bio-samtools 0.4.2 → 0.5.0

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  1. data/Gemfile.lock +1 -0
  2. data/README.rdoc +1 -0
  3. data/VERSION +1 -1
  4. data/bio-samtools.gemspec +19 -19
  5. data/doc/Bio.html +71 -4
  6. data/doc/Bio/DB.html +6 -4
  7. data/doc/Bio/DB/Alignment.html +8 -8
  8. data/doc/Bio/DB/Pileup.html +515 -0
  9. data/doc/Bio/DB/SAM.html +37 -37
  10. data/doc/Bio/DB/SAM/Library.html +4 -4
  11. data/doc/Bio/DB/SAM/Tools.html +4 -4
  12. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +4 -4
  13. data/doc/Bio/DB/SAM/Tools/Bam1T.html +4 -4
  14. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +4 -4
  15. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +4 -4
  16. data/doc/Bio/DB/SAM/Tools/SamfileT.html +4 -4
  17. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +4 -4
  18. data/doc/Bio/DB/SAMException.html +5 -5
  19. data/doc/Bio/DB/Tag.html +5 -5
  20. data/doc/Bio/DB/Vcf.html +467 -0
  21. data/doc/LICENSE_txt.html +57 -60
  22. data/doc/LibC.html +6 -4
  23. data/doc/created.rid +7 -7
  24. data/doc/index.html +4 -4
  25. data/doc/js/search_index.js +1 -1
  26. data/doc/lib/bio-samtools_rb.html +4 -4
  27. data/doc/lib/bio/db/pileup_rb.html +171 -0
  28. data/doc/lib/bio/db/sam/bam_rb.html +4 -4
  29. data/doc/lib/bio/db/sam/faidx_rb.html +4 -4
  30. data/doc/lib/bio/db/sam/library_rb.html +4 -4
  31. data/doc/lib/bio/db/sam/sam_rb.html +4 -4
  32. data/doc/lib/bio/db/sam_rb.html +4 -4
  33. data/doc/lib/bio/db/vcf_rb.html +124 -0
  34. data/doc/table_of_contents.html +16 -26
  35. data/doc/tutorial.html +26 -1
  36. data/doc/tutorial.pdf +0 -0
  37. data/lib/bio/db/{sam/pileup.rb → pileup.rb} +6 -4
  38. data/lib/bio/db/sam.rb +13 -12
  39. data/lib/bio/db/{sam/vcf.rb → vcf.rb} +6 -2
  40. data/test/samples/small/sorted.bam.bai +0 -0
  41. data/test/test_basic.rb +7 -5
  42. data/test/test_vcf.rb +5 -5
  43. metadata +29 -26
  44. data/test/basictest.rb +0 -322
  45. data/test/pileup.rb +0 -68
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data/doc/lib/bio/db/sam/sam_rb.html CHANGED
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+ <li><a href="../../../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
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data/doc/lib/bio/db/sam_rb.html CHANGED
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data/doc/lib/bio/db/vcf_rb.html ADDED
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ </nav>
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+ <nav id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Pages</h3>
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+ <ul>
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+ <li class="file"><a href="../../../LICENSE_txt.html">LICENSE</a>
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+ </nav>
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+ <nav id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class and Module Index</h3>
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+ <ul class="link-list">
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+
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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/Alignment.html">Bio::DB::Alignment</a>
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+
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+ <li><a href="../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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+
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+ <li><a href="../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
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+ <li><a href="../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
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+ <li><a href="../../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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+
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+ <li><a href="../../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
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+
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+ <li><a href="../../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
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+
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+ <li><a href="../../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
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+ <li><a href="../../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
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+
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+ <li><a href="../../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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+
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+ <li><a href="../../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
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+
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+ <li><a href="../../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
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+
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+ <li><a href="../../../Bio/DB/Sam.html">Bio::DB::Sam</a>
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+ <li><a href="../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
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+ <li><a href="../../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
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+ <li><a href="../../../LibC.html">LibC</a>
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+ </ul>
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+ </nav>
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+ </div>
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+ </nav>
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+
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+ <div id="documentation" class="description">
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+
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+ <h1 id="label-Vcf+">Vcf </h1>
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+
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+ <p>A class representing information in Variant Call Format Forked from vcfruby
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+ at <a
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+ href="https://github.com/jesserod/vcfruby">github.com/jesserod/vcfruby</a>
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+ Modified and tests written by Dan MacLean (tsl at dan.maclean.ac.uk) VCF is
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+ described at <a
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+ href="http://www.1000genomes.org/node/101">www.1000genomes.org/node/101</a></p>
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+ </div>
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+ <a href="Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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- <p>Not all the options SAMTools allows you to pass to mpileup are supported, those that cause mpileup to return BCF/VCF are ignored. Specifically these are g,u,e,h,I,L,o,p. The table below lists the SAMTools flags supported and the symbols you can use to call them in the mpileup command.
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+ <p>Not all the options SAMTools allows you to pass to mpileup will return a Pileup object, those that cause mpileup to return BCF/VCF will be ignored. Specifically these are g,u,e,h,I,L,o,p. The table below lists the SAMTools flags supported and the symbols you can use to call them in the mpileup command.
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  <tr><td><code>r</code></td><td>limit retrieval to a region</td><td><code>:r</code></td><td><code>:region</code></td><td>all positions</td><td><code>:r => "Chr1:1000-2000"</code></tr>
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+ <p>There is an 'experimental' function, <code>mpileup_plus</code>, that can return a Bio::DB::Vcf object when g,u,e,h,I,L,o,p options are passed. The list below shows the symbols you can use to invoke this behaviour:</p>
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+ <ul>
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+ <li><code>:genotype_calling, :g</code></li>
164
+ <li><code>:uncompressed_bcf , :u</code></li>
165
+ <li><code>:extension_sequencing_probability, :e</code></li>
166
+ <li><code>:homopolymer_error_coefficient, :h</code></li>
167
+ <li><code>:no_indels, :I</code></li>
168
+ <li><code>:skip_indel_over_average_depth, :L</code></li>
169
+ <li><code>:gap_open_sequencing_error_probability,:o</code></li>
170
+ <li><code>:platforms, :P</code></li>
171
+ </ul>
172
+ <br />
173
+ <h2>Tests</h2>
174
+ <p>The easiest way to run the built-in unit tests is to change to the bio-samtools installation directory (discoverable by typing 'gem which bio-samtools' at the command line) and running the separate test files individually.</p>
175
+ <pre><code class="ruby">gem which 'bio-samtools'
176
+ /some/path/ruby-1.x.x/bio-samtools-0.x.x/lib/bio-samtools.rb
177
+ cd /some/path/ruby-1.x.x/bio-samtools-0.x.x
178
+ ruby test/test_basic.rb
179
+ </code></pre>
180
+ <p> Each test file tests different aspects of the gem.
181
+ <ul>
182
+ <li>test_basic.rb - tests the general functionality of the gem, such as opening and closing BAM, creating indices, fetching regions, checks the correct Pileup format is returned when requested etc.</li>
183
+ <li>test_pileup.rb - tests the Pileup class, making sure attributes are set correctly when Pileup data are passed</li>
184
+ <li>test_vcf.rb - tests the Vcf class, making sure attributes are set correctly when Vcf data are passed</li>
160
185
  </div>
161
186
  </div>
162
187
  </div>
data/doc/tutorial.pdf CHANGED
Binary file
data/lib/bio/db/{sam/pileup.rb → pileup.rb} RENAMED
@@ -1,5 +1,5 @@
1
1
  # :title:Pileup
2
- # = Pileup
2
+ # = Bio::DB::Pileup
3
3
  # A class representing information in SAMTools pileup format
4
4
  # Author:: Dan MacLean (dan.maclean@tsl.ac.uk)
5
5
  # Pileup is described at http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_do_not_understand_the_columns_in_the_pileup_output.
@@ -24,13 +24,14 @@
24
24
  # Pileup provides accessors for all columns (6 or 10 column format) and a few other useful methods
25
25
  #
26
26
  #
27
-
27
+ module Bio
28
+ class DB
28
29
  class Pileup
29
30
  attr_accessor :ref_name, :pos, :ref_base, :coverage, :read_bases, :read_quals, :consensus, :consensus_quality, :snp_quality, :rms_mapq, :ar1, :ar2, :ar3
30
31
 
31
32
  #creates the Pileup object
32
33
  # pile_up_line = "seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9<;;7=<<<<<"
33
- # pile = Pileup.new(pile_up_line)
34
+ # pile = Bio::DB::Pileup.new(pile_up_line)
34
35
  def initialize(pile_up_line)
35
36
  cols = pile_up_line.split(/\t/)
36
37
  if cols.length == 6 ##should only be able to get 6 lines from mpileup
@@ -95,4 +96,5 @@ class Pileup
95
96
  end
96
97
 
97
98
  end
98
-
99
+ end
100
+ end
data/lib/bio/db/sam.rb CHANGED
@@ -2,8 +2,8 @@ require 'bio/db/sam/library'
2
2
  require 'bio/db/sam/bam'
3
3
  require 'bio/db/sam/faidx'
4
4
  require 'bio/db/sam/sam'
5
- require 'bio/db/sam/pileup'
6
- require 'bio/db/sam/vcf'
5
+ #require 'bio/db/pileup'
6
+ #require 'bio/db/vcf'
7
7
 
8
8
  module LibC
9
9
  extend FFI::Library
@@ -298,15 +298,15 @@ module Bio
298
298
  :min_mapping_quality => :q,
299
299
  :min_base_quality => :Q
300
300
  }
301
-
302
301
  ##convert any long_opts to short opts
302
+ temp_opts = opts.dup
303
303
  opts.each_pair do |k,v|
304
304
  if long_opts[k]
305
- opts[long_opts[k]] = v
306
- opts.delete(k)
305
+ temp_opts[long_opts[k]] = v
306
+ temp_opts.delete(k)
307
307
  end
308
308
  end
309
-
309
+ opts = temp_opts
310
310
  ##remove any calls to -g or -u for mpileup, bcf output is not yet supported
311
311
  ##and also associated output options
312
312
  [:g, :u, :e, :h, :I, :L, :o, :p].each {|x| opts.delete(x) }
@@ -325,7 +325,7 @@ module Bio
325
325
 
326
326
  sam_pipe = IO.popen(sam_command)
327
327
  while line = sam_pipe.gets
328
- yield Pileup.new(line)
328
+ yield Bio::DB::Pileup.new(line)
329
329
  end
330
330
  sam_pipe.close
331
331
  #strptrs << FFI::MemoryPointer.from_string('-f')
@@ -391,13 +391,14 @@ module Bio
391
391
  }
392
392
 
393
393
  ##convert any long_opts to short opts
394
+ temp_opts = opts.dup
394
395
  opts.each_pair do |k,v|
395
396
  if long_opts[k]
396
- opts[long_opts[k]] = v
397
- opts.delete(k)
397
+ temp_opts[long_opts[k]] = v
398
+ temp_opts.delete(k)
398
399
  end
399
400
  end
400
-
401
+ opts = temp_opts
401
402
  ##remove any calls to -g or -u for mpileup, bcf output is not yet supported
402
403
  ##and also associated output options
403
404
  #[:g, :u, :e, :h, :I, :L, :o, :p].each {|x| opts.delete(x) }
@@ -424,11 +425,11 @@ module Bio
424
425
  if opts[:u]
425
426
  while line = pipe.gets
426
427
  next if line[0,1] == '#' #skip any header or meta-lines, we dont do anything with those
427
- yield Vcf.new(line)
428
+ yield Bio::DB::Vcf.new(line)
428
429
  end
429
430
  else
430
431
  while line = pipe.gets
431
- yield Pileup.new(line)
432
+ yield Bio::DB::Pileup.new(line)
432
433
  end
433
434
  end
434
435
  pipe.close