bio-gngm 0.1.0

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  1. data/.document +5 -0
  2. data/Gemfile +20 -0
  3. data/Gemfile.lock +33 -0
  4. data/LICENSE.txt +20 -0
  5. data/README.rdoc +33 -0
  6. data/Rakefile +53 -0
  7. data/VERSION +1 -0
  8. data/bio-gngm.gemspec +173 -0
  9. data/doc/Bio.html +129 -0
  10. data/doc/Bio/DB.html +128 -0
  11. data/doc/Bio/DB/Pileup.html +316 -0
  12. data/doc/Bio/DB/Vcf.html +683 -0
  13. data/doc/Bio/Util.html +135 -0
  14. data/doc/Bio/Util/Gngm.html +1655 -0
  15. data/doc/LICENSE_txt.html +111 -0
  16. data/doc/_index.html +169 -0
  17. data/doc/class_list.html +47 -0
  18. data/doc/created.rid +4 -0
  19. data/doc/css/common.css +1 -0
  20. data/doc/css/full_list.css +55 -0
  21. data/doc/css/style.css +322 -0
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  23. data/doc/file_list.html +52 -0
  24. data/doc/frames.html +13 -0
  25. data/doc/images/add.png +0 -0
  26. data/doc/images/bands.png +0 -0
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  47. data/doc/images/threads.png +0 -0
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  52. data/doc/index.html +88 -0
  53. data/doc/js/app.js +205 -0
  54. data/doc/js/darkfish.js +153 -0
  55. data/doc/js/full_list.js +167 -0
  56. data/doc/js/jquery.js +18 -0
  57. data/doc/js/navigation.js +142 -0
  58. data/doc/js/search.js +94 -0
  59. data/doc/js/search_index.js +1 -0
  60. data/doc/js/searcher.js +228 -0
  61. data/doc/lib/bio-gngm_rb.html +103 -0
  62. data/doc/lib/bio/util/bio-gngm_rb.html +96 -0
  63. data/doc/method_list.html +382 -0
  64. data/doc/rdoc.css +543 -0
  65. data/doc/table_of_contents.html +161 -0
  66. data/examples/.DS_Store +0 -0
  67. data/examples/make_histograms.rb +40 -0
  68. data/examples/make_threads.rb +42 -0
  69. data/examples/make_threads_isize.rb +41 -0
  70. data/examples/use_indels.rb +36 -0
  71. data/lib/bio-gngm.rb +12 -0
  72. data/lib/bio/util/bio-gngm.rb +1029 -0
  73. data/scripts/get_subseq.rb +16 -0
  74. data/scripts/make_histograms_laerfyve.rb +83 -0
  75. data/scripts/make_histograms_laerfyve_stitched.rb +59 -0
  76. data/scripts/make_threads_isize_laerfyfe.rb +52 -0
  77. data/scripts/make_threads_unmapped_laerfyfe.rb +72 -0
  78. data/scripts/make_threads_unmapped_laerfyfe_pseudo.rb +56 -0
  79. data/scripts/make_threads_unmapped_simulation.rb +54 -0
  80. data/scripts/make_threads_unmapped_simulation_immediate_region.rb +59 -0
  81. data/scripts/optimise_freq_window_size.rb +82 -0
  82. data/stitched_contigs.zip +0 -0
  83. data/test/data/ids2.txt +1 -0
  84. data/test/data/sorted.bam +0 -0
  85. data/test/data/test +0 -0
  86. data/test/data/test.bam +0 -0
  87. data/test/data/test.fa +20 -0
  88. data/test/data/test.fai +0 -0
  89. data/test/data/test.sai +0 -0
  90. data/test/data/test.tam +10 -0
  91. data/test/data/test_chr.fasta +1000 -0
  92. data/test/data/test_chr.fasta.amb +2 -0
  93. data/test/data/test_chr.fasta.ann +3 -0
  94. data/test/data/test_chr.fasta.bwt +0 -0
  95. data/test/data/test_chr.fasta.fai +1 -0
  96. data/test/data/test_chr.fasta.pac +0 -0
  97. data/test/data/test_chr.fasta.rbwt +0 -0
  98. data/test/data/test_chr.fasta.rpac +0 -0
  99. data/test/data/test_chr.fasta.rsa +0 -0
  100. data/test/data/test_chr.fasta.sa +0 -0
  101. data/test/data/testu.bam +0 -0
  102. data/test/data/testu.bam.bai +0 -0
  103. data/test/helper.rb +18 -0
  104. data/test/test_bio-gngm.rb +126 -0
  105. metadata +276 -0
data/doc/lib/bio-gngm_rb.html ADDED
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+ <!DOCTYPE html>
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+ <html>
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+ <li><a href="../Bio.html">Bio</a>
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+ <p>Please require your code below, respecting the bioruby directory tree. For
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+ instance, perhaps the only uncommented line in this file might be
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+ something like this:</p>
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+
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+ <pre class="ruby"><span class="ruby-identifier">require</span> <span class="ruby-string">'bio/sequence/awesome_sequence_plugin_thingy'</span>
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+ </pre>
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+
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+ <p>and then create the ruby file ‘lib/bio/sequence/awesome_sequence_thingy.rb’
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+ and put your plugin’s code there. It is bad practice to write other code
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+ directly into this file, because doing so causes confusion if this biogem
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+ was ever to get merged into the main bioruby tree.</p>
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data/doc/lib/bio/util/bio-gngm_rb.html ADDED
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+ <li><a href="../../../Bio.html">Bio</a>
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+ <li><a href="../../../Bio/DB.html">Bio::DB</a>
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+ <li><a href="../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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+ <div id="documentation" class="description">
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+ <p>bio-gngm</p>
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+ <p>Created by Dan MacLean (TSL) on 2011-12-07. Copyright © . All rights
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+ reserved.</p>
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+ <span class='object_link'><a href="Bio/DB/Vcf.html#alternatives-instance_method" title="Bio::DB::Vcf#alternatives (method)">#alternatives</a></span>
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+ <small>Bio::DB::Vcf</small>
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+ </li>
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+ <li class="r2 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#calculate_clusters-instance_method" title="Bio::Util::Gngm#calculate_clusters (method)">#calculate_clusters</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ </li>
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+ <li class="r1 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#calculate_densities-instance_method" title="Bio::Util::Gngm#calculate_densities (method)">#calculate_densities</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ </li>
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+ <li class="r2 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#calculate_signal-instance_method" title="Bio::Util::Gngm#calculate_signal (method)">#calculate_signal</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ </li>
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+ <li class="r1 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#close-instance_method" title="Bio::Util::Gngm#close (method)">#close</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ </li>
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+ <li class="r2 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#clusters-instance_method" title="Bio::Util::Gngm#clusters (method)">#clusters</a></span>
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+
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+ <small>Bio::Util::Gngm</small>
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+ </li>
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+ <li class="r1 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#collect_threads-instance_method" title="Bio::Util::Gngm#collect_threads (method)">#collect_threads</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ </li>
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+ <li class="r2 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#densities-instance_method" title="Bio::Util::Gngm#densities (method)">#densities</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ </li>
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+ <li class="r1 ">
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+ <span class='object_link'><a href="Bio/DB/Pileup.html#discordant_chastity-instance_method" title="Bio::DB::Pileup#discordant_chastity (method)">#discordant_chastity</a></span>
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+ <small>Bio::DB::Pileup</small>
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+ </li>
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+ <li class="r2 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#draw_bands-instance_method" title="Bio::Util::Gngm#draw_bands (method)">#draw_bands</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ </li>
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+ <li class="r1 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#draw_hit_count-instance_method" title="Bio::Util::Gngm#draw_hit_count (method)">#draw_hit_count</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ <li class="r2 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#draw_peaks-instance_method" title="Bio::Util::Gngm#draw_peaks (method)">#draw_peaks</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ <li class="r1 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#draw_signal-instance_method" title="Bio::Util::Gngm#draw_signal (method)">#draw_signal</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ </li>
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+ <li class="r2 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#draw_threads-instance_method" title="Bio::Util::Gngm#draw_threads (method)">#draw_threads</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ </li>
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+ <li class="r1 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#file-instance_method" title="Bio::Util::Gngm#file (method)">#file</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ </li>
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+ <li class="r2 ">
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#get_band-instance_method" title="Bio::Util::Gngm#get_band (method)">#get_band</a></span>
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+ <small>Bio::Util::Gngm</small>
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#get_insert_size_frequency-instance_method" title="Bio::Util::Gngm#get_insert_size_frequency (method)">#get_insert_size_frequency</a></span>
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+ <span class='object_link'><a href="Bio/Util/Gngm.html#get_insert_size_frequency_from_bam-instance_method" title="Bio::Util::Gngm#get_insert_size_frequency_from_bam (method)">#get_insert_size_frequency_from_bam</a></span>
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+ <li class="r1 ">
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+ <span class='object_link'><a href="Bio/DB/Vcf.html#gq-instance_method" title="Bio::DB::Vcf#gq (method)">#gq</a></span>
189
+
190
+ <small>Bio::DB::Vcf</small>
191
+
192
+ </li>
193
+
194
+
195
+ <li class="r2 ">
196
+ <span class='object_link'><a href="Bio/DB/Vcf.html#has_just_one_variant%3F-instance_method" title="Bio::DB::Vcf#has_just_one_variant? (method)">#has_just_one_variant?</a></span>
197
+
198
+ <small>Bio::DB::Vcf</small>
199
+
200
+ </li>
201
+
202
+
203
+ <li class="r1 ">
204
+ <span class='object_link'><a href="Bio/Util/Gngm.html#hit_count-instance_method" title="Bio::Util::Gngm#hit_count (method)">#hit_count</a></span>
205
+
206
+ <small>Bio::Util::Gngm</small>
207
+
208
+ </li>
209
+
210
+
211
+ <li class="r2 ">
212
+ <span class='object_link'><a href="Bio/Util/Gngm.html#initialize-instance_method" title="Bio::Util::Gngm#initialize (method)">#initialize</a></span>
213
+
214
+ <small>Bio::Util::Gngm</small>
215
+
216
+ </li>
217
+
218
+
219
+ <li class="r1 ">
220
+ <span class='object_link'><a href="Bio/DB/Vcf.html#is_deletion%3F-instance_method" title="Bio::DB::Vcf#is_deletion? (method)">#is_deletion?</a></span>
221
+
222
+ <small>Bio::DB::Vcf</small>
223
+
224
+ </li>
225
+
226
+
227
+ <li class="r2 ">
228
+ <span class='object_link'><a href="Bio/DB/Vcf.html#is_indel%3F-instance_method" title="Bio::DB::Vcf#is_indel? (method)">#is_indel?</a></span>
229
+
230
+ <small>Bio::DB::Vcf</small>
231
+
232
+ </li>
233
+
234
+
235
+ <li class="r1 ">
236
+ <span class='object_link'><a href="Bio/DB/Vcf.html#is_insertion%3F-instance_method" title="Bio::DB::Vcf#is_insertion? (method)">#is_insertion?</a></span>
237
+
238
+ <small>Bio::DB::Vcf</small>
239
+
240
+ </li>
241
+
242
+
243
+ <li class="r2 ">
244
+ <span class='object_link'><a href="Bio/DB/Pileup.html#is_snp%3F-instance_method" title="Bio::DB::Pileup#is_snp? (method)">#is_snp?</a></span>
245
+
246
+ <small>Bio::DB::Pileup</small>
247
+
248
+ </li>
249
+
250
+
251
+ <li class="r1 ">
252
+ <span class='object_link'><a href="Bio/DB/Vcf.html#mq-instance_method" title="Bio::DB::Vcf#mq (method)">#mq</a></span>
253
+
254
+ <small>Bio::DB::Vcf</small>
255
+
256
+ </li>
257
+
258
+
259
+ <li class="r2 ">
260
+ <span class='object_link'><a href="Bio/DB/Vcf.html#non_ref_allele_count-instance_method" title="Bio::DB::Vcf#non_ref_allele_count (method)">#non_ref_allele_count</a></span>
261
+
262
+ <small>Bio::DB::Vcf</small>
263
+
264
+ </li>
265
+
266
+
267
+ <li class="r1 ">
268
+ <span class='object_link'><a href="Bio/DB/Vcf.html#non_ref_allele_freq-instance_method" title="Bio::DB::Vcf#non_ref_allele_freq (method)">#non_ref_allele_freq</a></span>
269
+
270
+ <small>Bio::DB::Vcf</small>
271
+
272
+ </li>
273
+
274
+
275
+ <li class="r2 ">
276
+ <span class='object_link'><a href="Bio/DB/Vcf.html#pass_quality%3F-instance_method" title="Bio::DB::Vcf#pass_quality? (method)">#pass_quality?</a></span>
277
+
278
+ <small>Bio::DB::Vcf</small>
279
+
280
+ </li>
281
+
282
+
283
+ <li class="r1 ">
284
+ <span class='object_link'><a href="Bio/Util/Gngm.html#peaks-instance_method" title="Bio::Util::Gngm#peaks (method)">#peaks</a></span>
285
+
286
+ <small>Bio::Util::Gngm</small>
287
+
288
+ </li>
289
+
290
+
291
+ <li class="r2 ">
292
+ <span class='object_link'><a href="Bio/DB/Vcf.html#pl-instance_method" title="Bio::DB::Vcf#pl (method)">#pl</a></span>
293
+
294
+ <small>Bio::DB::Vcf</small>
295
+
296
+ </li>
297
+
298
+
299
+ <li class="r1 ">
300
+ <span class='object_link'><a href="Bio/Util/Gngm.html#print_signal-instance_method" title="Bio::Util::Gngm#print_signal (method)">#print_signal</a></span>
301
+
302
+ <small>Bio::Util::Gngm</small>
303
+
304
+ </li>
305
+
306
+
307
+ <li class="r2 ">
308
+ <span class='object_link'><a href="Bio/DB/Pileup.html#second_non_ref_count-instance_method" title="Bio::DB::Pileup#second_non_ref_count (method)">#second_non_ref_count</a></span>
309
+
310
+ <small>Bio::DB::Pileup</small>
311
+
312
+ </li>
313
+
314
+
315
+ <li class="r1 ">
316
+ <span class='object_link'><a href="Bio/Util/Gngm.html#signal-instance_method" title="Bio::Util::Gngm#signal (method)">#signal</a></span>
317
+
318
+ <small>Bio::Util::Gngm</small>
319
+
320
+ </li>
321
+
322
+
323
+ <li class="r2 ">
324
+ <span class='object_link'><a href="Bio/Util/Gngm.html#snp_positions-instance_method" title="Bio::Util::Gngm#snp_positions (method)">#snp_positions</a></span>
325
+
326
+ <small>Bio::Util::Gngm</small>
327
+
328
+ </li>
329
+
330
+
331
+ <li class="r1 ">
332
+ <span class='object_link'><a href="Bio/DB/Pileup.html#third_non_ref_count-instance_method" title="Bio::DB::Pileup#third_non_ref_count (method)">#third_non_ref_count</a></span>
333
+
334
+ <small>Bio::DB::Pileup</small>
335
+
336
+ </li>
337
+
338
+
339
+ <li class="r2 ">
340
+ <span class='object_link'><a href="Bio/Util/Gngm.html#threads-instance_method" title="Bio::Util::Gngm#threads (method)">#threads</a></span>
341
+
342
+ <small>Bio::Util::Gngm</small>
343
+
344
+ </li>
345
+
346
+
347
+ <li class="r1 ">
348
+ <span class='object_link'><a href="Bio/DB/Vcf.html#to_s-instance_method" title="Bio::DB::Vcf#to_s (method)">#to_s</a></span>
349
+
350
+ <small>Bio::DB::Vcf</small>
351
+
352
+ </li>
353
+
354
+
355
+ <li class="r2 ">
356
+ <span class='object_link'><a href="Bio/DB/Pileup.html#top_non_ref_count-instance_method" title="Bio::DB::Pileup#top_non_ref_count (method)">#top_non_ref_count</a></span>
357
+
358
+ <small>Bio::DB::Pileup</small>
359
+
360
+ </li>
361
+
362
+
363
+ <li class="r1 ">
364
+ <span class='object_link'><a href="Bio/DB/Vcf.html#used_depth-instance_method" title="Bio::DB::Vcf#used_depth (method)">#used_depth</a></span>
365
+
366
+ <small>Bio::DB::Vcf</small>
367
+
368
+ </li>
369
+
370
+
371
+ <li class="r2 ">
372
+ <span class='object_link'><a href="Bio/DB/Vcf.html#variant%3F-instance_method" title="Bio::DB::Vcf#variant? (method)">#variant?</a></span>
373
+
374
+ <small>Bio::DB::Vcf</small>
375
+
376
+ </li>
377
+
378
+
379
+ </ul>
380
+ </div>
381
+ </body>
382
+ </html>