📄 showdb.txt
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ASTA file EMBL rodentsqanxfastaall N OK OK OK emboss sv,des special FASTA file EMBL rodents, all fields indexedqanxflat N OK OK OK emboss - special EMBL flatfilesqanxflatall N OK OK OK emboss des,org,key special EMBL flatfiles, all fields indexedqanxgcg N OK OK OK embossgcg - special GCG format EMBLqanxgcgall N OK OK OK embossgcg sv,des,org,key special GCG format EMBLqanxgcgexc N OK OK OK embossgcg - special GCG format EMBL without prokaryotesqanxgcginc N OK OK OK embossgcg - special GCG format EMBL only prokaryotesqapirexc N OK OK OK gcg - special PIRqasrswww N OK - - srswww sv,des,org,key special Remote SRS web serverqawfasta N OK OK OK emblcd - special FASTA file wormpep entriesqawxfasta N OK OK OK emboss - special FASTA file wormpep entriesqaxpirexc N OK OK OK embossgcg - special PIRtembl N OK OK OK emblcd sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM indextemblall N - - OK direct sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM indextemblrest N - - OK direct sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM indextemblvrt N - - OK direct sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM indextgb N OK - - srswww sv,des,org,key special Genbank IDstgenbank N OK OK OK emblcd sv,des,org,key special 01 GenBank in native format with EMBL CD-ROM indexCommand line arguments Standard (Mandatory) qualifiers: (none) Additional (Optional) qualifiers: -database string Name of a single database to give information on (Any string is accepted) -html boolean [N] Format output as an HTML table -[no]protein boolean [Y] Display protein databases -[no]nucleic boolean [Y] Display nucleic acid 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 standard output -filter boolean Read standard input, write 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. 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 messagesInput file format None. 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 P OK OK OK BLAST swissnewqapblastall P OK OK OK BLAST swissnew, all fields indexedqapblastsplit P OK OK OK BLAST swissnew split in 5 filesqapblastsplitexc P OK OK OK BLAST swissnew split in 5 files, not file 02qapblastsplitinc P OK OK OK BLAST swissnew split in 5 files, only file 02qapfasta P OK OK OK FASTA file swissnew entriesqapflat P OK OK OK Swissnew flatfilesqapflatall P OK OK OK Swissnew flatfiles, all fields indexedqapflatexc P OK OK OK Swissnew flatfiles, no updated sequence fileqapflatinc P OK OK OK Swissnew flatfiles, only updated sequence fileqapir P OK OK OK PIRqapirall P OK OK OK PIRqapirinc P OK OK OK PIRqapxfasta P OK OK OK FASTA file swissnew entriesqapxflat P OK OK OK Swissnew flatfilesqapxflatexc P OK OK OK Swissnew flatfiles, no updated sequence fileqapxflatinc P OK OK OK Swissnew flatfiles, only updated sequence fileqaxpir P OK OK OK PIRqaxpirall P OK OK OK PIRqaxpirinc P OK OK OK PIRtpir P OK OK OK PIR using NBRF access for 4 filestsw P OK OK OK Swissprot native format with EMBL CD-ROM indextswnew P OK OK OK Swissnew as 3 files in native format with EMBL CD-ROM indextwp P OK OK OK EMBL new in native format with EMBL CD-ROM indexgenbanksrs N OK - - Genbank IDsqanfasta N OK OK OK FASTA file EMBL rodentsqanfastaall N OK OK OK FASTA file EMBL rodents, all fields indexedqanflat N OK OK OK EMBL flatfilesqangcg N OK OK OK GCG format EMBLqangcgall N OK OK OK GCG format EMBLqangcgexc N OK OK OK GCG format EMBL without prokaryotesqangcginc N OK OK OK GCG format EMBL only prokaryotesqanxfasta N OK OK OK FASTA file EMBL rodentsqanxfastaall N OK OK OK FASTA file EMBL rodents, all fields indexedqanxflat N OK OK OK EMBL flatfilesqanxflatall N OK OK OK EMBL flatfiles, all fields indexedqanxgcg N OK OK OK GCG format EMBLqanxgcgall N OK OK OK GCG format EMBLqanxgcgexc N OK OK OK GCG format EMBL without prokaryotesqanxgcginc N OK OK OK GCG format EMBL only prokaryotesqapirexc N OK OK OK PIRqasrswww N OK - - Remote SRS web serverqawfasta N OK OK OK FASTA file wormpep entriesqawxfasta N OK OK OK FASTA file wormpep entriesqaxpirexc N OK OK OK PIRtembl N OK OK OK EMBL in native format with EMBL CD-ROM indextemblall N - - OK EMBL in native format with EMBL CD-ROM indextemblrest N - - OK EMBL in native format with EMBL CD-ROM indextemblvrt N - - OK EMBL in native format with EMBL CD-ROM indextgb N OK - - Genbank IDstgenbank N OK OK OK GenBank in native format with EMBL CD-ROM index The output is a simple 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 Note that 'OK' in the output 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. You can set up your own private databases by editing a file called '.embossrc' to contain database specifications. You can set up public databases by editing the file '/usr/local/share/EMBOSS/emboss.default' (if you have the permission to do this). The 'emboss.default' file will already have the definitions of the test databases in: tsw, tembl, tpir, etc. These are the databases that are used in the examples shown in the documentation of the programs. For details of the database definitions, you should first read David's Administration Guide: http://emboss.sourceforge.net/docs/adminguide/ especially: http://emboss.sourceforge.net/docs/adminguide/adminguide/node4.html See also: http://emboss.sourceforge.net/docs/themes/Databases.html for a lot of detail of the syntax of database definition. Just because showdb can display the database definitions, it does NOT mean that the databases are set up correctly. You must now test them using seqret.References None.Warnings None.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 abiview Reads ABI file and display the trace cirdna Draws circular maps of DNA constructs infoalign Information on a multiple sequence alignment infoseq Displays some simple information about sequences lindna Draws linear maps of DNA constructs pepnet Displays proteins as a helical net pepwheel Shows protein sequences as helices prettyplot Displays aligned sequences, with colouring and boxing prettyseq Output sequence with translated ranges remap Display sequence with restriction sites, translation etc seealso Finds programs sharing group names showalign Displays a multiple sequence alignment showfeat Show features of a sequence showseq Display a sequence with features, translation etc sixpack Display a DNA sequence with 6-frame translation and ORFs textsearch Search sequence documentation. Slow, use SRS and Entrez! tfm Displays a program's help documentation manual whichdb Search all databases for an entry wossname Finds programs by keywords in their one-line documentationAuthor(s) Gary Williams (gwilliam ⌨️ 快捷键说明
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