I tried the following two queries using wget, one to get 5'UTR sequences and coordinates and the other to get the 3'UTR. In the two result files however, the order of the attributes is not the same. Is there any way to control the order, or do attributes appear in random order? Here are the queries (in this case, DATASET=dmelanogaster_gene_ensembl):
wget -q 'http://www.biomart.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?> <Query virtualSchemaName = "default" header = "1" count = "" softwareVersion = "0.5" > <Dataset name = "'$DATASET'" interface = "default" > <Attribute name = "gene_stable_id" /> <Attribute name = "5utr" /> <Attribute name = "transcript_stable_id" /> <Attribute name = "str_chrom_name" /> <Attribute name = "transcript_chrom_strand" /> <Attribute name = "5utr_start" /> <Attribute name = "5utr_end" /> </Dataset> </Query>' -O 5utr.dat wget -q 'http://www.biomart.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?> <Query virtualSchemaName = "default" header = "1" count = "" softwareVersion = "0.5" > <Dataset name = "'$DATASET'" interface = "default" > <Attribute name = "gene_stable_id" /> <Attribute name = "3utr" /> <Attribute name = "transcript_stable_id" /> <Attribute name = "str_chrom_name" /> <Attribute name = "transcript_chrom_strand" /> <Attribute name = "3utr_start" /> <Attribute name = "3utr_end" /> </Dataset> </Query>' -O 3utr.dat
