bio-samtools 0.4.1 → 0.4.2
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/VERSION +1 -1
- data/bio-samtools.gemspec +60 -6
- data/doc/Bio.html +171 -0
- data/doc/Bio/DB.html +163 -0
- data/doc/Bio/DB/Alignment.html +780 -0
- data/doc/Bio/DB/SAM.html +1241 -0
- data/doc/Bio/DB/SAM/Library.html +217 -0
- data/doc/Bio/DB/SAM/Tools.html +331 -0
- data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +159 -0
- data/doc/Bio/DB/SAM/Tools/Bam1T.html +220 -0
- data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +249 -0
- data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +159 -0
- data/doc/Bio/DB/SAM/Tools/SamfileT.html +171 -0
- data/doc/Bio/DB/SAM/Tools/SamfileTX.html +159 -0
- data/doc/Bio/DB/SAMException.html +205 -0
- data/doc/Bio/DB/Tag.html +254 -0
- data/doc/LICENSE_txt.html +881 -0
- data/doc/LibC.html +153 -0
- data/doc/Pileup.html +571 -0
- data/doc/Vcf.html +473 -0
- data/doc/created.rid +10 -1
- data/doc/images/add.png +0 -0
- data/doc/images/brick.png +0 -0
- data/doc/images/brick_link.png +0 -0
- data/doc/images/bug.png +0 -0
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- data/doc/images/date.png +0 -0
- data/doc/images/delete.png +0 -0
- data/doc/images/find.png +0 -0
- data/doc/images/loadingAnimation.gif +0 -0
- data/doc/images/macFFBgHack.png +0 -0
- data/doc/images/package.png +0 -0
- data/doc/images/page_green.png +0 -0
- data/doc/images/page_white_text.png +0 -0
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- data/doc/images/plugin.png +0 -0
- data/doc/images/ruby.png +0 -0
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- data/doc/images/transparent.png +0 -0
- data/doc/images/wrench.png +0 -0
- data/doc/images/wrench_orange.png +0 -0
- data/doc/images/zoom.png +0 -0
- data/doc/index.html +109 -21
- data/doc/js/darkfish.js +153 -0
- data/doc/js/jquery.js +18 -0
- data/doc/js/navigation.js +142 -0
- data/doc/js/search.js +94 -0
- data/doc/js/search_index.js +1 -0
- data/doc/js/searcher.js +228 -0
- data/doc/lib/bio-samtools_rb.html +115 -0
- data/doc/lib/bio/db/sam/bam_rb.html +121 -0
- data/doc/lib/bio/db/sam/faidx_rb.html +117 -0
- data/doc/lib/bio/db/sam/library_rb.html +115 -0
- data/doc/lib/bio/db/sam/pileup_rb.html +171 -0
- data/doc/lib/bio/db/sam/sam_rb.html +121 -0
- data/doc/lib/bio/db/sam/vcf_rb.html +124 -0
- data/doc/lib/bio/db/sam_rb.html +115 -0
- data/doc/rdoc.css +543 -0
- data/doc/table_of_contents.html +186 -0
- data/ext/Makefile-bioruby.patch +1 -1
- data/ext/Rakefile +8 -1
- data/ext/mkrf_conf.rb +8 -1
- data/lib/bio/db/sam.rb +140 -27
- data/lib/bio/db/sam/vcf.rb +0 -1
- data/test/basictest.rb +4 -4
- data/test/test_basic.rb +50 -34
- metadata +79 -25
- data/test/coverage.rb +0 -26
- data/test/coverage_plot.rb +0 -28
- data/test/feature.rb +0 -0
- data/test/test_pileup.rb +0 -68
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<h2>Pages</h2>
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<h2 id="classes">Classes/Modules</h2>
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<a href="Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
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<a href="Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
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<a href="Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
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<a href="Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
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<a href="Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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<a href="Pileup.html">Pileup</a>
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<li><a href="Pileup.html#label-Pileup+">Pileup </a>
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<h2 id="methods">Methods</h2>
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<li class="method"><a href="Bio/DB/SAM/Tools.html#method-c-bam_sort">::bam_sort — Bio::DB::SAM::Tools</a>
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<li class="method"><a href="Bio/DB/Sam.html#method-c-new">::new — Bio::DB::Sam</a>
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<li class="method"><a href="Bio/DB/Sam.html#method-i-average_coverage">#average_coverage — Bio::DB::Sam</a>
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<li class="method"><a href="Bio/DB/Sam.html#method-i-chromosome_coverage">#chromosome_coverage — Bio::DB::Sam</a>
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<li class="method"><a href="Bio/DB/Sam.html#method-i-close">#close — Bio::DB::Sam</a>
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<li class="method"><a href="Bio/DB/Sam.html#method-i-fetch">#fetch — Bio::DB::Sam</a>
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<li class="method"><a href="Bio/DB/Sam.html#method-i-fetch_reference">#fetch_reference — Bio::DB::Sam</a>
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<li class="method"><a href="Bio/DB/Sam.html#method-i-index_stats">#index_stats — Bio::DB::Sam</a>
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<li class="method"><a href="Vcf.html#method-i-int_or_raw">#int_or_raw — Vcf</a>
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<li class="method"><a href="Bio/DB/Sam.html#method-i-load_index">#load_index — Bio::DB::Sam</a>
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<li class="method"><a href="Bio/DB/Sam.html#method-i-load_reference">#load_reference — Bio::DB::Sam</a>
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<p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
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data/ext/Makefile-bioruby.patch
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end #cd
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end
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end
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|
task :clean do
|
data/ext/mkrf_conf.rb
CHANGED
|
@@ -44,15 +44,22 @@ task :compile do
|
|
|
44
44
|
cp("libbam.a","#{path_external}")
|
|
45
45
|
#sh "CFLAGS='-g -Wall -O2 -fPIC' make -e libbam.so.1-local"
|
|
46
46
|
sh "make libbam.so.1-local"
|
|
47
|
+
cp("samtools", "#{path_external}")
|
|
47
48
|
cp("libbam.so.1","#{path_external}")
|
|
48
49
|
when /darwin/
|
|
49
50
|
sh "make"
|
|
50
51
|
cp("libbam.a","#{path_external}")
|
|
51
52
|
sh "make libbam.1.dylib-local"
|
|
52
|
-
cp("libbam.1.dylib","#{path_external}")
|
|
53
|
+
cp("libbam.1.dylib","#{path_external}")
|
|
54
|
+
sh "make"
|
|
55
|
+
cp('samtools', "#{path_external}")
|
|
53
56
|
when /mswin|mingw/ then raise NotImplementedError, "BWA library is not available for Windows platform"
|
|
54
57
|
end #case
|
|
55
58
|
end #cd
|
|
59
|
+
cd("samtools-#{Version}/bcftools") do
|
|
60
|
+
sh "make"
|
|
61
|
+
cp('bcftools', "#{path_external}")
|
|
62
|
+
end
|
|
56
63
|
end
|
|
57
64
|
|
|
58
65
|
task :clean do
|
data/lib/bio/db/sam.rb
CHANGED
|
@@ -311,44 +311,157 @@ module Bio
|
|
|
311
311
|
##and also associated output options
|
|
312
312
|
[:g, :u, :e, :h, :I, :L, :o, :p].each {|x| opts.delete(x) }
|
|
313
313
|
|
|
314
|
-
|
|
315
|
-
strptrs << FFI::MemoryPointer.from_string("mpileup")
|
|
314
|
+
sam_opts = []
|
|
315
|
+
#strptrs << FFI::MemoryPointer.from_string("mpileup")
|
|
316
316
|
opts.each do |k,v|
|
|
317
317
|
next unless opts[k] ##dont bother unless the values provided are true..
|
|
318
318
|
k = '6' if k == :six
|
|
319
319
|
k = '-' + k.to_s
|
|
320
|
-
strptrs << FFI::MemoryPointer.from_string(k)
|
|
321
|
-
|
|
320
|
+
sam_opts << k #strptrs << FFI::MemoryPointer.from_string(k)
|
|
321
|
+
sam_opts << v.to_s unless ["-R", "-B", "-E", "-6", "-A"].include?(k) #these are just flags so don't pass a value... strptrs << FFI::MemoryPointer.from_string(v.to_s)
|
|
322
322
|
end
|
|
323
|
-
|
|
324
|
-
|
|
325
|
-
strptrs << FFI::MemoryPointer.from_string(@sam)
|
|
326
|
-
strptrs << nil
|
|
323
|
+
sam_opts = sam_opts + ['-f', @fasta_path, @sam]
|
|
324
|
+
sam_command = "#{File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','samtools')} mpileup #{sam_opts.join(' ')} 2> /dev/null"
|
|
327
325
|
|
|
328
|
-
|
|
329
|
-
|
|
330
|
-
|
|
331
|
-
argv[i].put_pointer(0, p)
|
|
326
|
+
sam_pipe = IO.popen(sam_command)
|
|
327
|
+
while line = sam_pipe.gets
|
|
328
|
+
yield Pileup.new(line)
|
|
332
329
|
end
|
|
330
|
+
sam_pipe.close
|
|
331
|
+
#strptrs << FFI::MemoryPointer.from_string('-f')
|
|
332
|
+
#strptrs << FFI::MemoryPointer.from_string(@fasta_path)
|
|
333
|
+
#strptrs << FFI::MemoryPointer.from_string(@sam)
|
|
334
|
+
#strptrs << nil
|
|
333
335
|
|
|
334
|
-
|
|
335
|
-
|
|
336
|
-
|
|
336
|
+
# Now load all the pointers into a native memory block
|
|
337
|
+
#argv = FFI::MemoryPointer.new(:pointer, strptrs.length)
|
|
338
|
+
#strptrs.each_with_index do |p, i|
|
|
339
|
+
# argv[i].put_pointer(0, p)
|
|
340
|
+
#end
|
|
341
|
+
|
|
342
|
+
#old_stdout = STDOUT.clone
|
|
343
|
+
#read_pipe, write_pipe = IO.pipe()
|
|
344
|
+
#STDOUT.reopen(write_pipe)
|
|
337
345
|
#int bam_mpileup(int argc, char *argv[])
|
|
338
|
-
|
|
339
|
-
if fork
|
|
340
|
-
|
|
341
|
-
|
|
342
|
-
|
|
343
|
-
|
|
344
|
-
|
|
346
|
+
# Bio::DB::SAM::Tools.bam_mpileup(strptrs.length - 1,argv)
|
|
347
|
+
#if fork
|
|
348
|
+
# write_pipe.close
|
|
349
|
+
# STDOUT.reopen(old_stdout) #beware .. stdout from other processes eg tests calling this method can get mixed in...
|
|
350
|
+
# begin
|
|
351
|
+
# while line = read_pipe.readline
|
|
352
|
+
# yield Pileup.new(line)
|
|
353
|
+
# end
|
|
354
|
+
# rescue EOFError
|
|
355
|
+
# read_pipe.close
|
|
356
|
+
# Process.wait
|
|
357
|
+
# end
|
|
358
|
+
#end
|
|
359
|
+
end
|
|
360
|
+
|
|
361
|
+
#experimental method that spawns a samtools mpileup | bcftools view process and supports returning of pileup vcf
|
|
362
|
+
##otherwise works like mpileup
|
|
363
|
+
def mpileup_plus( opts )
|
|
364
|
+
|
|
365
|
+
raise SAMException.new(), "No BAMFile provided" unless @sam and @binary
|
|
366
|
+
raise SAMException.new(), "No FastA provided" unless @fasta_path
|
|
367
|
+
#long option form to short samtools form..
|
|
368
|
+
long_opts = {
|
|
369
|
+
:region => :r,
|
|
370
|
+
:illumina_quals => :six,
|
|
371
|
+
:count_anomalous => :A,
|
|
372
|
+
:no_baq => :B,
|
|
373
|
+
:adjust_mapq => :C,
|
|
374
|
+
:max_per_bam_depth => :d,
|
|
375
|
+
:extended_baq => :E,
|
|
376
|
+
:exclude_reads_file => :G,
|
|
377
|
+
:list_of_positions => :l,
|
|
378
|
+
:mapping_quality_cap => :M,
|
|
379
|
+
:ignore_rg => :R,
|
|
380
|
+
:min_mapping_quality => :q,
|
|
381
|
+
:min_base_quality => :Q,
|
|
382
|
+
###following options are for the -g -u option
|
|
383
|
+
:genotype_calling => :g,
|
|
384
|
+
:uncompressed_bcf => :u,
|
|
385
|
+
:extension_sequencing_probability => :e,
|
|
386
|
+
:homopolymer_error_coefficient => :h,
|
|
387
|
+
:no_indels => :I,
|
|
388
|
+
:skip_indel_over_average_depth => :L,
|
|
389
|
+
:gap_open_sequencing_error_probability => :o,
|
|
390
|
+
:platforms => :P
|
|
391
|
+
}
|
|
392
|
+
|
|
393
|
+
##convert any long_opts to short opts
|
|
394
|
+
opts.each_pair do |k,v|
|
|
395
|
+
if long_opts[k]
|
|
396
|
+
opts[long_opts[k]] = v
|
|
397
|
+
opts.delete(k)
|
|
398
|
+
end
|
|
399
|
+
end
|
|
400
|
+
|
|
401
|
+
##remove any calls to -g or -u for mpileup, bcf output is not yet supported
|
|
402
|
+
##and also associated output options
|
|
403
|
+
#[:g, :u, :e, :h, :I, :L, :o, :p].each {|x| opts.delete(x) }
|
|
404
|
+
opts[:u] = true if opts[:g] #so that we always get uncompressed output
|
|
405
|
+
opts.delete(:g)
|
|
406
|
+
|
|
407
|
+
sam_opts = []
|
|
408
|
+
#strptrs << FFI::MemoryPointer.from_string("mpileup")
|
|
409
|
+
opts.each do |k,v|
|
|
410
|
+
next unless opts[k] ##dont bother unless the values provided are true..
|
|
411
|
+
k = '6' if k == :six
|
|
412
|
+
k = '-' + k.to_s
|
|
413
|
+
sam_opts << k #strptrs << FFI::MemoryPointer.from_string(k)
|
|
414
|
+
sam_opts << v.to_s unless ["-R", "-B", "-E", "-6", "-A", "-g", "-u", "-I"].include?(k) #these are just flags so don't pass a value... strptrs << FFI::MemoryPointer.from_string(v.to_s)
|
|
345
415
|
end
|
|
346
|
-
|
|
347
|
-
|
|
348
|
-
|
|
416
|
+
sam_opts = sam_opts + ['-f', @fasta_path, @sam]
|
|
417
|
+
|
|
418
|
+
command = "#{File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','samtools')} mpileup #{sam_opts.join(' ')} 2> /dev/null"
|
|
419
|
+
if opts[:u]
|
|
420
|
+
command = command + " | #{File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','bcftools')} view -cg -"
|
|
421
|
+
end
|
|
422
|
+
pipe = IO.popen(command)
|
|
423
|
+
$stderr.puts command
|
|
424
|
+
if opts[:u]
|
|
425
|
+
while line = pipe.gets
|
|
426
|
+
next if line[0,1] == '#' #skip any header or meta-lines, we dont do anything with those
|
|
427
|
+
yield Vcf.new(line)
|
|
428
|
+
end
|
|
429
|
+
else
|
|
430
|
+
while line = pipe.gets
|
|
431
|
+
yield Pileup.new(line)
|
|
432
|
+
end
|
|
433
|
+
end
|
|
434
|
+
pipe.close
|
|
435
|
+
#strptrs << FFI::MemoryPointer.from_string('-f')
|
|
436
|
+
#strptrs << FFI::MemoryPointer.from_string(@fasta_path)
|
|
437
|
+
#strptrs << FFI::MemoryPointer.from_string(@sam)
|
|
438
|
+
#strptrs << nil
|
|
439
|
+
|
|
440
|
+
# Now load all the pointers into a native memory block
|
|
441
|
+
#argv = FFI::MemoryPointer.new(:pointer, strptrs.length)
|
|
442
|
+
#strptrs.each_with_index do |p, i|
|
|
443
|
+
# argv[i].put_pointer(0, p)
|
|
444
|
+
#end
|
|
445
|
+
|
|
446
|
+
#old_stdout = STDOUT.clone
|
|
447
|
+
#read_pipe, write_pipe = IO.pipe()
|
|
448
|
+
#STDOUT.reopen(write_pipe)
|
|
449
|
+
#int bam_mpileup(int argc, char *argv[])
|
|
450
|
+
# Bio::DB::SAM::Tools.bam_mpileup(strptrs.length - 1,argv)
|
|
451
|
+
#if fork
|
|
452
|
+
# write_pipe.close
|
|
453
|
+
# STDOUT.reopen(old_stdout) #beware .. stdout from other processes eg tests calling this method can get mixed in...
|
|
454
|
+
# begin
|
|
455
|
+
# while line = read_pipe.readline
|
|
456
|
+
# yield Pileup.new(line)
|
|
457
|
+
# end
|
|
458
|
+
# rescue EOFError
|
|
459
|
+
# read_pipe.close
|
|
460
|
+
# Process.wait
|
|
461
|
+
# end
|
|
462
|
+
#end
|
|
349
463
|
end
|
|
350
|
-
|
|
351
|
-
end
|
|
464
|
+
|
|
352
465
|
|
|
353
466
|
# utility method that does not use the samtools API, it calls samtools directly as if on the command line and catches the output,
|
|
354
467
|
# to use this method you must have a version of samtools that supports the pileup command (< 0.1.17)
|
data/lib/bio/db/sam/vcf.rb
CHANGED
|
@@ -11,7 +11,6 @@ public
|
|
|
11
11
|
|
|
12
12
|
#create the vcf object, use the ordered list of sample names to label samples if provided ['A', 'B', 'C'], otherwise uses, 1,2,3 etc
|
|
13
13
|
def initialize(line=nil, sample_names=nil)
|
|
14
|
-
next if line[0,1] == '#' #skip any header or meta-lines... inadvertantly passed..
|
|
15
14
|
@info = {}
|
|
16
15
|
@samples = {}
|
|
17
16
|
parse_line(line, sample_names) if line != nil
|
data/test/basictest.rb
CHANGED
|
@@ -29,7 +29,7 @@ class TestBioDbSam < Test::Unit::TestCase
|
|
|
29
29
|
rescue
|
|
30
30
|
end
|
|
31
31
|
end
|
|
32
|
-
|
|
32
|
+
=begi
|
|
33
33
|
def default_test
|
|
34
34
|
puts $LOAD_PATH
|
|
35
35
|
assert(true, "Unit test test")
|
|
@@ -165,7 +165,7 @@ class TestBioDbSam < Test::Unit::TestCase
|
|
|
165
165
|
assert(true, "Seems it ran the query")
|
|
166
166
|
#node_7263 238 60 has 550+, query from 0 to 500, something shall come....
|
|
167
167
|
end
|
|
168
|
-
|
|
168
|
+
=end
|
|
169
169
|
def test_read_invalid_reference
|
|
170
170
|
sam = Bio::DB::Sam.new({:bam=>@testBAMFile})
|
|
171
171
|
sam.open
|
|
@@ -281,11 +281,11 @@ class TestBioDbSam < Test::Unit::TestCase
|
|
|
281
281
|
def test_pileup
|
|
282
282
|
sam = Bio::DB::Sam.new(:fasta=>@testReference, :bam=>@testBAMFile )
|
|
283
283
|
pileup_list = []
|
|
284
|
-
sam.mpileup(:region => "chr_1:100-
|
|
284
|
+
sam.mpileup(:region => "chr_1:100-1100") do |pile|
|
|
285
285
|
next unless pile.ref_name == 'chr_1' ##required because in the test environment stdout gets mixed in with the captured stdout in the function and non pileup lines are passed...
|
|
286
286
|
pileup_list << pile
|
|
287
287
|
end
|
|
288
|
-
assert_equal(
|
|
288
|
+
assert_equal(1000,pileup_list.length)
|
|
289
289
|
pileup_list.each do |p|
|
|
290
290
|
assert_kind_of(Pileup, p)
|
|
291
291
|
end
|