genevalidator 1.6.6 → 1.6.8
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.
- checksums.yaml +4 -4
- data/README.md +1 -1
- data/aux/json_footer.erb +1 -1
- data/aux/template_footer.erb +1 -1
- data/bin/genevalidator +2 -1
- data/lib/genevalidator/blast.rb +5 -6
- data/lib/genevalidator/version.rb +1 -1
- metadata +2 -2
checksums.yaml
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: f1fdf73a212a4034bf683739c5cd37912704aa6f
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data.tar.gz: 3e14c4244654cbb5a33e74a73c03dd7939c32f81
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 51973ebeb66f9db5eb25e9c68a55417cea83eac7524cf30c8f810a2fe47f0c30038d11150910661630c54158f994ebf2fb0ac04bc448b6f0dc52c574e9fae1d2
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data.tar.gz: 167350002d32901144d799e713375d9fc008ea835748251372388170521cbea1bf29a8543475480709c116f781fb6934261be654c9ffd59506a814bcdb2fcff7
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data/README.md
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@@ -14,7 +14,7 @@ If you would like to use GeneValidator on a few sequences, see our online [GeneV
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If you use GeneValidator in your work, please cite us as follows:
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>
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> [Dragan M<sup>‡</sup>, Moghul MI<sup>‡</sup>, Priyam A, Bustos C & Wurm Y. 2016. GeneValidator: identify problems with protein-coding gene predictions. <em>Bioinformatics</em>, doi: 10.1093/bioinformatics/btw015](http://bioinformatics.oxfordjournals.org/content/early/2016/02/26/bioinformatics.btw015).
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data/aux/json_footer.erb
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<% output_files.each_with_index do |results_html, idx| %>
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<li><a href="<%=results_html%>"><%= idx + 1 %></a></li>
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<% end %></ul></nav><%end%>
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<footer><div class="container center-block"><p class="text-muted text-center">Please cite
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<footer><div class="container center-block"><p class="text-muted text-center">Please cite:<a href="http://bioinformatics.oxfordjournals.org/content/early/2016/02/26/bioinformatics.btw015"> "Dragan M<sup>‡</sup>, Moghul MI<sup>‡</sup>, Priyam A, Bustos C & Wurm Y <em>(2016)</em> GeneValidator: identify problematic gene predictions"</a><br/> Developed at <a href="https://wurmlab.github.io" target="_blank">Wurm Lab</a>, <a href="http://www.sbcs.qmul.ac.uk" target="_blank">QMUL</a> with funding by <a href="http://www.bbsrc.ac.uk/home/home.aspx" target="_blank">BBSRC</a> and <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2013" target="_blank">Google Summer of Code 2013</a><br/>This page was created by <a href="https://github.com/wurmlab/genevalidator" target="_blank" >GeneValidator</a> v<%= GeneValidator::VERSION %></p></div></footer></body></html>
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data/aux/template_footer.erb
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<% output_files.each_with_index do |results_html, idx| %>
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<li><a href="<%=results_html%>"><%= idx + 1 %></a></li>
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<% end %></ul></nav><%end%>
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<footer><div class="container center-block"><p class="text-muted text-center">Please cite
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<footer><div class="container center-block"><p class="text-muted text-center">Please cite:<a href="http://bioinformatics.oxfordjournals.org/content/early/2016/02/26/bioinformatics.btw015"> "Dragan M<sup>‡</sup>, Moghul MI<sup>‡</sup>, Priyam A, Bustos C & Wurm Y <em>(2016)</em> GeneValidator: identify problematic gene predictions"</a><br/> Developed at <a href="https://wurmlab.github.io" target="_blank">Wurm Lab</a>, <a href="http://www.sbcs.qmul.ac.uk" target="_blank">QMUL</a> with funding by <a href="http://www.bbsrc.ac.uk/home/home.aspx" target="_blank">BBSRC</a> and <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2013" target="_blank">Google Summer of Code 2013</a><br/>This page was created by <a href="https://github.com/wurmlab/genevalidator" target="_blank" >GeneValidator</a> v<%= GeneValidator::VERSION %></p></div></footer></body></html>
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data/bin/genevalidator
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#!/usr/bin/env ruby
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require 'optparse'
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require 'english'
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require 'genevalidator'
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require 'genevalidator/get_raw_sequences'
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@@ -116,7 +117,7 @@ begin
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exit 1
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end
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rescue OptionParser::ParseError
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$stderr.print 'Error: ' + $ERROR_INFO.to_s +
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$stderr.print 'Error: ' + $ERROR_INFO.to_s + "\n"
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exit 1
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end
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data/lib/genevalidator/blast.rb
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current_hsp.query_reading_frame = hsp.query_frame.to_i
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current_hsp.hit_alignment = hsp.hseq.to_s
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end
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seq_type = guess_sequence_type(current_hsp.hit_alignment)
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fail SequenceTypeError unless seq_type == :protein || seq_type.nil?
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current_hsp.query_alignment = hsp.qseq.to_s
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seq_type = guess_sequence_type(current_hsp.query_alignment)
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fail SequenceTypeError unless seq_type == :protein || seq_type.nil?
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current_hsp.align_len = hsp.align_len.to_i
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current_hsp.identity = hsp.identity.to_i
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current_hsp.pidentity = (100 * hsp.identity / hsp.align_len.to_f)
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metadata
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--- !ruby/object:Gem::Specification
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name: genevalidator
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version: !ruby/object:Gem::Version
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version: 1.6.
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version: 1.6.8
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platform: ruby
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authors:
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- Monica Dragan
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@@ -11,7 +11,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date:
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date: 2016-03-11 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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