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: x65921
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:6.4.0.0

   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 'qaxpir:x65921'
# Failed 'qaxpir:x65921'
# Trying 'qanxgcgexc:x65921'
# Failed 'qanxgcgexc:x65921'
# Trying 'qapblastsplitinc:x65921'
# Failed 'qapblastsplitinc:x65921'
# Trying 'qanxflatall:x65921'
qanxflatall:x65921
# Trying 'tgenbank:x65921'
tgenbank:x65921
# Trying 'tembl:x65921'
tembl:x65921
# Trying 'temblvrt:x65921'
temblvrt:x65921
# Trying 'qanxgcginc:x65921'
# Failed 'qanxgcginc:x65921'
# Trying 'qapirexc:x65921'
# Failed 'qapirexc:x65921'
# Trying 'qangcg:x65921'
# Failed 'qangcg:x65921'
# Trying 'qawxfasta:x65921'
# Failed 'qawxfasta:x65921'
# Trying 'tswnew:x65921'
# Failed 'tswnew:x65921'
# Trying 'qapirinc:x65921'
# Failed 'qapirinc:x65921'
# Trying 'qapfasta:x65921'
# Failed 'qapfasta:x65921'
# Trying 'tgenedashuman:x65921'
# Failed 'tgenedashuman:x65921'
# Trying 'qasrswww:x65921'
qasrswww:x65921
# Trying 'qangcgall:x65921'
# Failed 'qangcgall:x65921'
# Trying 'temblall:x65921'
temblall:x65921
# Trying 'qaxpirall:x65921'
# Failed 'qaxpirall:x65921'
# Trying 'qawfasta:x65921'
# Failed 'qawfasta:x65921'
# Trying 'qanxflatexc:x65921'
qanxflatexc:x65921
# Trying 'qanxflat:x65921'
# Failed 'qanxflat:x65921'
# Trying 'qanxfasta:x65921'
# Failed 'qanxfasta:x65921'
# Trying 'qapflat:x65921'
# Failed 'qapflat:x65921'
# Trying 'qanxflatinc:x65921'
# Failed 'qanxflatinc:x65921'


  [Part of this file has been deleted for brevity]

# Failed 'qapir:x65921'
# Trying 'qangcgexc:x65921'
# Failed 'qangcgexc:x65921'
# Trying 'qapxfasta:x65921'
# Failed 'qapxfasta:x65921'
# Trying 'qanfasta:x65921'
# Failed 'qanfasta:x65921'
# Trying 'qaxpirexc:x65921'
# Failed 'qaxpirexc:x65921'
# Trying 'qanxgcg:x65921'
# Failed 'qanxgcg:x65921'
# Trying 'qangcginc:x65921'
# Failed 'qangcginc:x65921'
# Trying 'qapblast:x65921'
# Failed 'qapblast:x65921'
# Trying 'tensembldasgrch37:x65921'
# Failed 'tensembldasgrch37:x65921'
# Trying 'qaxpirinc:x65921'
# Failed 'qaxpirinc:x65921'
# Trying 'qanxgcgall:x65921'
# Failed 'qanxgcgall:x65921'
# Trying 'qapblastall:x65921'
# Failed 'qapblastall:x65921'
# Trying 'qapblastsplit:x65921'
# Failed 'qapblastsplit:x65921'
# Trying 'qanflatexc:x65921'
qanflatexc:x65921
# Trying 'tsw:x65921'
# Failed 'tsw:x65921'
# Trying 'temblrest:x65921'
# Failed 'temblrest:x65921'
# Trying 'qapirall:x65921'
# Failed 'qapirall:x65921'
# Trying 'qanfastaall:x65921'
# Failed 'qanfastaall:x65921'
# Trying 'qanflatinc:x65921'
# Failed 'qanflatinc:x65921'
# Trying 'tgb:x65921'
tgb:x65921
# Trying 'qapblastsplitexc:x65921'
# Failed 'qapblastsplitexc:x65921'
# Trying 'qanxfastaall:x65921'
# Failed 'qanxfastaall:x65921'
# Trying 'qapxflat:x65921'
# Failed 'qapxflat:x65921'
# Trying 'qapflatall:x65921'
# Failed 'qapflatall:x65921'
# Trying 'qanflat:x65921'
# Failed 'qanflat:x65921'
# Trying 'testdb:x65921'
# Failed 'testdb:x65921'

   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       Retrieves 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
                    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

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