For example "embl:x13776". query One or more entries matching a wildcard string in the USA are retrieved (this can be slow for some methods). For example you can specify all of the human PAX proteins in SWISS_PROT by: swissprot:pax*_human. all All entries are read sequentially from a database. For example to specify all entries in the database use embl:*.
One or more query levels may be available for a database depending on the database in question and how it has been setup and indexed. Each database and access method must be configured for it to be available for use. This involves editing one of the EMBOSS configuration files, either your own personal .embossrc or the installation-wide emboss.default file. The emboss.default file will typically contain the definitions of the test databases (tsw, tembl, tpir, etc) used in the usage examples for the application documentation and serve as example database definitions. For more information, see the EMBOSS Administrators Manual. You can run showdb to see the databases and access methods that have been configured successfully.
References
None.Warnings
Where the string OK is given next to a database is listed in showdb output, this means showdb has read the database definition correctly and that this access method is in principle possible, in other words, the database has been configured correctly.. It does not mean that the database or access method are available or working correctly. You should check things are ok by running, for example, seqret to retrieve an entry.
Diagnostic Error Messages
"The database 'xyz' does not exist" You have supplied the name of a database with the -database qualifier, but that database does not exist as far as EMBOSS is concerned.Exit status
It always exits with status 0, unless the above diagnostic message is displayed.Known bugs
None noted.See also
| Program name | Description |
|---|---|
| cachedas | Generates server cache file for DAS servers or for the DAS registry |
| cachedbfetch | Generates server cache file for Dbfetch/WSDbfetch data sources |
| cacheebeyesearch | Generates server cache file for EB-eye search domains |
| cacheensembl | Generates server cache file for an Ensembl server |
| dbtell | Display information about a public database |
| servertell | Display information about a public server |
| showserver | Displays information on configured servers |
Author(s)
Gary Williams formerly at:MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.