parse_fasta 1.0.0 → 1.0.1
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- checksums.yaml +4 -4
- data/.gitignore +1 -0
- data/lib/parse_fasta/version.rb +1 -1
- metadata +1 -19
- data/doc/FastaFile.html +0 -292
- data/doc/File.html +0 -212
- data/doc/ParseFasta.html +0 -144
- data/doc/Sequence.html +0 -361
- data/doc/_index.html +0 -136
- data/doc/class_list.html +0 -54
- data/doc/css/common.css +0 -1
- data/doc/css/full_list.css +0 -57
- data/doc/css/style.css +0 -339
- data/doc/file.README.html +0 -161
- data/doc/file_list.html +0 -56
- data/doc/frames.html +0 -26
- data/doc/index.html +0 -161
- data/doc/js/app.js +0 -219
- data/doc/js/full_list.js +0 -178
- data/doc/js/jquery.js +0 -4
- data/doc/method_list.html +0 -71
- data/doc/top-level-namespace.html +0 -114
checksums.yaml
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data.tar.gz: d1bf3eb669efe8d5747315315b1cbb7370d70ed0614e64ea44beb9fd08990554e4609364ce623a54e896e74becd222c124da92ff5a716acfccc55b9887f5cf24
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data/.gitignore
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data/lib/parse_fasta/version.rb
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metadata
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--- !ruby/object:Gem::Specification
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name: parse_fasta
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version: !ruby/object:Gem::Version
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version: 1.0.
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version: 1.0.1
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platform: ruby
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authors:
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- Ryan Moore
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data/doc/FastaFile.html
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— Documentation by YARD 0.8.7.4
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<dd class="r2 last">lib/parse_fasta/fasta_file.rb</dd>
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<p>Provides simple interface for parsing fasta format files.</p>
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Instance Method Summary
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<p class="tag_title">Examples:</p>
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<p>Parsing a fasta file</p>
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<pre class="example code"><code><span class='const'>FastaFile</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>reads.fna</span><span class='tstring_end'>'</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>r</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_record'>each_record</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='op'>|</span>
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<span class='id identifier rubyid_puts'>puts</span> <span class='lbracket'>[</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='period'>.</span><span class='id identifier rubyid_gc'>gc</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>"</span><span class='tstring_content'>\t</span><span class='tstring_end'>"</span></span><span class='rparen'>)</span>
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<span class='kw'>end</span></code></pre>
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<pre class="code"><span class="info file"># File 'lib/parse_fasta/fasta_file.rb', line 35</span>
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<span class='kw'>def</span> <span class='id identifier rubyid_each_record'>each_record</span>
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<span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>"</span><span class='tstring_content'>\n></span><span class='tstring_end'>"</span></span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_line'>line</span><span class='op'>|</span>
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<span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span> <span class='op'>=</span> <span class='id identifier rubyid_parse_line'>parse_line</span><span class='lparen'>(</span><span class='id identifier rubyid_line'>line</span><span class='rparen'>)</span>
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<span class='kw'>yield</span><span class='lparen'>(</span><span class='id identifier rubyid_header'>header</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='comma'>,</span> <span class='const'>Sequence</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_sequence'>sequence</span><span class='rparen'>)</span><span class='rparen'>)</span>
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Generated on Tue Jun 3 22:55:41 2014 by
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0.8.7.4 (ruby-2.1.1).
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<pre class="code"><span class="info file"># File 'lib/parse_fasta/file.rb', line 20</span>
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<span class='kw'>def</span> <span class='id identifier rubyid_each_record'>each_record</span>
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<span class='kw'>yield</span> <span class='id identifier rubyid_header'>header</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span>
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