[Bioc-devel] seqnames missing in headerTabix()

Tue, Aug 23, 2011 9:14 AM

Hi Anita,

It looks like the download may not have worked. Check your gtfFn file to 
see if the data are really there,

     less Drosophila_melanogaster.BDGP5.25.62.gtf.gz

Once you are sure of the download you may want to check the file for the 
usual things -
(1) no comments lines starting with #
(2) the file is tab separated, not space separated

Coming from ensembl these should not be a problem.

Valerie

On 08/23/2011 07:02 AM, Anita Lerch wrote:

Hi,

I tried to stream a 'gtf' file from the ensemble with the Tabix methods.
The creation of the index files seems to work, but when I checked it
with headerTabix(tbx)$seqnames and got character(0).
Of course the scanTabix() didn't worked then too.
I do not have this problem with the example file in the Rsamtools
package.
Does anybody has an explanation for this?

Thanks in advance,
Anita

library(Rsamtools)
url<- "ftp://ftp.ensembl.org/pub/release-62/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP5.25.62.gtf.gz"
gtfFn<- "Drosophila_melanogaster.BDGP5.25.62.gtf.gz"
download.file(url, gtfFn, "wget")
indexTabix(gtfFn, format="gff")

[1] "Drosophila_melanogaster.BDGP5.25.62.gtf.gz.tbi"

tbx<- open(TabixFile(gtfFn))
headerTabix(tbx)

$seqnames
character(0)

$indexColumns
   seq start   end
     1     4     5

$skip
[1] 0

$comment
[1] "#"

$header
character(0)

seqnamesTabix(tbx)

character(0)

cat(yieldTabix(tbx, yieldSize=1L))
param<- GRanges(c("3L", "3R"), IRanges(c(1, 1), width=100000))
scanTabix(tbx, param=param)

Error: scanTabix: '3L' not present in tabix index
   path: /home_fmi/01/lerchani/workspace/Drosophila_melanogaster.BDGP5.25.62.gtf.gz

sessionInfo()

R Under development (unstable) (2011-08-23 r56776)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rsamtools_1.5.51     Biostrings_2.21.9    GenomicRanges_1.5.28 IRanges_1.11.24

loaded via a namespace (and not attached):
[1] BSgenome_1.21.3     RCurl_1.6-9         rtracklayer_1.13.11 tools_2.14.0        XML_3.4-2           zlibbioc_0.1.7

[Bioc-devel] seqnames missing in headerTabix()

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