genevalidator 1.6.6 → 1.6.8
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- 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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@@ -5,4 +5,4 @@
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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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@@ -5,4 +5,4 @@
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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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@@ -121,14 +121,13 @@ module GeneValidator
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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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