bio-samtools 0.6.2 → 2.0.3

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Files changed (160) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +3 -2
  3. data/README.md +4 -7
  4. data/VERSION +1 -1
  5. data/bio-samtools.gemspec +47 -105
  6. data/doc/Bio.html +68 -131
  7. data/doc/Bio/DB.html +51 -111
  8. data/doc/Bio/DB/Alignment.html +135 -363
  9. data/doc/Bio/DB/Pileup.html +183 -170
  10. data/doc/Bio/DB/SAM.html +1396 -820
  11. data/doc/Bio/DB/SAM/Library.html +73 -123
  12. data/doc/Bio/DB/SAM/Tools.html +51 -273
  13. data/doc/Bio/DB/Tag.html +78 -124
  14. data/doc/Bio/DB/Vcf.html +111 -147
  15. data/doc/LICENSE_txt.html +113 -148
  16. data/doc/created.rid +9 -10
  17. data/doc/fonts.css +167 -0
  18. data/doc/fonts/Lato-Light.ttf +0 -0
  19. data/doc/fonts/Lato-LightItalic.ttf +0 -0
  20. data/doc/fonts/Lato-Regular.ttf +0 -0
  21. data/doc/fonts/Lato-RegularItalic.ttf +0 -0
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  24. data/doc/images/add.png +0 -0
  25. data/doc/images/arrow_up.png +0 -0
  26. data/doc/images/delete.png +0 -0
  27. data/doc/images/tag_blue.png +0 -0
  28. data/doc/index.html +48 -54
  29. data/doc/js/darkfish.js +9 -22
  30. data/doc/js/search.js +20 -5
  31. data/doc/js/search_index.js +1 -1
  32. data/doc/rdoc.css +255 -218
  33. data/doc/table_of_contents.html +256 -137
  34. data/ext/Rakefile +57 -0
  35. data/lib/bio-samtools.rb +7 -2
  36. data/lib/bio/BIOExtensions.rb +89 -0
  37. data/lib/bio/db/alignment.rb +59 -0
  38. data/lib/bio/db/fastadb.rb +255 -0
  39. data/lib/bio/db/pileup.rb +221 -172
  40. data/lib/bio/db/sam.rb +639 -589
  41. data/lib/bio/db/sam/{faidx.rb → faidx_old.rb} +0 -0
  42. data/lib/bio/db/vcf.rb +69 -68
  43. data/test/.gitignore +1 -0
  44. data/test/{test_basic.rb → old_test_basic.rb} +33 -1
  45. data/test/samples/small/dupes.bam +0 -0
  46. data/test/samples/small/dupes.sam +274 -0
  47. data/test/samples/small/map_for_reheader.sam +8 -0
  48. data/test/samples/small/map_to_merge1.bam +0 -0
  49. data/test/samples/small/map_to_merge1.bam.bai +0 -0
  50. data/test/samples/small/map_to_merge1.sam +8 -0
  51. data/test/samples/small/map_to_merge2.bam +0 -0
  52. data/test/samples/small/map_to_merge2.bam.bai +0 -0
  53. data/test/samples/small/map_to_merge2.sam +8 -0
  54. data/test/samples/small/no_md.sam +8 -0
  55. data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
  56. data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
  57. data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
  58. data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
  59. data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
  60. data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
  61. data/test/samples/small/test_cov.svg +273 -0
  62. data/test/samples/small/testu.bam.bai +0 -0
  63. data/test/svg +133 -0
  64. data/test/test_pileup.rb +84 -0
  65. data/test/test_sam.rb +331 -0
  66. data/test/test_vcf.rb +11 -0
  67. data/{doc → tutorial}/tutorial.html +0 -0
  68. data/{doc → tutorial}/tutorial.pdf +0 -0
  69. metadata +56 -114
  70. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -159
  71. data/doc/Bio/DB/SAM/Tools/Bam1T.html +0 -220
  72. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +0 -249
  73. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +0 -159
  74. data/doc/Bio/DB/SAM/Tools/SamfileT.html +0 -171
  75. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +0 -159
  76. data/doc/Bio/DB/SAMException.html +0 -205
  77. data/doc/LibC.html +0 -155
  78. data/doc/Pileup.html +0 -571
  79. data/doc/Vcf.html +0 -473
  80. data/doc/basic_styles.css +0 -31
  81. data/doc/classes/Bio.html +0 -139
  82. data/doc/classes/Bio/DB.html +0 -137
  83. data/doc/classes/Bio/DB/Alignment.html +0 -441
  84. data/doc/classes/Bio/DB/Alignment.src/M000012.html +0 -19
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  88. data/doc/classes/Bio/DB/SAM.html +0 -510
  89. data/doc/classes/Bio/DB/SAM/Library.html +0 -135
  90. data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +0 -28
  91. data/doc/classes/Bio/DB/SAM/Tools.html +0 -278
  92. data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +0 -20
  93. data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -111
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  96. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +0 -169
  97. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +0 -19
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  99. data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +0 -111
  100. data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +0 -129
  101. data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +0 -111
  102. data/doc/classes/Bio/DB/SAMException.html +0 -140
  103. data/doc/classes/Bio/DB/SAMException.src/M000016.html +0 -18
  104. data/doc/classes/Bio/DB/Sam.src/M000017.html +0 -43
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  113. data/doc/classes/Bio/DB/Sam.src/M000026.html +0 -24
  114. data/doc/classes/Bio/DB/Sam.src/M000027.html +0 -19
  115. data/doc/classes/Bio/DB/Sam.src/M000028.html +0 -24
  116. data/doc/classes/Bio/DB/Sam.src/M000029.html +0 -41
  117. data/doc/classes/Bio/DB/Sam.src/M000030.html +0 -31
  118. data/doc/classes/Bio/DB/Sam.src/M000031.html +0 -86
  119. data/doc/classes/Bio/DB/Sam.src/M000032.html +0 -34
  120. data/doc/classes/Bio/DB/Tag.html +0 -160
  121. data/doc/classes/Bio/DB/Tag.src/M000011.html +0 -21
  122. data/doc/classes/LibC.html +0 -105
  123. data/doc/classes/Pileup.html +0 -374
  124. data/doc/classes/Pileup.src/M000001.html +0 -34
  125. data/doc/classes/Pileup.src/M000002.html +0 -21
  126. data/doc/classes/Pileup.src/M000003.html +0 -21
  127. data/doc/classes/Pileup.src/M000004.html +0 -21
  128. data/doc/classes/Pileup.src/M000005.html +0 -31
  129. data/doc/files/lib/bio-samtools_rb.html +0 -109
  130. data/doc/files/lib/bio/db/sam/bam_rb.html +0 -108
  131. data/doc/files/lib/bio/db/sam/faidx_rb.html +0 -108
  132. data/doc/files/lib/bio/db/sam/library_rb.html +0 -101
  133. data/doc/files/lib/bio/db/sam/pileup_rb.html +0 -178
  134. data/doc/files/lib/bio/db/sam/sam_rb.html +0 -113
  135. data/doc/files/lib/bio/db/sam_rb.html +0 -111
  136. data/doc/fr_class_index.html +0 -43
  137. data/doc/fr_file_index.html +0 -33
  138. data/doc/fr_method_index.html +0 -58
  139. data/doc/lib/bio-samtools_rb.html +0 -115
  140. data/doc/lib/bio/db/pileup_rb.html +0 -171
  141. data/doc/lib/bio/db/sam/bam_rb.html +0 -121
  142. data/doc/lib/bio/db/sam/faidx_rb.html +0 -117
  143. data/doc/lib/bio/db/sam/library_rb.html +0 -115
  144. data/doc/lib/bio/db/sam/pileup_rb.html +0 -171
  145. data/doc/lib/bio/db/sam/sam_rb.html +0 -121
  146. data/doc/lib/bio/db/sam/vcf_rb.html +0 -124
  147. data/doc/lib/bio/db/sam_rb.html +0 -115
  148. data/doc/lib/bio/db/vcf_rb.html +0 -124
  149. data/doc/rdoc-style.css +0 -208
  150. data/lib/bio/db/sam/bam.rb +0 -210
  151. data/lib/bio/db/sam/sam.rb +0 -86
  152. data/test/samples/pipe_char/test.bam +0 -0
  153. data/test/samples/pipe_char/test.bam.bai +0 -0
  154. data/test/samples/pipe_char/test.tam +0 -10
  155. data/test/samples/pipe_char/test_chr.fasta +0 -1000
  156. data/test/samples/pipe_char/test_chr.fasta.fai +0 -1
  157. data/test/samples/small/test +0 -0
  158. data/test/samples/small/test.bam +0 -0
  159. data/test/samples/small/test.fa +0 -20
  160. data/test/samples/small/test.fai +0 -0
data/doc/Vcf.html DELETED
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- <p>create the vcf object, use the ordered list of sample names to label
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- samples if provided [‘A’, ‘B’, ‘C’], otherwise uses, 1,2,3 etc</p>
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- <div class="method-source-code" id="new-source">
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- <pre><span class="ruby-comment"># File lib/bio/db/sam/vcf.rb, line 13</span>
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- <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">line</span>=<span class="ruby-keyword">nil</span>, <span class="ruby-identifier">sample_names</span>=<span class="ruby-keyword">nil</span>)
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- <span class="ruby-ivar">@info</span> = {}
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- <span class="ruby-ivar">@samples</span> = {}
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- <span class="ruby-identifier">parse_line</span>(<span class="ruby-identifier">line</span>, <span class="ruby-identifier">sample_names</span>) <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span>
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- <span class="ruby-keyword">end</span></pre>
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- </div><!-- new-source -->
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- </div>
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- </div><!-- new-method -->
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- </section><!-- public-class-method-details -->
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- <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
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- <h3 class="section-header">Public Instance Methods</h3>
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- <div id="method-i-int_or_raw" class="method-detail ">
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-
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- <div class="method-heading">
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- <span class="method-name">int_or_raw</span><span
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- class="method-args">(x)</span>
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- <span class="method-click-advice">click to toggle source</span>
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- </div>
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- <div class="method-description">
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- <div class="method-source-code" id="int_or_raw-source">
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- <pre><span class="ruby-comment"># File lib/bio/db/sam/vcf.rb, line 19</span>
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- <span class="ruby-keyword">def</span> <span class="ruby-identifier">int_or_raw</span>(<span class="ruby-identifier">x</span>)
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- <span class="ruby-constant">Integer</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">x</span>) <span class="ruby-keyword">rescue</span> <span class="ruby-identifier">x</span>
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- <span class="ruby-keyword">end</span></pre>
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- </div><!-- int_or_raw-source -->
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- </div>
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- </div><!-- int_or_raw-method -->
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- <div id="method-i-parse_line" class="method-detail ">
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- <div class="method-heading">
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- <span class="method-name">parse_line</span><span
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- class="method-args">(line, sample_names=nil)</span>
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- <span class="method-click-advice">click to toggle source</span>
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- </div>
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- <div class="method-description">
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-
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- <p>gets the info in the <a href="Vcf.html">Vcf</a> lines and parses the</p>
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- <div class="method-source-code" id="parse_line-source">
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- <pre><span class="ruby-comment"># File lib/bio/db/sam/vcf.rb, line 24</span>
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- <span class="ruby-keyword">def</span> <span class="ruby-identifier">parse_line</span>(<span class="ruby-identifier">line</span>, <span class="ruby-identifier">sample_names</span>=<span class="ruby-keyword">nil</span>)
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- <span class="ruby-keyword">return</span> <span class="ruby-keyword">false</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span>[<span class="ruby-value">0</span>,<span class="ruby-value">1</span>] <span class="ruby-operator">==</span> <span class="ruby-string">'#'</span>
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-
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- <span class="ruby-identifier">f</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;\t&quot;</span>, <span class="ruby-value">-1</span>)
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- <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;VCF lines must have at least 8 fields&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">&lt;</span> <span class="ruby-value">8</span>
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- <span class="ruby-ivar">@chrom</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">0</span>]
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- <span class="ruby-ivar">@pos</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_i</span>
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- <span class="ruby-ivar">@id</span> = <span class="ruby-string">'.'</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">2</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">2</span>]
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- <span class="ruby-ivar">@ref</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">3</span>]
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- <span class="ruby-ivar">@alt</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">4</span>]
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- <span class="ruby-ivar">@qual</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">5</span>].<span class="ruby-identifier">to_f</span>
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- <span class="ruby-ivar">@filter</span> = <span class="ruby-string">'.'</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">6</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">6</span>]
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- <span class="ruby-ivar">@info</span> = <span class="ruby-string">'.'</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">7</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> {}
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- <span class="ruby-keyword">if</span> <span class="ruby-ivar">@info</span>
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- <span class="ruby-identifier">info_vec</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">7</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;;&quot;</span>)
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- <span class="ruby-identifier">info_vec</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span>
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- <span class="ruby-identifier">keyval</span> = <span class="ruby-identifier">x</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;=&quot;</span>, <span class="ruby-value">-1</span>)
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- <span class="ruby-keyword">if</span> <span class="ruby-identifier">keyval</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">2</span> <span class="ruby-comment"># If it's key=value</span>
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- <span class="ruby-ivar">@info</span>[<span class="ruby-identifier">keyval</span>[<span class="ruby-value">0</span>]] = <span class="ruby-identifier">keyval</span>[<span class="ruby-value">1</span>]
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- <span class="ruby-keyword">else</span> <span class="ruby-comment"># Otherwise, it's just a flag</span>
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- <span class="ruby-ivar">@info</span>[<span class="ruby-identifier">x</span>] = <span class="ruby-keyword">nil</span>
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- <span class="ruby-keyword">end</span>
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- <span class="ruby-keyword">end</span>
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- <span class="ruby-keyword">end</span>
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-
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- <span class="ruby-ivar">@samples</span> = {}
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- <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">8</span> <span class="ruby-comment"># Has just upto info</span>
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- <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;Can't have format with no samples&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">9</span>
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- <span class="ruby-ivar">@format</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">8</span>]
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-
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- <span class="ruby-identifier">sample_keys</span> = <span class="ruby-ivar">@format</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;:&quot;</span>)
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-
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- <span class="ruby-identifier">num_samples</span> = <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">-</span> <span class="ruby-value">9</span> <span class="ruby-comment"># How many fields are past the format</span>
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- <span class="ruby-keyword">if</span> <span class="ruby-identifier">sample_names</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">nil</span> <span class="ruby-comment"># Make the sample names just [&quot;1&quot;, &quot;2&quot;, ... , &quot;num_samples}&quot;</span>
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- <span class="ruby-identifier">sample_names</span> = (<span class="ruby-value">1</span><span class="ruby-operator">..</span><span class="ruby-identifier">num_samples</span>).<span class="ruby-identifier">to_a</span>.<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span> <span class="ruby-identifier">i</span>.<span class="ruby-identifier">to_s</span>}
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- <span class="ruby-keyword">elsif</span> <span class="ruby-identifier">sample_names</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">num_samples</span>
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- <span class="ruby-identifier">raise</span> <span class="ruby-node">&quot;Unexpected number of samples (#{num_samples}) based on the provided sample names (#{sample_names.inspect})&quot;</span>
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- <span class="ruby-keyword">end</span>
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-
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- <span class="ruby-identifier">sample_names</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">sample_name</span>, <span class="ruby-identifier">sample_index</span><span class="ruby-operator">|</span>
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- <span class="ruby-identifier">i</span> = <span class="ruby-identifier">sample_index</span> <span class="ruby-operator">+</span> <span class="ruby-value">9</span> <span class="ruby-comment"># index into columns (f)</span>
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- <span class="ruby-identifier">sample_values</span> = <span class="ruby-identifier">f</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;:&quot;</span>)
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- <span class="ruby-identifier">raise</span> <span class="ruby-node">&quot;Expected number of sample values to be &lt;= number of sample keys in FORMAT column Format=#{@format} but sample=#{f[i]}&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">sample_values</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">sample_keys</span>.<span class="ruby-identifier">size</span>
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- <span class="ruby-ivar">@samples</span>[<span class="ruby-identifier">sample_name</span>] = {}
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- <span class="ruby-identifier">sample_keys</span>.<span class="ruby-identifier">each_with_index</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">key</span>, <span class="ruby-identifier">value_index</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@samples</span>[<span class="ruby-identifier">sample_name</span>][<span class="ruby-identifier">key</span>] = <span class="ruby-identifier">sample_values</span>[<span class="ruby-identifier">value_index</span>] <span class="ruby-operator">||</span> <span class="ruby-string">&quot;&quot;</span>}
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- <span class="ruby-keyword">end</span>
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- <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span>;
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- <span class="ruby-keyword">end</span></pre>
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- </div><!-- parse_line-source -->
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- </div>
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- </div><!-- parse_line-method -->
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- </section><!-- public-instance-method-details -->
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- </section><!-- 5Buntitled-5D -->
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- </div><!-- documentation -->
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- <footer id="validator-badges">
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- <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
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