good spec, but i can't get through the whole thing just now. this could
get you started

source("http://bioconductor.org/biocLite.R")
    biocLite("TxDb.Athaliana.BioMart.plantsmart12")
library(TxDb.Athaliana.BioMart.plantsmart12)
txdb = TxDb.Athaliana.BioMart.plantsmart12
tr = transcriptsBy(txdb, by="gene")

> tr
GRangesList of length 33602:
$AT1G01010
GRanges with 1 range and 2 elementMetadata cols:
      seqnames       ranges strand |     tx_id     tx_name
         <Rle>    <IRanges>  <Rle> | <integer> <character>
  [1]        1 [3631, 5899]      + |      9694 AT1G01010.1

$AT1G01020
GRanges with 2 ranges and 2 elementMetadata cols:
      seqnames       ranges strand | tx_id     tx_name
  [1]        1 [5928, 8737]      - | 29355 AT1G01020.1
  [2]        1 [6790, 8737]      - | 29354 AT1G01020.2

$AT1G01030
GRanges with 1 range and 2 elementMetadata cols:
      seqnames         ranges strand | tx_id     tx_name
  [1]        1 [11649, 13714]      - | 26358 AT1G01030.1

...
<33599 more elements>
---
seqlengths:
  3  4  1  5  2 Pt Mt
 NA NA NA NA NA NA NA

you could use an org.At* package a bit more simply, use the CHRLOC and CHRLOCEND
elements.  please look at the metadata page of bioconductor.org
INSTALL node for your
organism.  this should be a standard use case or faq, perhaps



On Sun, Jun 17, 2012 at 6:33 PM, Josh [guest] <guest@bioconductor.org>wrote:

>
> Dear listserv,
>
> I am a long-time R user, novice Bioconductor user. I am quickly realizing
> they are not the same thing. I have a very basic question that I hope you
> can help me with.
>
> I have a list of genes in Arabidopsis thaliana. I want to input this list
> into R/Bioconductor and output a table listing the start and end positions
> of each gene.
>
> Specific code that will get the job done will be the most helpful for me.
> Also, please tell me the specific packages and databases and such I must
> load into memory. I am a total newbie at this.
>
> Thanks in advance,
> -----------------------------------
> Josh Banta, Ph.D
> Assistant Professor
> Department of Biology
> The University of Texas at Tyler
> Tyler, TX 75799
> Tel: (903) 565-5655
> http://plantevolutionaryecology.org
>
>  -- output of sessionInfo():
>
> > gene.pos <- data.frame(matrix(nrow = 3, ncol = 4))
> > gene.list <- c("At5g35790", "AT5g60910", "AT1g16560")
> > gene.pos[,1] <- gene.list
> > colnames(gene.pos) <- c("gene", "chromosome", "nuc_sequence_start" ,
> "nuc_sequence_end")
> >
> > gene.pos
>       gene chromosome nuc_sequence_start nuc_sequence_end
> 1 At5g35790         NA                 NA               NA
> 2 AT5g60910         NA                 NA               NA
> 3 AT1g16560         NA                 NA               NA
> >
> > #now what? How do I fill in the blanks?
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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