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Download genome annotations from UCSC's MySQL database

I want to download a BED file of various genome annotations (introns, exons, 3' UTR, 5' UTR) for a given assembly. I can do this through the UCSC table browser following these instructions, however I'd like to do it programmatically. Currently I get these regions from the full refGene table using MySQL to download the table and a custom script to parse out the regions into BED format. Does UCSC already offer an established way to do this?

ucsc mysql bed
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by James Ashmore James Ashmore

1 answer 

Yes , you can access the mysql server using a simple sql script:

$ echo -e "chr1\t10000\t20000\nchr1\t30000\t40000" |\
awk -F '\t' '{printf("select \"%s\",\"%s\",\"%s\", G.name,G.txStart,G.txEnd from refGene as G  where chrom=\"%s\" and not(%s>txEnd or %s<txStart);\n",$1,$2,$3,$1,$2,$3);}' |\
mysql --user=genome --host=genome-mysql.cse.ucsc.edu  -A  -N -D hg38

chr1    10000    20000    NR_024540    14361    29370
chr1    10000    20000    NR_107063    17368    17436
chr1    10000    20000    NR_128720    17368    17436
chr1    10000    20000    NR_106918    17368    17436
chr1    10000    20000    NR_107062    17368    17436
chr1    10000    20000    NR_046018    11873    14409
chr1    30000    40000    NR_036267    30365    30503
chr1    30000    40000    NR_036266    30365    30503
chr1    30000    40000    NR_036268    30365    30503
chr1    30000    40000    NR_026822    34610    36081
chr1    30000    40000    NR_026820    34610    36081
chr1    30000    40000    NR_026818    34610    36081
chr1    30000    40000    NR_036051    30365    30503

I also remember Heng Li wrote a tool to batch-query the UCSC: https://github.com/lh3/misc/blob/master/biodb/batchUCSC.pl

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written by Pierre Lindenbaum Pierre Lindenbaum

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