Where do you actually download UCSC BLAT output?

Question

[rmartson]

Is it like BLAST output? Why do I only get results in my browser but no download option?

Answer 1

[GenoMax]

You could do "File save as" in your browser page with the results to save them. Copy/pasting psl output into a new file would avoid having to deal with the HTML code.

[rmartson]

I'm looking for xml, fasta or genbank format and not a html webpage

Anything I can work with in Biopython

[GenoMax]

With web blat you are limited to psl/psl without header output types. But if you are able to run blat locally then your options expand to ones below.

-out=type      Controls output file format.  Type is one of:
                    psl - Default.  Tab-separated format, no sequence
                    pslx - Tab-separated format with sequence
                    axt - blastz-associated axt format
                    maf - multiz-associated maf format
                    sim4 - similar to sim4 format
                    wublast - similar to wublast format
                    blast - similar to NCBI blast format
                    blast8- NCBI blast tabular format
                    blast9 - NCBI blast tabular format with comments

XML is not an option with blat. You could parse the psl or blast8/blast9 formats programmatically.