bio-svgenes 0.3.1 → 0.3.2
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.
- data/README.md +88 -0
- data/VERSION +1 -1
- data/bio-svgenes.gemspec +131 -8
- data/doc/classes/Bio.html +131 -0
- data/doc/classes/Bio/Graphics.html +142 -0
- data/doc/classes/Bio/Graphics/Glyph.html +987 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000001.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000002.html +27 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000003.html +32 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000004.html +27 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000005.html +25 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000006.html +29 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000007.html +107 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000008.html +51 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000009.html +23 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000010.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000011.html +75 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000012.html +51 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000013.html +23 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000014.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000015.html +27 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000016.html +32 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000017.html +27 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000018.html +25 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000019.html +29 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000020.html +107 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000021.html +51 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000022.html +23 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000023.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000024.html +75 -0
- data/doc/classes/Bio/Graphics/MiniFeature.html +243 -0
- data/doc/classes/Bio/Graphics/MiniFeature.src/M000001.html +25 -0
- data/doc/classes/Bio/Graphics/MiniFeature.src/M000003.html +25 -0
- data/doc/classes/Bio/Graphics/MiniFeature.src/M000024.html +25 -0
- data/doc/classes/Bio/Graphics/Page.html +705 -0
- data/doc/classes/Bio/Graphics/Page.src/M000010.html +35 -0
- data/doc/classes/Bio/Graphics/Page.src/M000011.html +83 -0
- data/doc/classes/Bio/Graphics/Page.src/M000012.html +24 -0
- data/doc/classes/Bio/Graphics/Page.src/M000013.html +29 -0
- data/doc/classes/Bio/Graphics/Page.src/M000014.html +24 -0
- data/doc/classes/Bio/Graphics/Page.src/M000015.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000016.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000017.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000018.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000019.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000020.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000021.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000022.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000023.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000024.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000025.html +35 -0
- data/doc/classes/Bio/Graphics/Page.src/M000026.html +83 -0
- data/doc/classes/Bio/Graphics/Page.src/M000027.html +24 -0
- data/doc/classes/Bio/Graphics/Page.src/M000028.html +29 -0
- data/doc/classes/Bio/Graphics/Page.src/M000029.html +24 -0
- data/doc/classes/Bio/Graphics/Page.src/M000030.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000031.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000032.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000033.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000034.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000035.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000036.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000037.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000038.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000039.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000040.html +107 -0
- data/doc/classes/Bio/Graphics/Page.src/M000041.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000042.html +23 -0
- data/doc/classes/Bio/Graphics/Page.src/M000043.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000044.html +18 -0
- data/doc/classes/Bio/Graphics/Primitive.html +204 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000001.html +21 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000002.html +20 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000008.html +21 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000009.html +20 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000022.html +21 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000023.html +20 -0
- data/doc/classes/Bio/Graphics/SVGEE.html +290 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000002.html +24 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000003.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000004.html +24 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000005.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000006.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000007.html +21 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000008.html +27 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000009.html +23 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000016.html +24 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000017.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000018.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000019.html +21 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000020.html +27 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000021.html +23 -0
- data/doc/classes/Bio/Graphics/Track.html +473 -0
- data/doc/classes/Bio/Graphics/Track.src/M000001.html +35 -0
- data/doc/classes/Bio/Graphics/Track.src/M000002.html +18 -0
- data/doc/classes/Bio/Graphics/Track.src/M000003.html +28 -0
- data/doc/classes/Bio/Graphics/Track.src/M000004.html +18 -0
- data/doc/classes/Bio/Graphics/Track.src/M000010.html +35 -0
- data/doc/classes/Bio/Graphics/Track.src/M000011.html +18 -0
- data/doc/classes/Bio/Graphics/Track.src/M000012.html +28 -0
- data/doc/classes/Bio/Graphics/Track.src/M000013.html +18 -0
- data/doc/created.rid +1 -9
- data/doc/files/lib/bio-svgenes_rb.html +131 -0
- data/doc/files/lib/bio/graphics/glyph_rb.html +101 -0
- data/doc/files/lib/bio/graphics/mini_feature_rb.html +101 -0
- data/doc/files/lib/bio/graphics/page_rb.html +111 -0
- data/doc/files/lib/bio/graphics/primitive_rb.html +101 -0
- data/doc/files/lib/bio/graphics/svgee_rb.html +101 -0
- data/doc/files/lib/bio/graphics/track_rb.html +101 -0
- data/doc/fr_class_index.html +34 -0
- data/doc/fr_file_index.html +33 -0
- data/doc/fr_method_index.html +70 -0
- data/doc/index.html +21 -91
- data/doc/manual/bootstrap/css/bootstrap-responsive.css +1109 -0
- data/doc/manual/bootstrap/css/bootstrap-responsive.min.css +9 -0
- data/doc/manual/bootstrap/css/bootstrap.css +6158 -0
- data/doc/manual/bootstrap/css/bootstrap.min.css +9 -0
- data/doc/manual/bootstrap/img/glyphicons-halflings-white.png +0 -0
- data/doc/manual/bootstrap/img/glyphicons-halflings.png +0 -0
- data/doc/manual/bootstrap/js/bootstrap.js +2276 -0
- data/doc/manual/bootstrap/js/bootstrap.min.js +6 -0
- data/doc/manual/img/circle.png +0 -0
- data/doc/manual/img/directed.png +0 -0
- data/doc/manual/img/down_triangle.png +0 -0
- data/doc/manual/img/histogram.png +0 -0
- data/doc/manual/img/span.png +0 -0
- data/doc/manual/img/transcript.png +0 -0
- data/doc/manual/img/up_triangle.png +0 -0
- data/doc/manual/manual.html +360 -0
- data/doc/manual/manual.md +307 -0
- data/doc/rdoc-style.css +208 -0
- data/examples/example.rb +12 -8
- data/examples/{make_example.rb → example2.rb} +5 -16
- data/lib/bio/graphics/glyph.rb +293 -126
- data/lib/bio/graphics/mini_feature.rb +24 -17
- data/lib/bio/graphics/page.rb +112 -54
- data/lib/bio/graphics/primitive.rb +12 -9
- data/lib/bio/graphics/svgee.rb +9 -11
- data/lib/bio/graphics/track.rb +92 -10
- metadata +132 -9
- data/README.rdoc +0 -19
- data/examples/annotate_snps.rb +0 -86
- data/examples/eg2.rb +0 -40
- data/examples/get_coverage_in_windows.rb +0 -176
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<title>new (Bio::Graphics::Page)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 16</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>]
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<span class="ruby-ivar">@width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:width</span>]
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<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:style</span>] = <span class="ruby-node">"background-color:#{args[:background_color]};"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:background_color</span>]
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<span class="ruby-ivar">@svg</span> = <span class="ruby-constant">SVGEE</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-ivar">@scale_start</span> = <span class="ruby-value">1.0</span><span class="ruby-operator">/</span><span class="ruby-value">0</span><span class="ruby-value">.0</span>
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<span class="ruby-ivar">@scale_stop</span> = <span class="ruby-value">-1.0</span><span class="ruby-operator">/</span><span class="ruby-value">0</span><span class="ruby-value">.0</span>
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<span class="ruby-ivar">@tracks</span> = [] <span class="ruby-comment cmt">#array of track objects with loads of features in it...</span>
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<span class="ruby-ivar">@nt_per_percent</span> = <span class="ruby-value">1</span>;
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<span class="ruby-ivar">@num_intervals</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:number_of_intervals</span>]
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<span class="ruby-ivar">@track_top</span> = <span class="ruby-value">30</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">update_height</span>(<span class="ruby-identifier">height</span>)
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<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">height</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt">#def @svg.update_width(width)</span>
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<span class="ruby-comment cmt"># @width = width</span>
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<span class="ruby-comment cmt">#end</span>
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<span class="ruby-keyword kw">end</span></pre>
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<html>
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<title>from_json (Bio::Graphics::Page)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 39</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span><span class="ruby-keyword kw">self</span>..<span class="ruby-identifier">from_json</span><span class="ruby-identifier">from_json</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-identifier">require</span> <span class="ruby-value str">'rubygems'</span>
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<span class="ruby-identifier">require</span> <span class="ruby-value str">'json'</span>
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<span class="ruby-identifier">data</span> = <span class="ruby-constant">JSON</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:json</span>], <span class="ruby-value str">'r'</span>).<span class="ruby-identifier">read</span>)
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<span class="ruby-identifier">p</span> = <span class="ruby-constant">Page</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-value str">"Page"</span>][<span class="ruby-value str">"width"</span>],
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<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-value str">"Page"</span>][<span class="ruby-value str">"height"</span>],
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<span class="ruby-identifier">:number_of_intervals</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-value str">"Page"</span>][<span class="ruby-value str">"intervals"</span>])
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<span class="ruby-identifier">data</span>[<span class="ruby-value str">"Tracks"</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
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<span class="ruby-comment cmt">#prep the track args</span>
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<span class="ruby-identifier">track_args</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">dup</span>
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<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value str">"file"</span>)
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<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value str">"file_type"</span>)
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<span class="ruby-identifier">track_args</span> = <span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">inject</span>({}) { <span class="ruby-operator">|</span><span class="ruby-identifier">memo</span>, (<span class="ruby-identifier">k</span>, <span class="ruby-identifier">v</span>)<span class="ruby-operator">|</span> <span class="ruby-identifier">memo</span>[<span class="ruby-identifier">k</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">v</span>; <span class="ruby-identifier">memo</span> }
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<span class="ruby-comment cmt">##convert any of the pre-made gradient strings in the keys to symbol</span>
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<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">each_key</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
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<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">respond_to?</span>(<span class="ruby-identifier">:to_sym</span>)
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<span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>] = <span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">to_sym</span> <span class="ruby-keyword kw">if</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradients</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">to_sym</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-identifier">svg_track</span> = <span class="ruby-identifier">p</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">track_args</span>)
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<span class="ruby-identifier">features</span> = [] <span class="ruby-comment cmt">##set up the features...</span>
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<span class="ruby-keyword kw">case</span> <span class="ruby-identifier">track</span>[<span class="ruby-value str">"file_type"</span>] <span class="ruby-comment cmt">##deal with the gff and data files</span>
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<span class="ruby-keyword kw">when</span> <span class="ruby-value str">"gff"</span>
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<span class="ruby-identifier">groups</span> = {}
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<span class="ruby-identifier">parentless_features</span> = []
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<span class="ruby-constant">Page</span>.<span class="ruby-identifier">parse_gff</span>(<span class="ruby-identifier">track</span>[<span class="ruby-value str">"file"</span>]).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gff</span><span class="ruby-operator">|</span> <span class="ruby-comment cmt">#gets features in a list and links their children to them as members of the array at the key</span>
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<span class="ruby-identifier">parent_id</span> = <span class="ruby-identifier">gff</span>.<span class="ruby-identifier">attributes</span>.<span class="ruby-identifier">select</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">first</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'Parent'</span> }
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">empty?</span>
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<span class="ruby-identifier">parentless_features</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>].<span class="ruby-identifier">nil?</span>
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<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] = []
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<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span>
|
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<span class="ruby-comment cmt">#now flick through the parentless features and add any exons / UTRs</span>
|
|
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|
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<span class="ruby-identifier">parentless_features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">plf</span><span class="ruby-operator">|</span>
|
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|
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<span class="ruby-identifier">require</span> <span class="ruby-value str">'pp'</span>
|
|
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|
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<span class="ruby-comment cmt">#pp parentless_features</span>
|
|
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|
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<span class="ruby-identifier">gff_id</span> = <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">attributes</span>.<span class="ruby-identifier">select</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">first</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'ID'</span> }
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<span class="ruby-identifier">gff_id</span> = <span class="ruby-identifier">gff_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>
|
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<span class="ruby-identifier">exons</span> = []
|
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<span class="ruby-identifier">utrs</span> = []
|
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<span class="ruby-identifier">children</span> = <span class="ruby-identifier">groups</span>[<span class="ruby-identifier">gff_id</span>] <span class="ruby-operator">||</span> <span class="ruby-identifier">children</span> = []
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<span class="ruby-identifier">children</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">child</span><span class="ruby-operator">|</span>
|
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'exon'</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'CDS'</span>
|
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<span class="ruby-identifier">exons</span> <span class="ruby-operator">+=</span> [<span class="ruby-identifier">child</span>.<span class="ruby-identifier">start</span>, <span class="ruby-identifier">child</span>.<span class="ruby-identifier">end</span>]
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/utr/i</span>
|
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<span class="ruby-identifier">utrs</span> <span class="ruby-operator">+=</span> [<span class="ruby-identifier">child</span>.<span class="ruby-identifier">start</span>, <span class="ruby-identifier">child</span>.<span class="ruby-identifier">end</span>]
|
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span>
|
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<span class="ruby-identifier">features</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">MiniFeature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:start</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">start</span>, <span class="ruby-identifier">:end</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">end</span>, <span class="ruby-identifier">:exons</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">exons</span>, <span class="ruby-identifier">:utrs</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">utrs</span>, <span class="ruby-identifier">:strand</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">strand</span>, <span class="ruby-identifier">:id</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">gff_id</span>)
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<span class="ruby-keyword kw">end</span> <span class="ruby-comment cmt">#parentless features end</span>
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<span class="ruby-keyword kw">when</span> <span class="ruby-value str">"data"</span>
|
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<span class="ruby-comment cmt">##each line is a data feature</span>
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<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">track</span>[<span class="ruby-value str">"file"</span>], <span class="ruby-value str">"r"</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">start</span>, <span class="ruby-identifier">stop</span>, <span class="ruby-identifier">value</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\t/</span>)
|
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<span class="ruby-identifier">features</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">MiniFeature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:start</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">start</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-identifier">:end</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">stop</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-identifier">:segment_height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">value</span>.<span class="ruby-identifier">to_f</span>)
|
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span> <span class="ruby-comment cmt">#data end</span>
|
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|
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<span class="ruby-identifier">features</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">svg_track</span>.<span class="ruby-identifier">add</span>(<span class="ruby-identifier">f</span>) }
|
|
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|
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<span class="ruby-keyword kw">end</span> <span class="ruby-comment cmt">#track end</span>
|
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|
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<span class="ruby-identifier">p</span>.<span class="ruby-identifier">write</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:outfile</span>])
|
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<span class="ruby-keyword kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 111</span>
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">parse_gff</span>(<span class="ruby-identifier">gff_file</span>)
|
|
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|
+
<span class="ruby-identifier">require</span> <span class="ruby-value str">'bio'</span>
|
|
16
|
+
<span class="ruby-identifier">a</span> = []
|
|
17
|
+
<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">gff_file</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
|
|
18
|
+
<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">line</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/^#/</span>
|
|
19
|
+
<span class="ruby-identifier">a</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">GFF</span><span class="ruby-operator">::</span><span class="ruby-constant">GFF3</span><span class="ruby-operator">::</span><span class="ruby-constant">Record</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
|
|
20
|
+
<span class="ruby-keyword kw">end</span>
|
|
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|
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<span class="ruby-identifier">a</span>
|
|
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|
+
<span class="ruby-keyword kw">end</span></pre>
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<title>add_track (Bio::Graphics::Page)</title>
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 206</span>
|
|
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|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">args</span>)
|
|
15
|
+
<span class="ruby-comment cmt">#sort out the colour/gradient options</span>
|
|
16
|
+
[<span class="ruby-identifier">:fill_color</span>, <span class="ruby-identifier">:exon_fill_color</span>, <span class="ruby-identifier">:utr_fill_color</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">colour_tag</span><span class="ruby-operator">|</span>
|
|
17
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradients</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>])
|
|
18
|
+
<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>]))
|
|
19
|
+
<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>] = <span class="ruby-node">"url(##{args[colour_tag]})"</span>
|
|
20
|
+
<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>].<span class="ruby-identifier">instance_of?</span>(<span class="ruby-constant">Hash</span>)
|
|
21
|
+
<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>])
|
|
22
|
+
<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>] = <span class="ruby-node">"url(##{args[colour_tag][:id]})"</span>
|
|
23
|
+
<span class="ruby-keyword kw">end</span>
|
|
24
|
+
<span class="ruby-keyword kw">end</span>
|
|
25
|
+
<span class="ruby-ivar">@tracks</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Track</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">args</span>)
|
|
26
|
+
<span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">last</span>
|
|
27
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
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|
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|
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|
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<title>get_limits (Bio::Graphics::Page)</title>
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 222</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_limits</span>
|
|
15
|
+
<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
|
16
|
+
<span class="ruby-identifier">lowest</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">x</span>, <span class="ruby-identifier">y</span><span class="ruby-operator">|</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">y</span>.<span class="ruby-identifier">start</span> }.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">start</span>
|
|
17
|
+
<span class="ruby-identifier">highest</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">x</span>, <span class="ruby-identifier">y</span><span class="ruby-operator">|</span> <span class="ruby-identifier">y</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">end</span> }.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">end</span>
|
|
18
|
+
<span class="ruby-ivar">@scale_start</span> = <span class="ruby-identifier">lowest</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">lowest</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@scale_start</span>
|
|
19
|
+
<span class="ruby-ivar">@scale_stop</span> = <span class="ruby-identifier">highest</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">highest</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@scale_stop</span>
|
|
20
|
+
<span class="ruby-ivar">@nt_per_px_x</span> = (<span class="ruby-ivar">@scale_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@width</span>.<span class="ruby-identifier">to_f</span>
|
|
21
|
+
<span class="ruby-keyword kw">end</span>
|
|
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|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
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<title>draw_scale (Bio::Graphics::Page)</title>
|
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 233</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_scale</span>
|
|
15
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">scale</span>(<span class="ruby-identifier">:start</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@scale_start</span>,
|
|
16
|
+
<span class="ruby-identifier">:stop</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@scale_stop</span>,
|
|
17
|
+
<span class="ruby-identifier">:number_of_intervals</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@num_intervals</span>, <span class="ruby-identifier">:page_width</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@width</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
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|
+
<span class="ruby-keyword kw">end</span></pre>
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<title>draw_label (Bio::Graphics::Page)</title>
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 241</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_label</span>(<span class="ruby-identifier">args</span>)
|
|
15
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">label</span>(<span class="ruby-identifier">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:text</span>],
|
|
16
|
+
<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x</span>],
|
|
17
|
+
<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>]).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
18
|
+
<span class="ruby-keyword kw">end</span></pre>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_generic</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment cmt">#remember presentation info comes from track@args when the track is defined</span>
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">generic</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_directed</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 256</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_circle</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">circle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 260</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_transcript</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">transcript</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 264</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_histogram</span>(<span class="ruby-identifier">args</span>)
|
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|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">generic</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 268</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_up_triangle</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">up_triangle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 272</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_down_triangle</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">down_triangle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 276</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_span</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">span</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 16</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>]
|
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<span class="ruby-ivar">@width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:width</span>]
|
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<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:style</span>] = <span class="ruby-node">"background-color:#{args[:background_color]};"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:background_color</span>]
|
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<span class="ruby-ivar">@svg</span> = <span class="ruby-constant">SVGEE</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-ivar">@scale_start</span> = <span class="ruby-value">1.0</span><span class="ruby-operator">/</span><span class="ruby-value">0</span><span class="ruby-value">.0</span>
|
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<span class="ruby-ivar">@scale_stop</span> = <span class="ruby-value">-1.0</span><span class="ruby-operator">/</span><span class="ruby-value">0</span><span class="ruby-value">.0</span>
|
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<span class="ruby-ivar">@tracks</span> = [] <span class="ruby-comment cmt">#array of track objects with loads of features in it...</span>
|
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<span class="ruby-ivar">@nt_per_percent</span> = <span class="ruby-value">1</span>;
|
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<span class="ruby-ivar">@num_intervals</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:number_of_intervals</span>]
|
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|
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<span class="ruby-ivar">@track_top</span> = <span class="ruby-value">30</span>
|
|
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|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">update_height</span>(<span class="ruby-identifier">height</span>)
|
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|
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<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">height</span>
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|
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<span class="ruby-comment cmt">#def @svg.update_width(width)</span>
|
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|
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<span class="ruby-comment cmt">#end</span>
|
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|
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<span class="ruby-keyword kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 39</span>
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span><span class="ruby-keyword kw">self</span>..<span class="ruby-identifier">from_json</span><span class="ruby-identifier">from_json</span>(<span class="ruby-identifier">args</span>)
|
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|
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<span class="ruby-identifier">require</span> <span class="ruby-value str">'rubygems'</span>
|
|
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|
+
<span class="ruby-identifier">require</span> <span class="ruby-value str">'json'</span>
|
|
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|
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<span class="ruby-identifier">data</span> = <span class="ruby-constant">JSON</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:json</span>], <span class="ruby-value str">'r'</span>).<span class="ruby-identifier">read</span>)
|
|
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|
+
<span class="ruby-identifier">p</span> = <span class="ruby-constant">Page</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-value str">"Page"</span>][<span class="ruby-value str">"width"</span>],
|
|
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|
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<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-value str">"Page"</span>][<span class="ruby-value str">"height"</span>],
|
|
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|
+
<span class="ruby-identifier">:number_of_intervals</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-value str">"Page"</span>][<span class="ruby-value str">"intervals"</span>])
|
|
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|
+
<span class="ruby-identifier">data</span>[<span class="ruby-value str">"Tracks"</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
|
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|
+
<span class="ruby-comment cmt">#prep the track args</span>
|
|
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|
+
<span class="ruby-identifier">track_args</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">dup</span>
|
|
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|
+
<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value str">"file"</span>)
|
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25
|
+
<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value str">"file_type"</span>)
|
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26
|
+
<span class="ruby-identifier">track_args</span> = <span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">inject</span>({}) { <span class="ruby-operator">|</span><span class="ruby-identifier">memo</span>, (<span class="ruby-identifier">k</span>, <span class="ruby-identifier">v</span>)<span class="ruby-operator">|</span> <span class="ruby-identifier">memo</span>[<span class="ruby-identifier">k</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">v</span>; <span class="ruby-identifier">memo</span> }
|
|
27
|
+
<span class="ruby-comment cmt">##convert any of the pre-made gradient strings in the keys to symbol</span>
|
|
28
|
+
<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">each_key</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
|
|
29
|
+
<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">respond_to?</span>(<span class="ruby-identifier">:to_sym</span>)
|
|
30
|
+
<span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>] = <span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">to_sym</span> <span class="ruby-keyword kw">if</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradients</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">to_sym</span>)
|
|
31
|
+
<span class="ruby-keyword kw">end</span>
|
|
32
|
+
|
|
33
|
+
<span class="ruby-identifier">svg_track</span> = <span class="ruby-identifier">p</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">track_args</span>)
|
|
34
|
+
<span class="ruby-identifier">features</span> = [] <span class="ruby-comment cmt">##set up the features...</span>
|
|
35
|
+
|
|
36
|
+
<span class="ruby-keyword kw">case</span> <span class="ruby-identifier">track</span>[<span class="ruby-value str">"file_type"</span>] <span class="ruby-comment cmt">##deal with the gff and data files</span>
|
|
37
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-value str">"gff"</span>
|
|
38
|
+
<span class="ruby-identifier">groups</span> = {}
|
|
39
|
+
<span class="ruby-identifier">parentless_features</span> = []
|
|
40
|
+
<span class="ruby-constant">Page</span>.<span class="ruby-identifier">parse_gff</span>(<span class="ruby-identifier">track</span>[<span class="ruby-value str">"file"</span>]).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gff</span><span class="ruby-operator">|</span> <span class="ruby-comment cmt">#gets features in a list and links their children to them as members of the array at the key</span>
|
|
41
|
+
<span class="ruby-identifier">parent_id</span> = <span class="ruby-identifier">gff</span>.<span class="ruby-identifier">attributes</span>.<span class="ruby-identifier">select</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">first</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'Parent'</span> }
|
|
42
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">empty?</span>
|
|
43
|
+
<span class="ruby-identifier">parentless_features</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
|
|
44
|
+
<span class="ruby-keyword kw">else</span>
|
|
45
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>].<span class="ruby-identifier">nil?</span>
|
|
46
|
+
<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] = []
|
|
47
|
+
<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
|
|
48
|
+
<span class="ruby-keyword kw">else</span>
|
|
49
|
+
<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
|
|
50
|
+
<span class="ruby-keyword kw">end</span>
|
|
51
|
+
<span class="ruby-keyword kw">end</span>
|
|
52
|
+
<span class="ruby-keyword kw">end</span>
|
|
53
|
+
<span class="ruby-comment cmt">#now flick through the parentless features and add any exons / UTRs</span>
|
|
54
|
+
<span class="ruby-identifier">parentless_features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">plf</span><span class="ruby-operator">|</span>
|
|
55
|
+
<span class="ruby-identifier">require</span> <span class="ruby-value str">'pp'</span>
|
|
56
|
+
<span class="ruby-comment cmt">#pp parentless_features</span>
|
|
57
|
+
<span class="ruby-identifier">gff_id</span> = <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">attributes</span>.<span class="ruby-identifier">select</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">first</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'ID'</span> }
|
|
58
|
+
<span class="ruby-identifier">gff_id</span> = <span class="ruby-identifier">gff_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>
|
|
59
|
+
<span class="ruby-identifier">exons</span> = []
|
|
60
|
+
<span class="ruby-identifier">utrs</span> = []
|
|
61
|
+
<span class="ruby-identifier">children</span> = <span class="ruby-identifier">groups</span>[<span class="ruby-identifier">gff_id</span>] <span class="ruby-operator">||</span> <span class="ruby-identifier">children</span> = []
|
|
62
|
+
<span class="ruby-identifier">children</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">child</span><span class="ruby-operator">|</span>
|
|
63
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'exon'</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'CDS'</span>
|
|
64
|
+
<span class="ruby-identifier">exons</span> <span class="ruby-operator">+=</span> [<span class="ruby-identifier">child</span>.<span class="ruby-identifier">start</span>, <span class="ruby-identifier">child</span>.<span class="ruby-identifier">end</span>]
|
|
65
|
+
<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/utr/i</span>
|
|
66
|
+
<span class="ruby-identifier">utrs</span> <span class="ruby-operator">+=</span> [<span class="ruby-identifier">child</span>.<span class="ruby-identifier">start</span>, <span class="ruby-identifier">child</span>.<span class="ruby-identifier">end</span>]
|
|
67
|
+
<span class="ruby-keyword kw">end</span>
|
|
68
|
+
<span class="ruby-keyword kw">end</span>
|
|
69
|
+
<span class="ruby-identifier">features</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">MiniFeature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:start</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">start</span>, <span class="ruby-identifier">:end</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">end</span>, <span class="ruby-identifier">:exons</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">exons</span>, <span class="ruby-identifier">:utrs</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">utrs</span>, <span class="ruby-identifier">:strand</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">strand</span>, <span class="ruby-identifier">:id</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">gff_id</span>)
|
|
70
|
+
<span class="ruby-keyword kw">end</span> <span class="ruby-comment cmt">#parentless features end</span>
|
|
71
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-value str">"data"</span>
|
|
72
|
+
<span class="ruby-comment cmt">##each line is a data feature</span>
|
|
73
|
+
<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">track</span>[<span class="ruby-value str">"file"</span>], <span class="ruby-value str">"r"</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
|
|
74
|
+
<span class="ruby-identifier">start</span>, <span class="ruby-identifier">stop</span>, <span class="ruby-identifier">value</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\t/</span>)
|
|
75
|
+
<span class="ruby-identifier">features</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">MiniFeature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:start</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">start</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-identifier">:end</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">stop</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-identifier">:segment_height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">value</span>.<span class="ruby-identifier">to_f</span>)
|
|
76
|
+
<span class="ruby-keyword kw">end</span>
|
|
77
|
+
<span class="ruby-keyword kw">end</span> <span class="ruby-comment cmt">#data end</span>
|
|
78
|
+
<span class="ruby-identifier">features</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">svg_track</span>.<span class="ruby-identifier">add</span>(<span class="ruby-identifier">f</span>) }
|
|
79
|
+
<span class="ruby-keyword kw">end</span> <span class="ruby-comment cmt">#track end</span>
|
|
80
|
+
<span class="ruby-identifier">p</span>.<span class="ruby-identifier">write</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:outfile</span>])
|
|
81
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
82
|
+
</body>
|
|
83
|
+
</html>
|