[Seqinr-forum] RFC: where.is.this.acc

[Jean lobry]

Dear seqinr,

this is a RFC (Request For Comments) about the interest of commiting
in the seqinR package a function that would make the following job:
to look in all available databases if there is a given accession number.

A call to this function would look like this:

#######
>  library(seqinr)
>  where.is.this.acc("NC_001416")
Looking for available databases
Looking for sequence with accession number NC_001416 in the following 
ACNUC databases:
  [1] "genbank"        "embl"           "emblwgs"        "swissprot" 
"ensembl"
  [6] "refseq"         "refseqViruses"  "nrsub"          "hobacnucl" 
"hobacprot"
[11] "hovergendna"    "hovergen"       "hogenom5"       "hogenom5dna" 
"hogenom"
[16] "hogenomdna"     "homolens"       "homolensdna"    "greviews" 
"polymorphix"
[21] "emglib"         "taxobacgen"     "apis"           "anopheles" 
"caenorhabditis"
[26] "cionasavignyi"  "danio"          "drosophila"     "felis" 
"gallus"
[31] "human"          "mouse"          "saccharomyces"  "tetraodon" 
"xenopus"

Trying to open bank with name --->genbank<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank genbank ...... not found here.

Trying to open bank with name --->embl<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank embl ...... not found here.

Trying to open bank with name --->emblwgs<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank emblwgs ...... not found here.

Trying to open bank with name --->swissprot<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank swissprot ...... not found here.

Trying to open bank with name --->ensembl<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank ensembl ...... not found here.

Trying to open bank with name --->refseq<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank refseq ...... not found here.

Trying to open bank with name --->refseqViruses<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank refseqViruses ...... 
*** FOUND *** here.

Trying to open bank with name --->nrsub<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank nrsub ...... not found here.

Trying to open bank with name --->hobacnucl<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank hobacnucl ...... not found here.

Trying to open bank with name --->hobacprot<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank hobacprot ...... not found here.

Trying to open bank with name --->hovergendna<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank hovergendna ...... not 
found here.

Trying to open bank with name --->hovergen<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank hovergen ...... not found here.

Trying to open bank with name --->hogenom5<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank hogenom5 ...... not found here.

Trying to open bank with name --->hogenom5dna<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank hogenom5dna ...... not 
found here.

Trying to open bank with name --->hogenom<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank hogenom ...... not found here.

Trying to open bank with name --->hogenomdna<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank hogenomdna ...... not found here.

Trying to open bank with name --->homolens<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank homolens ...... not found here.

Trying to open bank with name --->homolensdna<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank homolensdna ...... not 
found here.

Trying to open bank with name --->greviews<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank greviews ...... not found here.

Trying to open bank with name --->polymorphix<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank polymorphix ...... not 
found here.

Trying to open bank with name --->emglib<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank emglib ...... not found here.

Trying to open bank with name --->taxobacgen<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank taxobacgen ...... not found here.

Trying to open bank with name --->apis<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank apis ...... not found here.

Trying to open bank with name --->anopheles<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank anopheles ...... not found here.

Trying to open bank with name --->caenorhabditis<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank caenorhabditis ...... 
not found here.

Trying to open bank with name --->cionasavignyi<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank cionasavignyi ...... 
not found here.

Trying to open bank with name --->danio<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank danio ...... not found here.

Trying to open bank with name --->drosophila<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank drosophila ...... not found here.

Trying to open bank with name --->felis<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank felis ...... not found here.

Trying to open bank with name --->gallus<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank gallus ...... not found here.

Trying to open bank with name --->human<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank human ...... not found here.

Trying to open bank with name --->mouse<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank mouse ...... not found here.

Trying to open bank with name --->saccharomyces<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank saccharomyces ...... 
not found here.

Trying to open bank with name --->tetraodon<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank tetraodon ...... not found here.

Trying to open bank with name --->xenopus<--- ...... and opening was OK.
==> Trying to find sequence NC_001416 in bank xenopus ...... not found here.


Sequence with accesion number NC_001416 was found in the following database(s):
[1] "refseqViruses"

#######

Is it usefull? (I include the code source just in case you want to 
play with it).

I'm inclined to say yes given the number of people who just don't know where to
start from.

Best,

Z.
-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo  : +33 472 43 27 56     fax    : +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/
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