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whichdb
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
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
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 (c) 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
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