genomer-plugin-view 0.0.2 → 0.0.3
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Feature: Producing a gff3 view of a scaffold's annotations
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In order to view scaffold annotations
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A user can use the "gff" command
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to generate gff3 view of scaffold annotations
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@disable-bundler
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Scenario: A single annotation on a single contig
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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 gff --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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##gff-version 3
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genome . gene 1 3 . + 1 .
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"""
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@disable-bundler
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Scenario: Two annotations on a single contig
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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 gff --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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##gff-version 3
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genome . gene 1 3 . + 1 .
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genome . gene 4 6 . + 1 .
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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 gff --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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##gff-version 3
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genome . gene 1 3 . + 1 ID=000001
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genome . gene 4 6 . + 1 ID=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 gff --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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##gff-version 3
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genome . gene 1 3 . + 1 ID=000005
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genome . gene 4 6 . + 1 ID=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 gff --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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##gff-version 3
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genome . gene 1 3 . + 1 ID=000001
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genome . gene 4 6 . + 1 ID=000002
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genome . gene 7 9 . + 1 ID=000003
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genome . gene 10 12 . + 1 ID=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 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 gff --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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##gff-version 3
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genome . gene 1 3 . + 1 ID=pre_gene1
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genome . gene 4 6 . + 1 ID=pre_gene2
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"""
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require 'genomer'
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class GenomerPluginView::Gff < Genomer::Plugin
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DEFAULT = '.'
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def run
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options = GenomerPluginView.convert_command_line_flags(flags)
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annotations(options).
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map{|i| i.seqname = options[:identifier] || DEFAULT; i}.
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map(&:to_s).
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map(&:strip).
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unshift("##gff-version 3").
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join("\n") + "\n"
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end
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end
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require 'spec_helper'
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require 'genomer-plugin-view/gff'
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describe GenomerPluginView::Gff do
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describe "#run" do
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let(:annotations){ [] }
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let(:flags){ {} }
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before(:each) do
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stub(subject).annotations do
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annotations
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end
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stub(subject).flags do
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flags
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end
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end
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subject do
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described_class.new([],{})
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end
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describe "with no annotations or flags" do
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it "should return the header line" do
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subject.run.should == "##gff-version 3\n"
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end
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end
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describe "with one gene annotation" do
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let(:annotations){ [gene] }
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it "should return a single gene gff entry " do
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subject.run.should == <<-EOS.unindent
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##gff-version 3
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.\t.\tgene\t1\t3\t.\t+\t1\t.
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EOS
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end
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end
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describe "with two gene annotations" do
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let(:annotations) do
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[
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gene,
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gene(:start => 4, :end => 6)
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]
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end
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it "should return a single gene gff entry " do
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subject.run.should == <<-EOS.unindent
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##gff-version 3
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.\t.\tgene\t1\t3\t.\t+\t1\t.
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.\t.\tgene\t4\t6\t.\t+\t1\t.
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EOS
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end
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end
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describe "with the identifier flag" do
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let(:flags){ {:identifier => 'genome'} }
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let(:annotations){ [gene] }
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it "should return a single gene gff entry " do
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subject.run.should == <<-EOS.unindent
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##gff-version 3
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genome\t.\tgene\t1\t3\t.\t+\t1\t.
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EOS
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end
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end
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end
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end
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: genomer-plugin-view
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3
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version: !ruby/object:Gem::Version
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-
version: 0.0.
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version: 0.0.3
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prerelease:
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platform: ruby
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7
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authors:
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2012-05-
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date: 2012-05-29 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: genomer
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@@ -139,6 +139,7 @@ files:
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139
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- features/agp/generation.feature
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140
140
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- features/fasta/contigs.feature
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- features/fasta/single_sequence.feature
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- features/gff/core.feature
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143
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- features/mappings/core.feature
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143
144
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- features/support/env.rb
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145
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- features/table/cds_entries.feature
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@@ -148,6 +149,7 @@ files:
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148
149
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- lib/genomer-plugin-view.rb
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149
150
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- lib/genomer-plugin-view/agp.rb
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- lib/genomer-plugin-view/fasta.rb
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152
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+
- lib/genomer-plugin-view/gff.rb
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151
153
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- lib/genomer-plugin-view/gff_record_helper.rb
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152
154
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- lib/genomer-plugin-view/mapping.rb
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153
155
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- lib/genomer-plugin-view/table.rb
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@@ -157,6 +159,7 @@ files:
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- spec/genomer-view-plugin/agp_spec.rb
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158
160
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- spec/genomer-view-plugin/fasta_spec.rb
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159
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- spec/genomer-view-plugin/gff_record_helper_spec.rb
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162
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+
- spec/genomer-view-plugin/gff_spec.rb
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160
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- spec/genomer-view-plugin/mapping_spec.rb
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- spec/genomer-view-plugin/table_spec.rb
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162
165
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- spec/genomer-view-plugin_spec.rb
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@@ -176,7 +179,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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version: '0'
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segments:
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- 0
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-
hash:
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+
hash: -3689932046879280024
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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