Clojure implementation of IGV client to control IGV via its Port Commands
Add the following to your :dependencies:
(require '[igv-client.core :as igv])
(def client (igv/connect "127.0.0.1" 60151))
(igv/set-snapshot-dir! client "/path/to/snapshot/dir")
(igv/reset client)
(igv/load-file client "/path/to/your/input/file")
(igv/goto client "chr1" 123456)
(igv/collapse client)
(igv/snapshot client)
(.close client)
;; or you can also write the same thing with the threading macro:
(-> client
igv/reset
(igv/load-file "/path/to/your/input/file")
(igv/goto "chr1" 123456)
igv/collapse
igv/snapshot
.close)Following is the list of commands available:
| Command Name | Function Signature |
|---|---|
version |
(version <client>) |
new/reset/clear |
(reset <client>) |
load/loadfile |
(load-file <client> <path>) |
remove |
(remove <client> <track>) |
genome |
(genome <client> <genome>) |
goto |
(goto <client> <locus>) |
(goto <client> <chr> <pos>) |
|
gototrack |
(goto-track <client> <track>) |
setsleepinterval |
(set-sleep-interval! <client> <msec>) |
snapshotdirectory |
(set-snapshot-dir! <client> <dir>) |
snapshot |
(snapshot <client>) |
zoomin |
(zoom-in <client>) |
zoomout |
(zoom-out <client>) |
collapse |
(collapse <client> [<track>]) |
expand |
(expand <client> [<track>]) |
squish |
(squish <client> [<track>]) |
tofront |
(bring-to-front! <client>) |
Copyright © 2019 Shogo Ohta
This program and the accompanying materials are made available under the terms of the Eclipse Public License 2.0 which is available at http://www.eclipse.org/legal/epl-2.0.
This Source Code may also be made available under the following Secondary Licenses when the conditions for such availability set forth in the Eclipse Public License, v. 2.0 are satisfied: GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version, with the GNU Classpath Exception which is available at https://www.gnu.org/software/classpath/license.html.