bacterial-annotator 0.8.8 → 0.8.9
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- checksums.yaml +4 -4
- data/bin/bacterial-annotator +10 -0
- data/lib/bacterial-annotator.rb +16 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 1dc26e2ae283ea0c8163e7c487c95bf0f0b7cffa4095d841b38e709262698a52
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4
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+
data.tar.gz: be699876985f29d8269119852b6f027f562c541263abb6afe29b84783375ad3b
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: a7615dee5f7d89e8224477dc94798621d72ab8923d1b7027c9b912f46f9fca85beb71bf1b3cd7a058fa27503b07a244ecd97a71330c0816d4b3c41b4f8795e55
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7
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+
data.tar.gz: 813dc52e3732accd812e54a9ad998fee65e01cdec8bf79c136c59262512683ed32656e88e860476f405e08441723eef6681648d972f17237ec80d88a64a8a46d
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data/bin/bacterial-annotator
CHANGED
@@ -194,6 +194,11 @@ def parseOptions_compare
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194
194
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options[:software] = "fasttree"
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195
195
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options[:bootstrap] = 100
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196
196
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197
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+
if ARGV.length == 0
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198
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usage_compare
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199
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abort
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200
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end
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201
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197
202
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while x = ARGV.shift
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198
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case x.downcase
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@@ -254,6 +259,11 @@ def parseOptions_identify
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254
259
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options[:genome_list] = []
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255
260
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options[:output] = "tsv"
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256
261
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262
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+
if ARGV.length == 0
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263
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usage_identify
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264
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abort
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265
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end
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266
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+
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257
267
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while x = ARGV.shift
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268
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259
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case x.downcase
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data/lib/bacterial-annotator.rb
CHANGED
@@ -369,6 +369,20 @@ class BacterialAnnotator
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369
369
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inference: inference
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370
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}
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371
371
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372
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+
@annotation_stats[:flagged_cds].each do |flag|
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373
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if flag.include? "#{k}"
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374
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if v[:homology][:assert_cutoff].inject(:+) > 2
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375
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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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376
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+
elsif v[:homology][:assert_cutoff] == [1,1,0]
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377
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flag.replace("#{flag}\tPossible pseudogene (coverage subject = #{cov_subject} with #{v[:homology][:hits][0]}))")
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378
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elsif v[:homology][:assert_cutoff] == [1,0,1]
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379
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+
flag.replace("#{flag}\tPossible pseudogene (coverage query = #{cov_query} with #{v[:homology][:hits][0]}))")
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380
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+
elsif v[:homology][:assert_cutoff] == [0,1,1]
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381
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flag.replace("#{flag}\tLow similarity (percent identity = #{v[:homology][:pId]} with #{v[:homology][:hits][0]}))")
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382
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end
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383
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end
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384
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end
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385
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+
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372
386
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end
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373
387
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374
388
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end
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@@ -463,6 +477,7 @@ class BacterialAnnotator
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463
477
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flag += "\t#{(@prot_synteny_refgenome.query_sequences[prot][:homology][:cov_query]*100).round(2)}"
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464
478
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flag += "\t#{(@prot_synteny_refgenome.query_sequences[prot][:homology][:cov_subject]*100).round(2)}"
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465
479
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@annotation_stats[:flagged_cds] << flag
|
480
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+
remaining_cds << prot
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466
481
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end
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467
482
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468
483
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else
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@@ -515,7 +530,7 @@ class BacterialAnnotator
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515
530
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516
531
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file_flagged_cds = file_dir + "/Prot-flagged.tsv"
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517
532
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File.open(file_flagged_cds, "w") do |fopen|
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518
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-
fopen.write("CDS locus\tAssertion-CutOff\tAA Identity\tCovQuery(%)\tCovSubject(%)\n")
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533
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+
fopen.write("CDS locus\tAssertion-CutOff\tAA Identity\tCovQuery(%)\tCovSubject(%)\tNote\n")
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519
534
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@annotation_stats[:flagged_cds].each do |fcds|
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520
535
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fopen.write("#{fcds}\n")
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521
536
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end
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: bacterial-annotator
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.8.
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4
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+
version: 0.8.9
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Maxime Deraspe
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8
8
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autorequire:
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9
9
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bindir: bin
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10
10
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cert_chain: []
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11
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-
date: 2018-
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11
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+
date: 2018-10-17 00:00:00.000000000 Z
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12
12
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dependencies:
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13
13
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- !ruby/object:Gem::Dependency
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14
14
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name: bio
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