ruby-igv 0.0.3 → 0.0.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/README.md +5 -1
- data/lib/igv.rb +24 -15
- data/lib/igv/version.rb +1 -1
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 8915f9a26a6b4b4bbe15dc5dd35d156ca9c84a5b2737c4b81ffa1441b5049e2d
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data.tar.gz: 44980727b24b348a3167566179e9a75755cda0023761624de1fb72fdfe3701cd
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 232bc8a829604e65fb67e7b39aa0480e3c0165e1291022c1162469ed5d126caefe0881b124e70fb4c386a51937e1530d812fb5ec459d8067fa9264e78b368202
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data.tar.gz: c57afdcf2dcbf5d9829fd3815e4fdc91148a1757906027f663690598438ec3e284b54ff75b07f8ab8c699be93b7674192b78821953cc0846cc333a48bc4572f8
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data/README.md
CHANGED
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@@ -23,9 +23,13 @@ igv.load 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwR
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igv.go 'chr18:78,016,233-78,016,640'
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igv.save '/tmp/r/region.svg'
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igv.save '/tmp/r/region.png'
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-
igv.
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igv.snapshot_dir = '/tmp/r2/'
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igv.save 'region.jpg' # save to /tmp/r2/region.png
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igv.send 'echo' # whatever you want
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```
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* [Controlling IGV through a Port](https://software.broadinstitute.org/software/igv/PortCommands)
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## Contributing
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* [Report bugs](https://github.com/kojix2/ruby-igv/issues)
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data/lib/igv.rb
CHANGED
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@@ -5,11 +5,11 @@ require 'fileutils'
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class IGV
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class Error < StandardError; end
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attr_reader :host, :port, :snapshot_dir, :
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attr_reader :host, :port, :snapshot_dir, :history
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def initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
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@host = host
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@port = port
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-
@
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@history = []
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connect
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set_snapshot_dir(snapshot_dir)
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end
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@@ -30,11 +30,20 @@ class IGV
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alias goto go
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def genome(name_or_path)
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-
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path = File.expand_path(name_or_path)
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if File.exist?(path)
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send 'genome ' + path
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else
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send 'genome ' + name_or_path
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end
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end
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def load(path_or_url)
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-
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if URI.parse(path_or_url).scheme
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send 'load ' + path_or_url
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else
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send 'load ' + File.expand_path(path_or_url)
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end
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end
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def region(contig, start, end_)
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@@ -49,16 +58,6 @@ class IGV
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end
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end
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-
def snapshot_dir=(snapshot_dir)
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snapshot_dir = File.expand_path(snapshot_dir)
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return if snapshot_dir == @snaphot_dir
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-
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FileUtils.mkdir_p(snapshot_dir)
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send "snapshotDirectory #{snapshot_dir}"
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@snapshot_dir = snapshot_dir
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end
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alias set_snapshot_dir snapshot_dir=
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-
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def expand(_track = '')
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send "expand #{track}"
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end
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@@ -77,11 +76,21 @@ class IGV
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alias quit exit
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def send(cmd)
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@
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@history << cmd
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@socket.puts(cmd.encode(Encoding::UTF_8))
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@socket.gets&.chomp("\n")
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end
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def snapshot_dir=(snapshot_dir)
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snapshot_dir = File.expand_path(snapshot_dir)
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return if snapshot_dir == @snaphot_dir
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FileUtils.mkdir_p(snapshot_dir)
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send "snapshotDirectory #{snapshot_dir}"
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@snapshot_dir = snapshot_dir
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end
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alias set_snapshot_dir snapshot_dir=
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def save(file_path = nil)
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if file_path
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# igv assumes the path is just a single filename, but
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data/lib/igv/version.rb
CHANGED
metadata
CHANGED
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@@ -1,14 +1,14 @@
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1
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--- !ruby/object:Gem::Specification
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name: ruby-igv
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version: !ruby/object:Gem::Version
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version: 0.0.
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version: 0.0.4
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platform: ruby
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authors:
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- kojix2
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2020-
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date: 2020-08-23 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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