bacterial-annotator 0.8.8 → 0.8.9

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@@ -194,6 +194,11 @@ def parseOptions_compare
194
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  options[:software] = "fasttree"
195
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  options[:bootstrap] = 100
196
196
 
197
+ if ARGV.length == 0
198
+ usage_compare
199
+ abort
200
+ end
201
+
197
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  while x = ARGV.shift
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199
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  case x.downcase
@@ -254,6 +259,11 @@ def parseOptions_identify
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  options[:genome_list] = []
255
260
  options[:output] = "tsv"
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261
 
262
+ if ARGV.length == 0
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+ usage_identify
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+ abort
265
+ end
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+
257
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  while x = ARGV.shift
258
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259
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  case x.downcase
@@ -369,6 +369,20 @@ class BacterialAnnotator
369
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  inference: inference
370
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  }
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372
+ @annotation_stats[:flagged_cds].each do |flag|
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+ if flag.include? "#{k}"
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+ if v[:homology][:assert_cutoff].inject(:+) > 2
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+ flag.replace("#{flag}\tAnnotated by externaldb (#{v[:homology][:hits][0]}|#{v[:homology][:pId]}|#{cov_query}|#{cov_subject}))")
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+ elsif v[:homology][:assert_cutoff] == [1,1,0]
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+ flag.replace("#{flag}\tPossible pseudogene (coverage subject = #{cov_subject} with #{v[:homology][:hits][0]}))")
378
+ elsif v[:homology][:assert_cutoff] == [1,0,1]
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+ flag.replace("#{flag}\tPossible pseudogene (coverage query = #{cov_query} with #{v[:homology][:hits][0]}))")
380
+ elsif v[:homology][:assert_cutoff] == [0,1,1]
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+ flag.replace("#{flag}\tLow similarity (percent identity = #{v[:homology][:pId]} with #{v[:homology][:hits][0]}))")
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+ end
383
+ end
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+ end
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+
372
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  end
373
387
 
374
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  end
@@ -463,6 +477,7 @@ class BacterialAnnotator
463
477
  flag += "\t#{(@prot_synteny_refgenome.query_sequences[prot][:homology][:cov_query]*100).round(2)}"
464
478
  flag += "\t#{(@prot_synteny_refgenome.query_sequences[prot][:homology][:cov_subject]*100).round(2)}"
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  @annotation_stats[:flagged_cds] << flag
480
+ remaining_cds << prot
466
481
  end
467
482
 
468
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  else
@@ -515,7 +530,7 @@ class BacterialAnnotator
515
530
 
516
531
  file_flagged_cds = file_dir + "/Prot-flagged.tsv"
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  File.open(file_flagged_cds, "w") do |fopen|
518
- fopen.write("CDS locus\tAssertion-CutOff\tAA Identity\tCovQuery(%)\tCovSubject(%)\n")
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+ fopen.write("CDS locus\tAssertion-CutOff\tAA Identity\tCovQuery(%)\tCovSubject(%)\tNote\n")
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  @annotation_stats[:flagged_cds].each do |fcds|
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  fopen.write("#{fcds}\n")
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  end
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bacterial-annotator
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.8.8
4
+ version: 0.8.9
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5
  platform: ruby
6
6
  authors:
7
7
  - Maxime Deraspe
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2018-08-02 00:00:00.000000000 Z
11
+ date: 2018-10-17 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: bio