genomer-plugin-view 0.0.2
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.
- data/.document +5 -0
- data/.gitignore +52 -0
- data/Gemfile +2 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +19 -0
- data/Rakefile +9 -0
- data/features/agp/generation.feature +285 -0
- data/features/fasta/contigs.feature +173 -0
- data/features/fasta/single_sequence.feature +144 -0
- data/features/mappings/core.feature +181 -0
- data/features/support/env.rb +13 -0
- data/features/table/cds_entries.feature +304 -0
- data/features/table/core.feature +302 -0
- data/features/table/feature_type.feature +180 -0
- data/genomer-plugin-view.gemspec +34 -0
- data/lib/genomer-plugin-view/agp.rb +62 -0
- data/lib/genomer-plugin-view/fasta.rb +36 -0
- data/lib/genomer-plugin-view/gff_record_helper.rb +61 -0
- data/lib/genomer-plugin-view/mapping.rb +14 -0
- data/lib/genomer-plugin-view/table.rb +56 -0
- data/lib/genomer-plugin-view/version.rb +3 -0
- data/lib/genomer-plugin-view.rb +29 -0
- data/man/genomer-view-agp.ronn +46 -0
- data/man/genomer-view.ronn +153 -0
- data/spec/genomer-view-plugin/agp_spec.rb +79 -0
- data/spec/genomer-view-plugin/fasta_spec.rb +96 -0
- data/spec/genomer-view-plugin/gff_record_helper_spec.rb +244 -0
- data/spec/genomer-view-plugin/mapping_spec.rb +89 -0
- data/spec/genomer-view-plugin/table_spec.rb +279 -0
- data/spec/genomer-view-plugin_spec.rb +103 -0
- data/spec/spec_helper.rb +32 -0
- metadata +192 -0
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Feature: Producing a annotation view of a scaffold
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In order to submit genome annotations
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A user can use the "table" command
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to generate the genbank annotation table format
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@disable-bundler
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Scenario: Generating a table file from a single annotation
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Given I successfully run `genomer init project`
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And I cd to "project"
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And I write to "assembly/scaffold.yml" with:
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"""
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---
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- sequence:
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source: contig1
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig1
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AAAAATTTTTGGGGGCCCCC
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"""
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And I write to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 3 . + 1 .
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"""
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And I append to "Gemfile" with:
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"""
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gem 'genomer-plugin-view', :path => '../../../'
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"""
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When I run `genomer view table --identifier=genome`
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Then the exit status should be 0
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And the output should contain:
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"""
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>Feature genome annotation_table
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1 3 gene
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"""
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@disable-bundler
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Scenario: Generating a table file from two annotations
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Given I successfully run `genomer init project`
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And I cd to "project"
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And I write to "assembly/scaffold.yml" with:
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"""
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---
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- sequence:
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source: contig1
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig1
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AAAAATTTTTGGGGGCCCCC
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"""
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And I write to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 3 . + 1
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contig1 . gene 4 6 . + 1
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"""
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And I append to "Gemfile" with:
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"""
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gem 'genomer-plugin-view', :path => '../../../'
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"""
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When I run `genomer view table --identifier=genome`
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Then the exit status should be 0
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And the output should contain:
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"""
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>Feature genome annotation_table
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1 3 gene
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4 6 gene
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"""
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@disable-bundler
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Scenario: Generating a table file from a gene with ID attribute
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Given I successfully run `genomer init project`
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And I cd to "project"
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And I write to "assembly/scaffold.yml" with:
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"""
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---
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- sequence:
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source: contig1
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig1
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AAAAATTTTTGGGGGCCCCC
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"""
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And I write to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 3 . - 1 ID=gene1
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"""
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And I append to "Gemfile" with:
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"""
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gem 'genomer-plugin-view', :path => '../../../'
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"""
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When I run `genomer view table --identifier=genome`
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Then the exit status should be 0
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And the output should contain:
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"""
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>Feature genome annotation_table
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3 1 gene
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locus_tag gene1
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"""
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@disable-bundler
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Scenario: Generating a table file from a gene with ID and name attributes
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Given I successfully run `genomer init project`
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And I cd to "project"
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And I write to "assembly/scaffold.yml" with:
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"""
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---
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- sequence:
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source: contig1
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig1
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AAAAATTTTTGGGGGCCCCC
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"""
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And I write to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 3 . - 1 ID=gene1;Name=abcd
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"""
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And I append to "Gemfile" with:
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"""
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gem 'genomer-plugin-view', :path => '../../../'
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"""
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When I run `genomer view table --identifier=genome`
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Then the exit status should be 0
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And the output should contain:
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"""
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>Feature genome annotation_table
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3 1 gene
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locus_tag gene1
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gene abcd
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"""
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@disable-bundler
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Scenario: Reseting locus tag numbering at the scaffold origin
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Given I successfully run `genomer init project`
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And I cd to "project"
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And I write to "assembly/scaffold.yml" with:
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"""
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---
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- sequence:
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source: contig1
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig1
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AAAAATTTTTGGGGGCCCCC
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"""
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And I write to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 3 . + 1 ID=gene1
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contig1 . gene 4 6 . + 1 ID=gene2
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"""
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And I append to "Gemfile" with:
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"""
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gem 'genomer-plugin-view', :path => '../../../'
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"""
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When I run `genomer view table --identifier=genome --reset_locus_numbering`
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Then the exit status should be 0
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And the output should contain:
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"""
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>Feature genome annotation_table
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1 3 gene
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locus_tag 000001
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4 6 gene
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locus_tag 000002
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"""
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@disable-bundler
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Scenario: Reseting locus tag numbering at specified start value
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Given I successfully run `genomer init project`
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And I cd to "project"
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And I write to "assembly/scaffold.yml" with:
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"""
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---
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- sequence:
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source: contig1
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig1
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AAAAATTTTTGGGGGCCCCC
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"""
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And I write to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 3 . + 1 ID=gene1
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contig1 . gene 4 6 . + 1 ID=gene2
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"""
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And I append to "Gemfile" with:
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"""
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gem 'genomer-plugin-view', :path => '../../../'
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"""
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When I run `genomer view table --identifier=genome --reset_locus_numbering=5`
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Then the exit status should be 0
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And the output should contain:
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"""
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>Feature genome annotation_table
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1 3 gene
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locus_tag 000005
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4 6 gene
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locus_tag 000006
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"""
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@disable-bundler
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Scenario: Reseting locus tag at the scaffold origin with unordered annotations
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Given I successfully run `genomer init project`
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And I cd to "project"
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And I write to "assembly/scaffold.yml" with:
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"""
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---
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- sequence:
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source: contig1
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig1
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AAAAATTTTTGGGGGCCCCC
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"""
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And I write to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 10 12 . + 1 ID=gene4
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contig1 . gene 4 6 . + 1 ID=gene2
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contig1 . gene 1 3 . + 1 ID=gene1
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contig1 . gene 7 9 . + 1 ID=gene3
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"""
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And I append to "Gemfile" with:
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"""
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gem 'genomer-plugin-view', :path => '../../../'
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"""
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When I run `genomer view table --identifier=genome --reset_locus_numbering`
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Then the exit status should be 0
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And the output should contain:
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"""
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>Feature genome annotation_table
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1 3 gene
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locus_tag 000001
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4 6 gene
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locus_tag 000002
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7 9 gene
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locus_tag 000003
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10 12 gene
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locus_tag 000004
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"""
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@disable-bundler
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Scenario: Adding a prefix to annotation locus tags
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Given I successfully run `genomer init project`
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And I cd to "project"
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And I write to "assembly/scaffold.yml" with:
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"""
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---
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- sequence:
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source: contig1
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig1
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AAAAATTTTTGGGGGCCCCC
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"""
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And I write to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 10 12 . + 1 ID=gene4
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contig1 . gene 4 6 . + 1 ID=gene2
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contig1 . gene 1 3 . + 1 ID=gene1
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contig1 . gene 7 9 . + 1 ID=gene3
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"""
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And I append to "Gemfile" with:
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"""
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gem 'genomer-plugin-view', :path => '../../../'
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"""
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When I run `genomer view table --identifier=genome --prefix=pre_`
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Then the exit status should be 0
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And the output should contain:
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"""
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>Feature genome annotation_table
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1 3 gene
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locus_tag pre_gene1
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4 6 gene
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locus_tag pre_gene2
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7 9 gene
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locus_tag pre_gene3
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10 12 gene
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locus_tag pre_gene4
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"""
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@@ -0,0 +1,180 @@
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Feature: Producing an table view of alternate entries
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2
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In order to submit non-CDS genome annotations
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3
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A user can use the "table" command with --generate_encoded_features
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4
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to generate the genbank annotation table format with non-CDS
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@disable-bundler
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Scenario: Creating an unknown feature type using 'feature_type'
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Given I successfully run `genomer init project`
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And I cd to "project"
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And I write to "assembly/scaffold.yml" with:
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"""
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---
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- sequence:
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source: contig1
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig1
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AAAAATTTTTGGGGGCCCCC
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"""
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And I write to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 3 . - 1 ID=gene1;feature_type=unknown;product=something
|
|
25
|
+
"""
|
|
26
|
+
And I append to "Gemfile" with:
|
|
27
|
+
"""
|
|
28
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
|
29
|
+
"""
|
|
30
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
|
31
|
+
Then the exit status should be 1
|
|
32
|
+
And the output should contain:
|
|
33
|
+
"""
|
|
34
|
+
Error. Unknown feature_type 'unknown'
|
|
35
|
+
"""
|
|
36
|
+
|
|
37
|
+
@disable-bundler
|
|
38
|
+
Scenario: Creating a tRNA entry from using the 'feature_type' field
|
|
39
|
+
Given I successfully run `genomer init project`
|
|
40
|
+
And I cd to "project"
|
|
41
|
+
And I write to "assembly/scaffold.yml" with:
|
|
42
|
+
"""
|
|
43
|
+
---
|
|
44
|
+
- sequence:
|
|
45
|
+
source: contig1
|
|
46
|
+
"""
|
|
47
|
+
And I write to "assembly/sequence.fna" with:
|
|
48
|
+
"""
|
|
49
|
+
>contig1
|
|
50
|
+
AAAAATTTTTGGGGGCCCCC
|
|
51
|
+
"""
|
|
52
|
+
And I write to "assembly/annotations.gff" with:
|
|
53
|
+
"""
|
|
54
|
+
##gff-version 3
|
|
55
|
+
contig1 . gene 1 3 . - 1 ID=gene1;feature_type=tRNA;product=tRNA-Gly;Note=something
|
|
56
|
+
"""
|
|
57
|
+
And I append to "Gemfile" with:
|
|
58
|
+
"""
|
|
59
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
|
60
|
+
"""
|
|
61
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
|
62
|
+
Then the exit status should be 0
|
|
63
|
+
And the output should contain:
|
|
64
|
+
"""
|
|
65
|
+
3 1 gene
|
|
66
|
+
locus_tag gene1
|
|
67
|
+
3 1 tRNA
|
|
68
|
+
product tRNA-Gly
|
|
69
|
+
note something
|
|
70
|
+
|
|
71
|
+
"""
|
|
72
|
+
|
|
73
|
+
@disable-bundler
|
|
74
|
+
Scenario: Creating a rRNA entry from using the 'feature_type' field
|
|
75
|
+
Given I successfully run `genomer init project`
|
|
76
|
+
And I cd to "project"
|
|
77
|
+
And I write to "assembly/scaffold.yml" with:
|
|
78
|
+
"""
|
|
79
|
+
---
|
|
80
|
+
- sequence:
|
|
81
|
+
source: contig1
|
|
82
|
+
"""
|
|
83
|
+
And I write to "assembly/sequence.fna" with:
|
|
84
|
+
"""
|
|
85
|
+
>contig1
|
|
86
|
+
AAAAATTTTTGGGGGCCCCC
|
|
87
|
+
"""
|
|
88
|
+
And I write to "assembly/annotations.gff" with:
|
|
89
|
+
"""
|
|
90
|
+
##gff-version 3
|
|
91
|
+
contig1 . gene 1 3 . - 1 ID=gene1;feature_type=rRNA;product=ribosomal RNA;Note=something
|
|
92
|
+
"""
|
|
93
|
+
And I append to "Gemfile" with:
|
|
94
|
+
"""
|
|
95
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
|
96
|
+
"""
|
|
97
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
|
98
|
+
Then the exit status should be 0
|
|
99
|
+
And the output should contain:
|
|
100
|
+
"""
|
|
101
|
+
3 1 gene
|
|
102
|
+
locus_tag gene1
|
|
103
|
+
3 1 rRNA
|
|
104
|
+
product ribosomal RNA
|
|
105
|
+
note something
|
|
106
|
+
|
|
107
|
+
"""
|
|
108
|
+
|
|
109
|
+
@disable-bundler
|
|
110
|
+
Scenario: Creating a tmRNA entry from using the 'feature_type' field
|
|
111
|
+
Given I successfully run `genomer init project`
|
|
112
|
+
And I cd to "project"
|
|
113
|
+
And I write to "assembly/scaffold.yml" with:
|
|
114
|
+
"""
|
|
115
|
+
---
|
|
116
|
+
- sequence:
|
|
117
|
+
source: contig1
|
|
118
|
+
"""
|
|
119
|
+
And I write to "assembly/sequence.fna" with:
|
|
120
|
+
"""
|
|
121
|
+
>contig1
|
|
122
|
+
AAAAATTTTTGGGGGCCCCC
|
|
123
|
+
"""
|
|
124
|
+
And I write to "assembly/annotations.gff" with:
|
|
125
|
+
"""
|
|
126
|
+
##gff-version 3
|
|
127
|
+
contig1 . gene 1 3 . - 1 ID=gene1;feature_type=tmRNA;product=tmRNA;Note=something
|
|
128
|
+
"""
|
|
129
|
+
And I append to "Gemfile" with:
|
|
130
|
+
"""
|
|
131
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
|
132
|
+
"""
|
|
133
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
|
134
|
+
Then the exit status should be 0
|
|
135
|
+
And the output should contain:
|
|
136
|
+
"""
|
|
137
|
+
3 1 gene
|
|
138
|
+
locus_tag gene1
|
|
139
|
+
3 1 tmRNA
|
|
140
|
+
product tmRNA
|
|
141
|
+
note something
|
|
142
|
+
|
|
143
|
+
"""
|
|
144
|
+
|
|
145
|
+
@disable-bundler
|
|
146
|
+
Scenario: Creating a miscRNA entry from using the 'feature_type' field
|
|
147
|
+
Given I successfully run `genomer init project`
|
|
148
|
+
And I cd to "project"
|
|
149
|
+
And I write to "assembly/scaffold.yml" with:
|
|
150
|
+
"""
|
|
151
|
+
---
|
|
152
|
+
- sequence:
|
|
153
|
+
source: contig1
|
|
154
|
+
"""
|
|
155
|
+
And I write to "assembly/sequence.fna" with:
|
|
156
|
+
"""
|
|
157
|
+
>contig1
|
|
158
|
+
AAAAATTTTTGGGGGCCCCC
|
|
159
|
+
"""
|
|
160
|
+
And I write to "assembly/annotations.gff" with:
|
|
161
|
+
"""
|
|
162
|
+
##gff-version 3
|
|
163
|
+
contig1 . gene 1 3 . - 1 ID=gene1;feature_type=miscRNA;product=RNA signal;Note=something
|
|
164
|
+
"""
|
|
165
|
+
And I append to "Gemfile" with:
|
|
166
|
+
"""
|
|
167
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
|
168
|
+
"""
|
|
169
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
|
170
|
+
Then the exit status should be 0
|
|
171
|
+
And the output should contain:
|
|
172
|
+
"""
|
|
173
|
+
3 1 gene
|
|
174
|
+
locus_tag gene1
|
|
175
|
+
3 1 miscRNA
|
|
176
|
+
product RNA signal
|
|
177
|
+
note something
|
|
178
|
+
|
|
179
|
+
"""
|
|
180
|
+
|