igv-client

Clojure implementation of IGV client to control IGV via its Port Commands

Installation

Add the following to your :dependencies:

Usage

(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)

Available Commands

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>)

License

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.