Hi,

I have a problem running getSequence in biomaRt.

I've found a thread two years old, but there was no solution mentioned
there, so I am not sure whether it was fixed or not.

The behavior is though exactly as Julie showed in her example. When I ran
the command for several files in a for loop, I get this error for some of
the queries but not for all.

this is what I do:
library(biomaRt)
ensembl<-useMart("ensembl", dataset="dmelanogaster_gene_ensembl")
...
for (j in 1:length(dirs)){
 ...
    files<-list.files()
    for (i in 1:length(files)) {
        ...
                    ids<-read.table(files[i])[,1]
                    cat("in the list of genes we have here", ids[1],"genes
\n")
                    result<-getSequence(id=as.character(ids),
type="flybase_gene_id", seqType="coding_gene_flank", upstream="1000",
mart=ensembl)
                   ...
              }
      }

ids is a vector of flybase IDs (FBgn0030073 FBgn0038346 FBgn0025366
FBgn0011770 FBgn0029828 FBgn0031701 ...)

This is how the output looks like:
[1] "working directory is: /home/ayeroslaviz/myProject/4_genelists/geneids"
unpaired_downregulated_0.1_nonRed.txt
in the list of genes we have here 48 genes
saving to ../martSequences/unpaired_downregulated_0.1_nonRed.txt
unpaired_downregulated_0.1.txt
in the list of genes we have here 48 genes
saving to  ../martSequences/unpaired_downregulated_0.1.txt
unpaired_listfile_decreasing.tsv
unpaired_listfile_decreasing.txt
unpaired_listfile_increasing.tsv
unpaired_listfile_increasing.txt
unpaired_upregulated_0.1_nonRed.txt
in the list of genes we have here 28 genes
Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"),  :
  Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT
FOUND

the output lists the files created during the loop for the different input
files.
I ran the complete loop again and it shows no error messages. The third
time I ran it it gave the same error message.

The problem happens mainly, when I am running this lines as a script from
the shell.
home@vm1-pipeline:~/myProject$ ./run.sh config.txt
the config file is at: ...
my working directory is at: ...

Run full analysis? (y)es, (n)o:
n

Select STEPS to run:
...

8
8
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"),  :
  Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT
FOUND
Calls: getSequence -> getBM
Execution halted

I would appreciate ant ideas to solve this problem.

Thanks
Assa


> date()
[1] "Mon Dec 19 14:12:10 2011"
> R.version
               _
platform       x86_64-pc-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          14.0
year           2011
month          10
day            31
svn rev        57496
language       R
version.string R version 2.14.0 (2011-10-31)
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] biomaRt_2.10.0 stringr_0.5    affy_1.32.0    Biobase_2.14.0

loaded via a namespace (and not attached):
[1] affyio_1.22.0         BiocInstaller_1.2.1   plyr_1.6
[4] preprocessCore_1.16.0 RCurl_1.7-0           tools_2.14.0
[7] XML_3.6-0             zlibbioc_1.0.0

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