whichdb

 

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Function

Search all sequence databases for an entry and retrieve it

Description

whichdb searches all available sequence databases for sequences with a specified ID name or accession number. The uniform sequence address (USA) of matching database entries is written to an output file. whichdb will, optionally, write out the sequences it finds to files. An "available" database is one that has been defined in the EMBOSS system file (.embossrc or emboss.login) and is available from the system you are running EMBOSS. If you do not know which database(s) contain the entry you are interested in, whichdb will tell you.

Usage

Here is a sample session with whichdb 


% whichdb -showall 
Search all sequence databases for an entry and retrieve it
ID or Accession number: x65923
Output file [outfile.whichdb]:

Go to the output files for this example

Command line arguments 

Search all sequence databases for an entry and retrieve it
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-entry]             string     ID or Accession number (Any string)
*  -outfile            outfile    [*.whichdb] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -get                toggle     [N] Retrieve sequences
   -showall            boolean    [N] Show failed attempts

   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
[-entry]
(Parameter 1)		 string ID or Accession number Any string  
-outfile outfile Output file name Output file <*>.whichdb
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-get toggle Retrieve sequences Toggle value Yes/No No
-showall boolean Show failed attempts Boolean value Yes/No No
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

None.

Output file format

Output files for usage example

File: outfile.whichdb

# Trying 'bpembl:x65923'
bpembl:x65923
# Trying 'bpgb:x65923'
bpgb:x65923
# Trying 'bpsw:x65923'
# Failed 'bpsw:x65923'
# Trying 'bpworm:x65923'
# Failed 'bpworm:x65923'
# Trying 'ena:x65923'
ena:x65923
# Trying 'qanfasta:x65923'
# Failed 'qanfasta:x65923'
# Trying 'qanfastaall:x65923'
# Failed 'qanfastaall:x65923'
# Trying 'qanflat:x65923'
# Failed 'qanflat:x65923'
# Trying 'qanflatall:x65923'
qanflatall:x65923
# Trying 'qanflatexc:x65923'
qanflatexc:x65923
# Trying 'qanflatinc:x65923'
# Failed 'qanflatinc:x65923'
# Trying 'qangcg:x65923'
qangcg:x65923
# Trying 'qangcgall:x65923'
qangcgall:x65923
# Trying 'qangcgexc:x65923'
qangcgexc:x65923
# Trying 'qangcginc:x65923'
# Failed 'qangcginc:x65923'
# Trying 'qanxfasta:x65923'
# Failed 'qanxfasta:x65923'
# Trying 'qanxfastaall:x65923'
# Failed 'qanxfastaall:x65923'
# Trying 'qanxflat:x65923'
# Failed 'qanxflat:x65923'
# Trying 'qanxflatall:x65923'
qanxflatall:x65923
# Trying 'qanxflatexc:x65923'
qanxflatexc:x65923
# Trying 'qanxflatinc:x65923'
# Failed 'qanxflatinc:x65923'
# Trying 'qanxgcg:x65923'
qanxgcg:x65923
# Trying 'qanxgcgall:x65923'
qanxgcgall:x65923
# Trying 'qanxgcgexc:x65923'
qanxgcgexc:x65923
# Trying 'qanxgcginc:x65923'
# Failed 'qanxgcginc:x65923'


  [Part of this file has been deleted for brevity]

# Failed 'qapir:x65923'
# Trying 'qapirall:x65923'
# Failed 'qapirall:x65923'
# Trying 'qapirexc:x65923'
# Failed 'qapirexc:x65923'
# Trying 'qapirinc:x65923'
# Failed 'qapirinc:x65923'
# Trying 'qapxfasta:x65923'
# Failed 'qapxfasta:x65923'
# Trying 'qapxflat:x65923'
# Failed 'qapxflat:x65923'
# Trying 'qasrswww:x65923'
# Failed 'qasrswww:x65923'
# Trying 'qawfasta:x65923'
# Failed 'qawfasta:x65923'
# Trying 'qawxfasta:x65923'
# Failed 'qawxfasta:x65923'
# Trying 'qaxembl:x65923'
qaxembl:x65923
# Trying 'qaxpir:x65923'
# Failed 'qaxpir:x65923'
# Trying 'qaxpirall:x65923'
# Failed 'qaxpirall:x65923'
# Trying 'qaxpirexc:x65923'
# Failed 'qaxpirexc:x65923'
# Trying 'qaxpirinc:x65923'
# Failed 'qaxpirinc:x65923'
# Trying 'tembl:x65923'
tembl:x65923
# Trying 'temblall:x65923'
temblall:x65923
# Trying 'temblrest:x65923'
# Failed 'temblrest:x65923'
# Trying 'temblvrt:x65923'
temblvrt:x65923
# Trying 'tensembldasgrch37:x65923'
# Failed 'tensembldasgrch37:x65923'
# Trying 'testdb:x65923'
# Failed 'testdb:x65923'
# Trying 'tgb:x65923'
tgb:x65923
# Trying 'tgenbank:x65923'
tgenbank:x65923
# Trying 'tgenedashuman:x65923'
# Failed 'tgenedashuman:x65923'
# Trying 'tpir:x65923'
# Failed 'tpir:x65923'
# Trying 'tsw:x65923'
# Failed 'tsw:x65923'
# Trying 'tswnew:x65923'
# Failed 'tswnew:x65923'

The reported database entries are written out to the specified output file.

Each database that is defined in the local implementation of EMBOSS which contains an entry called 'x65923' is reported.

Note that where a database is defined under several names ('embl', 'em'), each definition of that database containing the entry is reported.

When the '-get' option is used to output the sequences, they are written to separate files. The sequence format they are written in is always 'Fasta' format. The normal command-line qualifiers for changing the output formats etc. will not work in this program.

The names of the files that the sequences are written to is reported as they are written, for example: 

Writing x65923.embl
Writing x65923.human
Writing x65923.tembl
Writing x65923.em
Writing x65923.genbank
Writing x65923.gb

Data files

None.

Notes

The Uniform Sequence Addresss (USA) method used by EMBOSS for referencing sequences does not allow database entries to be specified by just the ID name or accession number. You must specify both the name of the database and the entry, for example embl:x65923, not just x65923. whichdb is useful where you do not know the database that a sequence entry is found in.

IDs and Accessions

An entry in a database must have some way of being uniquely identified in that database. Most sequence databases have two such identifiers for each sequence - an ID name and an Accession number.

Why are there two such identifiers? The ID name was originally intended to be a human-readable name that had some indication of the function of its sequence. In the early years of EMBL and GenBank the first two (or three) letters indicated the species and the rest indicated the function, for example HSFAU was the Homo Sapiens FAU pseudogene. This naming scheme started to be a problem when the number of entries added each day was so vast that people could not make up the ID names fast enough. Instead, the Accession numbers were used as the ID name. Therefore you will now find ID names like X65923, the same as the Accession number for that sequence in EMBL. The protein sequence databases continue to use recognizable names for entries (for example AMIR_PSEAE for the AmiR gene product of Pseudomonas aeruginosa in UniProt/SwissProt).

ID names are not guaranteed to remain the same between different versions of a database (although in practice they usually do). In contrast, accession numbers are unique alphanumeric identifiers that are guaranteed to remain with that sequence through the rest of the life of the database. If two sequences are merged into one, then the new sequence will get a new Accession number and the Accession numbers of the merged sequences will be retained as 'secondary' Accession numbers. EMBL, GenBank and UniProt/SwissProt share an Accession numbering scheme - an Accession number uniquely identifies a sequence within these three databases.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
abiview Display the trace in an ABI sequencer file
coderet Extract CDS, mRNA and translations from feature tables
entret Retrieve sequence entries from flatfile databases and files
extractalign Extract regions from a sequence alignment
infoalign Display basic information about a multiple sequence alignment
infoseq Display basic information about sequences
refseqget Get reference sequence
seqxref Retrieve all database cross-references for a sequence entry
seqxrefget Retrieve all cross-referenced data for a sequence entry
showalign Display a multiple sequence alignment in pretty format
variationget Get sequence variations

Author(s)

Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Written (Jan 2002) - Alan Bleasby.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None