features/mappings/core.feature in genomer-plugin-view-0.0.4 vs features/mappings/core.feature in genomer-plugin-view-0.0.5
- old
+ new
@@ -2,13 +2,20 @@
In order to use map annotation IDs between versions
A user can use the "mapping" command
to generate a list of the original and updated annotations
@disable-bundler
+ Scenario: Getting the man page for the genomer view plugin
+ Given I create a new genomer project
+ When I run `genomer man view mapping`
+ Then the exit status should be 0
+ And the output should contain a valid man page
+ And the output should contain "GENOMER-VIEW-MAPPING(1)"
+
+ @disable-bundler
Scenario: Two genes with locus tag numbering reset at the scaffold origin
- Given I successfully run `genomer init project`
- And I cd to "project"
+ Given I create a new genomer project
And I write to "assembly/scaffold.yml" with:
"""
---
- sequence:
source: contig1
@@ -22,26 +29,21 @@
"""
##gff-version 3
contig1 . gene 1 3 . + 1 ID=gene1
contig1 . gene 4 6 . + 1 ID=gene2
"""
- And I append to "Gemfile" with:
- """
- gem 'genomer-plugin-view', :path => '../../../'
- """
When I run `genomer view mapping --reset_locus_numbering`
Then the exit status should be 0
And the output should contain:
"""
gene1 000001
gene2 000002
"""
@disable-bundler
Scenario: Two genes with locus tag numbering reset at specified start value
- Given I successfully run `genomer init project`
- And I cd to "project"
+ Given I create a new genomer project
And I write to "assembly/scaffold.yml" with:
"""
---
- sequence:
source: contig1
@@ -55,26 +57,21 @@
"""
##gff-version 3
contig1 . gene 1 3 . + 1 ID=gene1
contig1 . gene 4 6 . + 1 ID=gene2
"""
- And I append to "Gemfile" with:
- """
- gem 'genomer-plugin-view', :path => '../../../'
- """
When I run `genomer view mapping --reset_locus_numbering=5`
Then the exit status should be 0
And the output should contain:
"""
gene1 000005
gene2 000006
"""
@disable-bundler
Scenario: Four unordered genes with locus tag reset at the scaffold origin
- Given I successfully run `genomer init project`
- And I cd to "project"
+ Given I create a new genomer project
And I write to "assembly/scaffold.yml" with:
"""
---
- sequence:
source: contig1
@@ -90,14 +87,10 @@
contig1 . gene 10 12 . + 1 ID=gene4
contig1 . gene 4 6 . + 1 ID=gene2
contig1 . gene 1 3 . + 1 ID=gene1
contig1 . gene 7 9 . + 1 ID=gene3
"""
- And I append to "Gemfile" with:
- """
- gem 'genomer-plugin-view', :path => '../../../'
- """
When I run `genomer view mapping --reset_locus_numbering`
Then the exit status should be 0
And the output should contain:
"""
gene1 000001
@@ -106,12 +99,11 @@
gene4 000004
"""
@disable-bundler
Scenario: Four genes with a prefix added to the locus tags
- Given I successfully run `genomer init project`
- And I cd to "project"
+ Given I create a new genomer project
And I write to "assembly/scaffold.yml" with:
"""
---
- sequence:
source: contig1
@@ -127,14 +119,10 @@
contig1 . gene 10 12 . + 1 ID=gene4
contig1 . gene 4 6 . + 1 ID=gene2
contig1 . gene 1 3 . + 1 ID=gene1
contig1 . gene 7 9 . + 1 ID=gene3
"""
- And I append to "Gemfile" with:
- """
- gem 'genomer-plugin-view', :path => '../../../'
- """
When I run `genomer view mapping --prefix=pre_`
Then the exit status should be 0
And the output should contain:
"""
gene1 pre_gene1
@@ -143,12 +131,11 @@
gene4 pre_gene4
"""
@disable-bundler
Scenario: Four genes prefixes and locus tag reset at the scaffold origin
- Given I successfully run `genomer init project`
- And I cd to "project"
+ Given I create a new genomer project
And I write to "assembly/scaffold.yml" with:
"""
---
- sequence:
source: contig1
@@ -163,13 +150,9 @@
##gff-version 3
contig1 . gene 10 12 . + 1 ID=gene4
contig1 . gene 4 6 . + 1 ID=gene2
contig1 . gene 1 3 . + 1 ID=gene1
contig1 . gene 7 9 . + 1 ID=gene3
- """
- And I append to "Gemfile" with:
- """
- gem 'genomer-plugin-view', :path => '../../../'
"""
When I run `genomer view mapping --reset_locus_numbering=5 --prefix=pre_`
Then the exit status should be 0
And the output should contain:
"""