full_lengther_next 0.6.2 → 0.9.8
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 +7 -0
- data/.gitignore +9 -0
- data/.rspec +2 -0
- data/.travis.yml +5 -0
- data/CODE_OF_CONDUCT.md +49 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +21 -0
- data/{README.rdoc → README.md} +0 -0
- data/Rakefile +6 -37
- data/bin/console +14 -0
- data/bin/download_fln_dbs.rb +2 -7
- data/bin/full_lengther_next +85 -6
- data/bin/make_user_db.rb +13 -5
- data/bin/setup +8 -0
- data/full_lengther_next.gemspec +42 -0
- data/lib/full_lengther_next.rb +2 -10
- data/lib/full_lengther_next/artifacts.rb +74 -0
- data/lib/full_lengther_next/{classes/blast_functions.rb → blast_functions.rb} +0 -0
- data/lib/full_lengther_next/{classes/cdhit.rb → cdhit.rb} +0 -0
- data/lib/full_lengther_next/{classes/chimeric_seqs.rb → chimeric_seqs.rb} +0 -0
- data/lib/full_lengther_next/{classes/common_functions.rb → common_functions.rb} +0 -0
- data/lib/full_lengther_next/{classes/exonerate_result.rb → exonerate_result.rb} +0 -0
- data/lib/full_lengther_next/{classes/fl_analysis.rb → fl_analysis.rb} +0 -0
- data/lib/full_lengther_next/{classes/fl_string_utils.rb → fl_string_utils.rb} +0 -0
- data/lib/full_lengther_next/fln_stats.rb +613 -0
- data/lib/full_lengther_next/go_methods.rb +42 -0
- data/lib/full_lengther_next/{classes/handle_db.rb → handle_db.rb} +0 -0
- data/lib/full_lengther_next/mapping.rb +296 -0
- data/lib/full_lengther_next/{classes/my_worker.rb → my_worker.rb} +71 -9
- data/lib/full_lengther_next/{classes/my_worker_EST.rb → my_worker_EST.rb} +0 -0
- data/lib/full_lengther_next/{classes/my_worker_manager_EST.rb → my_worker_manager_EST.rb} +0 -0
- data/lib/full_lengther_next/{classes/my_worker_manager_fln.rb → my_worker_manager_fln.rb} +181 -16
- data/lib/full_lengther_next/{classes/nc_rna.rb → nc_rna.rb} +0 -0
- data/lib/full_lengther_next/{classes/orf.rb → orf.rb} +0 -0
- data/lib/full_lengther_next/{classes/reptrans.rb → reptrans.rb} +9 -5
- data/lib/full_lengther_next/{classes/sequence.rb → sequence.rb} +26 -1
- data/lib/full_lengther_next/{classes/test_code.rb → test_code.rb} +1 -1
- data/lib/full_lengther_next/{classes/types.rb → types.rb} +3 -2
- data/lib/full_lengther_next/{classes/une_los_hit.rb → une_los_hit.rb} +0 -0
- data/lib/full_lengther_next/version.rb +3 -0
- data/lib/full_lengther_next/{classes/warnings.rb → warnings.rb} +0 -0
- data/report_templates/general_summary.erb +140 -0
- data/report_templates/mapping_summary.erb +98 -0
- data/report_templates/reptrans_summary.erb +32 -0
- metadata +112 -134
- data/.gemtest +0 -0
- data/History.txt +0 -32
- data/Manifest.txt +0 -44
- data/PostInstall.txt +0 -6
- data/bin/plot_fln.rb +0 -270
- data/bin/plot_taxonomy.rb +0 -70
- data/lib/expresscanvas.zip +0 -0
- data/lib/full_lengther_next/classes/artifacts.rb +0 -66
- data/lib/full_lengther_next/classes/fln_stats.rb +0 -641
- data/script/console +0 -10
- data/script/destroy +0 -14
- data/script/generate +0 -14
- data/test/test_full_lengther_next.rb +0 -11
- data/test/test_helper.rb +0 -3
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<%
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base_pie_config = {
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header: true,
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width: '650px',
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height: '650px',
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responsive: false,
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title: nil,
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config: {
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'fontName' => 'Arial',
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'showPieValues' => false,
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'pieSegmentPrecision' => 3,
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'maxPieSectors' => 30,
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'legendBox' => false,
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'legendScaleFontFactor' => 0.9
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}
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}
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%>
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<center>
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<div style="float: center; font-size: 30; margin:10px">
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<b>Full-LengtherNEXT Mapping Summary</b>
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</div>
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<div style="overflow: hidden; width: 1320px; heigth: 800px; padding: 10">
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<div style="margin: 0; float: left">
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<%= table_title('Mean coverage <br>') %>
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<%=sccater2D(
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id: :mean_coverage,
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x_label: 'Transcripts',
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y_label: 'Coverage (reads)',
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title: nil,
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responsive: false
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<div style="margin: 0; float: rigth">
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<%= table_title('Normalized partial coverage') %>
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<%=sccater2D(
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id: :normalized_partial_coverage,
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x_label: 'Transcript sequence mapped (%)',
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y_label: 'Normalized difference (%)',
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<div style="margin: 0; float: left">
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<%= table_title('Coverage analysis on transcripts') %>
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<%=sccater2D(
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id: :normalized_coverages_sorted_by_npc,
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x_label: 'Transcript sequence mapped (%)',
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y_label: 'Mean coverage (reads)',
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<div style="margin: 0; float: left">
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<%= table_title('GO: Molecular function') %>
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<%= pie(base_pie_config.merge({
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id: :function_go,
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row_names: true,
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</div>
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<div style="margin: 0; float: rigth">
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<%= table_title('GO: Biological process') %>
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<%= pie(base_pie_config.merge({
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id: :process_go,
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<%= table_title('GO: Cellular component') %>
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<%= pie(base_pie_config.merge({
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id: :component_go,
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<% base_table_config = {
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header: true,
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border: 2,
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cell_align: ['left', 'right', 'right'],
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attrib: {
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'cellspacing' => 0,
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'cellpadding' => 2
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}
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} %>
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<center>
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<div style="float: center; font-size: 30; margin: 10px">
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<b> Full-LengtherNEXT Representative Transcriptome Summary </b>
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</div>
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<div style="width: 850px; height: 350px; padding: 10">
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<%= table_title('Sequences info') %>
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<%= table(base_table_config.merge({
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id: :general_report,
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}
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<div style="margin: 0; float: rigth">
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<%= table_title('Sequences summary (Acumulative)') %>
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<%= table(base_table_config.merge({
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id: :acumulative_report,
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</center>
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metadata
CHANGED
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--- !ruby/object:Gem::Specification
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name: full_lengther_next
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version: 0.
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version: 0.9.8
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platform: ruby
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authors:
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- Pedro Seoane
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- Noe Fernandez
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- Dario Guerrero
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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: 2018-02-14 00:00:00.000000000 Z
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dependencies:
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type: :runtime
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description: FULL-LENGTHERNEXT is a tool adapted to NGS technologies, able to work
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in parallel and in a distributed way to minimise computing time. It is able to classify
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unigenes to full-length, 5’-end, 3’-end and internal, suggesting which unknown genes
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one of the main mistake found in wrong entries of full-length sequences databases,
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and it is a fast tool to compare different transcriptome assemblies.
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email:
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|
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|
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|
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+
homepage: https://github.com/seoanezonjic
|
|
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|
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licenses:
|
|
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|
+
- MIT
|
|
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+
metadata: {}
|
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post_install_message:
|
|
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|
+
rdoc_options: []
|
|
243
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|
require_paths:
|
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- lib
|
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required_ruby_version: !ruby/object:Gem::Requirement
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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|
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version: '0'
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requirements: []
|
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rubyforge_project:
|
|
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|
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rubygems_version:
|
|
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|
+
rubyforge_project:
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rubygems_version: 2.4.8
|
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|
signing_key:
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specification_version:
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summary:
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|
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|
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|
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test_files:
|
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|
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|
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|
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specification_version: 4
|
|
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|
+
summary: Tool to annotate transcriptomes and it is able to stablish the integrity
|
|
243
|
+
of each transcript. Also, FLN can detect novel genes on a target organism.
|
|
244
|
+
test_files: []
|