[BioC] Howto annotate blast subject.id with AnnotationDbi

[Arnaud Mounier]

Hi,

I try to annotate a blastp result (not so much, just 270 query) with the 
org.At.tair.db from AnnotationDBi package throw bioconductor.

First I read blast output with RFLPtools :

 > df.blast.report <- read.blast(file = f.blast.report)
 > head(df.blast.report)
          query.id  subject.id identity alignment.length mismatches 
gap.opens q.start q.end s.start s.end evalue bit.score
1 medtr8g018420.1 AT1G55020.1    59.77              860        314 
    9       9   856      20   859      0      1058
2 medtr8g018420.1 AT3G22400.1    56.16              869        344 
   10       9   856      34   886      0      1004
3 medtr8g018420.1 AT1G72520.1    45.19              821        433 
   10      45   856     114   926      0       729

The subject ID have version number (.1 or .2) and the original 
ATH_GO_GOSLIM.txt from tair site two. But this version number is not 
present in the org.At.tait.dbTAIR :
 > head(keys(org.At.tair.db, keytype="TAIR"))
[1] "AT1G01010" "AT1G01020" "AT1G01030" "AT1G01040" "AT1G01050" "AT1G01060"


* Is this relevant or can I annotate without taking care of the version 
number ?
Does Org.At.tair.db keep the version number elsewhere ?
Because the source file for this package 
(ftp://ftp.arabidopsis.org/Ontologies/Gene_Ontology/ATH_GO_GOSLIM.txt) 
store it initialy.

* As the query must be selected in function of her subjects annotations 
and GO.db, I want to merge all info (blast report, org.At.tair.db + 
GO.db) in one db with a bioconductor package (annotationForge perhaps).
So, is there a package or a GNU script to manage this association easily 
or do i wrote my own R scripts ?

Any links are welcomes !
Thank's in advance,
Ar.

-- 
« Le soleil filtre à travers les branches des arbres par éclairs, comme 
le sens à travers la langue. »
Nancy Huston

Arnaud Mounier
INRA - UMR Agroécologie 1347
CNRS - ERL IPM 6300 (Plant-Microorganism Interaction)
17, rue Sully - BP 86510 - F-21065 Dijon Cedex - France
Work phone : +33 380 693 167 - Fax : +33 380 693 753

https://www6.dijon.inra.fr/umragroecologie/Personnel/IPM/ITA/MOUNIER-Arnaud