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 fasta view of a scaffold
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In order to produce fasta output from a scaffold
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A user can use the "view" command
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to generate the required fasta output
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@disable-bundler
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Scenario: Generating simple fasta
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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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-
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sequence:
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source: "contig00001"
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig00001
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ATGGC
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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 fasta`
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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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>.
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ATGGC
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"""
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@disable-bundler
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Scenario: Generating simple fasta with a sequence identifier
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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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-
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sequence:
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source: "contig00001"
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig00001
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ATGGC
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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 fasta --identifier=scaffold`
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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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>scaffold
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ATGGC
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"""
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@disable-bundler
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Scenario: Generating fasta with a organism name modifier
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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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-
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sequence:
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source: "contig00001"
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig00001
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ATGGC
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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 fasta --organism='genus species'`
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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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>. [organism=genus species]
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ATGGC
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"""
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@disable-bundler
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Scenario: Generating fasta with a strain modifier
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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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-
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sequence:
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source: "contig00001"
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig00001
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ATGGC
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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 fasta --strain=strain_name`
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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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>. [strain=strain_name]
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ATGGC
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"""
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@disable-bundler
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Scenario: Generating fasta with identifier and strain modifier
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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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-
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sequence:
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source: "contig00001"
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"""
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And I write to "assembly/sequence.fna" with:
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"""
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>contig00001
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ATGGC
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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 fasta --strain=strain_name --identifier=name`
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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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>name [strain=strain_name]
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ATGGC
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"""
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Feature: Producing a map of annotations IDs
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In order to use map annotation IDs between versions
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A user can use the "mapping" command
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to generate a list of the original and updated annotations
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@disable-bundler
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Scenario: Two genes with locus tag numbering reset 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 mapping --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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gene1 000001
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gene2 000002
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"""
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@disable-bundler
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Scenario: Two genes with locus tag numbering reset 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 mapping --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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gene1 000005
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gene2 000006
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"""
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@disable-bundler
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Scenario: Four unordered genes with locus tag reset 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 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 mapping --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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gene1 000001
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gene2 000002
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gene3 000003
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gene4 000004
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"""
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@disable-bundler
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Scenario: Four genes with a prefix added to the 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 mapping --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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gene1 pre_gene1
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gene2 pre_gene2
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gene3 pre_gene3
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gene4 pre_gene4
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"""
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@disable-bundler
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Scenario: Four genes prefixes and locus tag reset 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 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 mapping --reset_locus_numbering=5 --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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gene1 pre_000005
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gene2 pre_000006
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gene3 pre_000007
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gene4 pre_000008
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"""
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@@ -0,0 +1,13 @@
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require 'bundler'
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begin
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Bundler.setup(:default, :development)
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rescue Bundler::BundlerError => e
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$stderr.puts e.message
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$stderr.puts "Run `bundle install` to install missing gems"
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exit e.status_code
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end
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$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
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$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../spec')
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require 'aruba/cucumber'
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@@ -0,0 +1,304 @@
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Feature: Producing cds annotation view from a scaffold
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In order to submit CDS genome annotations
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A user can use the "table" command with --generate_encoded_features
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to generate the genbank annotation table format with CDS
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@disable-bundler
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Scenario: A CDS entry with no 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 .
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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 --generate_encoded_features`
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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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+
1 3 CDS
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+
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"""
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+
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@disable-bundler
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+
Scenario: A CDS entry with a prefixed ID
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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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54
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+
"""
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55
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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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64
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+
When I run `genomer view table --identifier=genome --generate_encoded_features=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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68
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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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3 1 CDS
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protein_id pre_gene1
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"""
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+
|
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|
+
@disable-bundler
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+
Scenario: A CDS entry with a Name 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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84
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source: contig1
|
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+
"""
|
|
86
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+
And I write to "assembly/sequence.fna" with:
|
|
87
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+
"""
|
|
88
|
+
>contig1
|
|
89
|
+
AAAAATTTTTGGGGGCCCCC
|
|
90
|
+
"""
|
|
91
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+
And I write to "assembly/annotations.gff" with:
|
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92
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+
"""
|
|
93
|
+
##gff-version 3
|
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94
|
+
contig1 . gene 4 6 . + 1 ID=gene2;Name=defg
|
|
95
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+
"""
|
|
96
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+
And I append to "Gemfile" with:
|
|
97
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+
"""
|
|
98
|
+
gem 'genomer-plugin-view', :path => '../../../'
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|
99
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+
"""
|
|
100
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
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Then the exit status should be 0
|
|
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+
And the output should contain:
|
|
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|
+
"""
|
|
104
|
+
>Feature genome annotation_table
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|
105
|
+
4 6 gene
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|
106
|
+
locus_tag gene2
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|
107
|
+
gene defg
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|
108
|
+
4 6 CDS
|
|
109
|
+
protein_id gene2
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|
110
|
+
product Defg
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111
|
+
|
|
112
|
+
"""
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|
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|
+
|
|
114
|
+
@disable-bundler
|
|
115
|
+
Scenario: A CDS entry with a product attribute
|
|
116
|
+
Given I successfully run `genomer init project`
|
|
117
|
+
And I cd to "project"
|
|
118
|
+
And I write to "assembly/scaffold.yml" with:
|
|
119
|
+
"""
|
|
120
|
+
---
|
|
121
|
+
- sequence:
|
|
122
|
+
source: contig1
|
|
123
|
+
"""
|
|
124
|
+
And I write to "assembly/sequence.fna" with:
|
|
125
|
+
"""
|
|
126
|
+
>contig1
|
|
127
|
+
AAAAATTTTTGGGGGCCCCC
|
|
128
|
+
"""
|
|
129
|
+
And I write to "assembly/annotations.gff" with:
|
|
130
|
+
"""
|
|
131
|
+
##gff-version 3
|
|
132
|
+
contig1 . gene 4 6 . + 1 ID=gene2;product=defg
|
|
133
|
+
"""
|
|
134
|
+
And I append to "Gemfile" with:
|
|
135
|
+
"""
|
|
136
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
|
137
|
+
"""
|
|
138
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
|
139
|
+
Then the exit status should be 0
|
|
140
|
+
And the output should contain:
|
|
141
|
+
"""
|
|
142
|
+
>Feature genome annotation_table
|
|
143
|
+
4 6 gene
|
|
144
|
+
locus_tag gene2
|
|
145
|
+
4 6 CDS
|
|
146
|
+
protein_id gene2
|
|
147
|
+
product defg
|
|
148
|
+
|
|
149
|
+
"""
|
|
150
|
+
|
|
151
|
+
@disable-bundler
|
|
152
|
+
Scenario: A CDS entry with Name and product attributes
|
|
153
|
+
Given I successfully run `genomer init project`
|
|
154
|
+
And I cd to "project"
|
|
155
|
+
And I write to "assembly/scaffold.yml" with:
|
|
156
|
+
"""
|
|
157
|
+
---
|
|
158
|
+
- sequence:
|
|
159
|
+
source: contig1
|
|
160
|
+
"""
|
|
161
|
+
And I write to "assembly/sequence.fna" with:
|
|
162
|
+
"""
|
|
163
|
+
>contig1
|
|
164
|
+
AAAAATTTTTGGGGGCCCCC
|
|
165
|
+
"""
|
|
166
|
+
And I write to "assembly/annotations.gff" with:
|
|
167
|
+
"""
|
|
168
|
+
##gff-version 3
|
|
169
|
+
contig1 . gene 4 6 . + 1 ID=gene2;Name=defg;product=xyz
|
|
170
|
+
"""
|
|
171
|
+
And I append to "Gemfile" with:
|
|
172
|
+
"""
|
|
173
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
|
174
|
+
"""
|
|
175
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
|
176
|
+
Then the exit status should be 0
|
|
177
|
+
And the output should contain:
|
|
178
|
+
"""
|
|
179
|
+
>Feature genome annotation_table
|
|
180
|
+
4 6 gene
|
|
181
|
+
locus_tag gene2
|
|
182
|
+
gene defg
|
|
183
|
+
4 6 CDS
|
|
184
|
+
protein_id gene2
|
|
185
|
+
product Defg
|
|
186
|
+
function xyz
|
|
187
|
+
|
|
188
|
+
"""
|
|
189
|
+
|
|
190
|
+
@disable-bundler
|
|
191
|
+
Scenario: A CDS entry with product and function attributes
|
|
192
|
+
Given I successfully run `genomer init project`
|
|
193
|
+
And I cd to "project"
|
|
194
|
+
And I write to "assembly/scaffold.yml" with:
|
|
195
|
+
"""
|
|
196
|
+
---
|
|
197
|
+
- sequence:
|
|
198
|
+
source: contig1
|
|
199
|
+
"""
|
|
200
|
+
And I write to "assembly/sequence.fna" with:
|
|
201
|
+
"""
|
|
202
|
+
>contig1
|
|
203
|
+
AAAAATTTTTGGGGGCCCCC
|
|
204
|
+
"""
|
|
205
|
+
And I write to "assembly/annotations.gff" with:
|
|
206
|
+
"""
|
|
207
|
+
##gff-version 3
|
|
208
|
+
contig1 . gene 4 6 . + 1 ID=gene2;product=defg;function=xyz
|
|
209
|
+
"""
|
|
210
|
+
And I append to "Gemfile" with:
|
|
211
|
+
"""
|
|
212
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
|
213
|
+
"""
|
|
214
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
|
215
|
+
Then the exit status should be 0
|
|
216
|
+
And the output should contain:
|
|
217
|
+
"""
|
|
218
|
+
>Feature genome annotation_table
|
|
219
|
+
4 6 gene
|
|
220
|
+
locus_tag gene2
|
|
221
|
+
4 6 CDS
|
|
222
|
+
protein_id gene2
|
|
223
|
+
product defg
|
|
224
|
+
function xyz
|
|
225
|
+
|
|
226
|
+
"""
|
|
227
|
+
|
|
228
|
+
@disable-bundler
|
|
229
|
+
Scenario: A CDS entry with Name, product and function attributes
|
|
230
|
+
Given I successfully run `genomer init project`
|
|
231
|
+
And I cd to "project"
|
|
232
|
+
And I write to "assembly/scaffold.yml" with:
|
|
233
|
+
"""
|
|
234
|
+
---
|
|
235
|
+
- sequence:
|
|
236
|
+
source: contig1
|
|
237
|
+
"""
|
|
238
|
+
And I write to "assembly/sequence.fna" with:
|
|
239
|
+
"""
|
|
240
|
+
>contig1
|
|
241
|
+
AAAAATTTTTGGGGGCCCCC
|
|
242
|
+
"""
|
|
243
|
+
And I write to "assembly/annotations.gff" with:
|
|
244
|
+
"""
|
|
245
|
+
##gff-version 3
|
|
246
|
+
contig1 . gene 4 6 . + 1 ID=gene2;Name=abcd;product=efgh;function=ijkl
|
|
247
|
+
"""
|
|
248
|
+
And I append to "Gemfile" with:
|
|
249
|
+
"""
|
|
250
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
|
251
|
+
"""
|
|
252
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
|
253
|
+
Then the exit status should be 0
|
|
254
|
+
And the output should contain:
|
|
255
|
+
"""
|
|
256
|
+
>Feature genome annotation_table
|
|
257
|
+
4 6 gene
|
|
258
|
+
locus_tag gene2
|
|
259
|
+
gene abcd
|
|
260
|
+
4 6 CDS
|
|
261
|
+
protein_id gene2
|
|
262
|
+
product Abcd
|
|
263
|
+
function efgh
|
|
264
|
+
|
|
265
|
+
"""
|
|
266
|
+
|
|
267
|
+
@disable-bundler
|
|
268
|
+
Scenario: A CDS entry with ec_number and note attributes
|
|
269
|
+
Given I successfully run `genomer init project`
|
|
270
|
+
And I cd to "project"
|
|
271
|
+
And I write to "assembly/scaffold.yml" with:
|
|
272
|
+
"""
|
|
273
|
+
---
|
|
274
|
+
- sequence:
|
|
275
|
+
source: contig1
|
|
276
|
+
"""
|
|
277
|
+
And I write to "assembly/sequence.fna" with:
|
|
278
|
+
"""
|
|
279
|
+
>contig1
|
|
280
|
+
AAAAATTTTTGGGGGCCCCC
|
|
281
|
+
"""
|
|
282
|
+
And I write to "assembly/annotations.gff" with:
|
|
283
|
+
"""
|
|
284
|
+
##gff-version 3
|
|
285
|
+
contig1 . gene 1 3 . - 1 ID=gene1;ec_number=3.5.2.3;Note=my protein
|
|
286
|
+
"""
|
|
287
|
+
And I append to "Gemfile" with:
|
|
288
|
+
"""
|
|
289
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
|
290
|
+
"""
|
|
291
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
|
292
|
+
Then the exit status should be 0
|
|
293
|
+
And the output should contain:
|
|
294
|
+
"""
|
|
295
|
+
>Feature genome annotation_table
|
|
296
|
+
3 1 gene
|
|
297
|
+
locus_tag gene1
|
|
298
|
+
3 1 CDS
|
|
299
|
+
protein_id gene1
|
|
300
|
+
EC_number 3.5.2.3
|
|
301
|
+
note my protein
|
|
302
|
+
|
|
303
|
+
"""
|
|
304
|
+
|