ruby-igv 0.0.1 → 0.0.2

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Files changed (5) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +11 -7
  3. data/lib/igv.rb +3 -3
  4. data/lib/igv/version.rb +1 -1
  5. metadata +1 -1
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data/README.md CHANGED
@@ -1,6 +1,10 @@
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  # Ruby-IGV
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- Using Integrative Genomics Viewer (IGV) with the Ruby language.
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+ [![Gem Version](https://badge.fury.io/rb/ruby-igv.svg)](https://badge.fury.io/rb/ruby-igv)
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+ [![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://rubydoc.info/gems/ruby-igv)
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+ [![The MIT License](https://img.shields.io/badge/license-MIT-orange.svg)](LICENSE.txt)
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+
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+ Using [Integrative Genomics Viewer (IGV)](http://software.broadinstitute.org/software/igv/) with the Ruby language.
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  Based on [brentp/bio-playground/igv](https://github.com/brentp/bio-playground).
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@@ -14,12 +18,12 @@ gem install ruby-igv
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  ```ruby
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  igv = IGV.new
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- igv.gnome 'hg19'
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- igv.load 'http://www.broadinstitute.org/igvdata/1KG/pilot2Bams/NA12878.SLX.bam'
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- igv.go 'chr1:45,600-45,800'
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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.send 'echo' #whatever
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+ igv.genome 'hg19'
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+ igv.load 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562G1AlnRep1.bam'
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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.send 'echo' #whatever
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  ```
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  ## Contributing
data/lib/igv.rb CHANGED
@@ -7,7 +7,7 @@ class IGV
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  class Error < StandardError; end
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  attr_reader :host, :port, :snapshot_dir, :commands
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- def initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: '/tmp/igv')
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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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  @commands = []
@@ -83,8 +83,8 @@ class IGV
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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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  # we can set the snapshot dir. then just use the filename.
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- dir_path = Pathname(File.expand_path(file_path)).dirname
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- set_snapshot_dir(dir_path)
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+ dir_path = File.dirname(file_path)
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+ set_snapshot_dir(File.expand_path(dir_path)) if dir_path != '.'
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  send 'snapshot ' + File.basename(file_path)
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  else
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  send 'snapshot'
@@ -1,3 +1,3 @@
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  class IGV
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- VERSION = '0.0.1'.freeze
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+ VERSION = '0.0.2'.freeze
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
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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: 0.0.1
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+ version: 0.0.2
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  platform: ruby
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  authors:
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  - kojix2