Pipeable command to Liftover (UCSC) builds?
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6.8 years ago
Tafelplankje ▴ 120

I was wondering if anyone has trick to make the UCSC LiftOver program pipable in bash? (https://genome.ucsc.edu/cgi-bin/hgLiftOver)

As I understand the application creates files from files, which is quite annoying sometimes; it would be handy if it could use stdin and stdout for the input/output.

liftover genome bash build • 2.3k views
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6.8 years ago
Ram 37k

The link in the bottom of that page gives you a resource where you can download an executable (and other required files) from.

EDIT: I'm assuming you've already downloaded the executable and are looking to bypass the input file creation step. To do this, take a look at process substitution. Essentially, you can feed in your input generator pipeline as a sub-process to the liftOver tool using <().

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