Entering edit mode
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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