Hello,

I'm a student in bioinformatics in Tel Aviv University.
I'm working with you biomaRt API in order to generate automatically FASTA
sequences downloading.
I experienced some problem, here is my code:

#open biomart libaray
library(biomaRt)
#open data set of human
human = useDataset("hsapiens_gene_ensembl",mart=ensembl)
#select the attributes that we want from the data set
attr<-c('ensembl_gene_id','ensembl_transcript_id',
'external_gene_id','chromosome_name','strand','transcript_start')
#downloading the map between transcript id and transcript name
tmpgene<-getBM(attr, 'biotype', values = 'protein_coding', human)
#save in a TSV format (the file is saved in txt)
write.table(tmpgene,"Z:/tomhait/organisms/human/transcript_names.txt",
row.names=FALSE, quote=FALSE)
#collect all sequences with upstream flank 3000 bases based on the first
column (ensembl_id) of tmpgene
i<-1
for(id1 in tmpgene[,2]){
 #retrieve sequence
 sequence<-getSequence(id=id1,
type='ensembl_transcript_id',seqType='transcript_flank',upstream = 3000,
mart = human)
 #check if sequence was retrieved
 sLengths <- with(sequence, nchar(as.character(transcript_flank)))

#writing to a new file in "Z:/tomhait/organisms/human/mart_export_new.txt"
#you can change it to "mart_export_new.txt" and it will create a new file
in R directory
 if(length(sLengths) > 0){
  x<-sequence[,1]
  y<-y<-strsplit(gsub("([[:alnum:]]{60})", "\\1 ", x), " ")[[1]]
  title<-paste(paste(">",tmpgene[i,1],sep=""),tmpgene[i,2],tmpgene[i,3],tmpgene[i,4],tmpgene[i,5],tmpgene[i,6],
sep="|")
  write(title,file="Z:/tomhait/organisms/human/mart_export_new.txt",ncolumns
= 1, append=TRUE,sep="")
  write(y,file="Z:/tomhait/organisms/human/mart_export_new.txt",ncolumns =
1, append=TRUE,sep="\n")
  write("\n",file="Z:/tomhait/organisms/human/mart_export_new.txt",ncolumns
= 1, append=TRUE,sep="\n")
 }
 i<-i+1
}

I got the message:
Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"),  :
  Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT
FOUND

Could you please help me to solve this problem?

Best Regards,

Tom Hait.

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