features/api/annotation_location.feature in genomer-0.0.6 vs features/api/annotation_location.feature in genomer-0.0.7
- old
+ new
@@ -5,29 +5,29 @@
@disable-bundler
Scenario: Two annotations on a single contig
Given I run the genomer command with the arguments "init project"
And I cd to "project"
- And I append to "Gemfile" with:
+ And I overwrite "Gemfile" with:
"""
gem 'genomer', :path => '../../../'
gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
"""
- And I append to "assembly/scaffold.yml" with:
+ And I overwrite "assembly/scaffold.yml" with:
"""
---
-
sequence:
source: contig1
"""
- And I append to "assembly/sequence.fna" with:
+ And I overwrite "assembly/sequence.fna" with:
"""
>contig1
ATGCATGC
"""
- And I append to "assembly/annotations.gff" with:
+ And I overwrite "assembly/annotations.gff" with:
"""
##gff-version 3
contig1 . gene 1 3 . + 1 .
contig1 . gene 5 7 . + 1 .
"""
@@ -42,34 +42,34 @@
@disable-bundler
Scenario: Two annotations on a two contigs
Given I run the genomer command with the arguments "init project"
And I cd to "project"
- And I append to "Gemfile" with:
+ And I overwrite "Gemfile" with:
"""
gem 'genomer', :path => '../../../'
gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
"""
- And I append to "assembly/scaffold.yml" with:
+ And I overwrite "assembly/scaffold.yml" with:
"""
---
-
sequence:
source: contig1
-
sequence:
source: contig2
"""
- And I append to "assembly/sequence.fna" with:
+ And I overwrite "assembly/sequence.fna" with:
"""
>contig1
ATGCATGC
>contig2
ATGCATGC
"""
- And I append to "assembly/annotations.gff" with:
+ And I overwrite "assembly/annotations.gff" with:
"""
##gff-version 3
contig1 . gene 1 3 . + 1 .
contig2 . gene 5 7 . + 1 .
"""
@@ -84,29 +84,29 @@
@disable-bundler
Scenario: Two annotations on a single contig with an unused annotation
Given I run the genomer command with the arguments "init project"
And I cd to "project"
- And I append to "Gemfile" with:
+ And I overwrite "Gemfile" with:
"""
gem 'genomer', :path => '../../../'
gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
"""
- And I append to "assembly/scaffold.yml" with:
+ And I overwrite "assembly/scaffold.yml" with:
"""
---
-
sequence:
source: contig1
"""
- And I append to "assembly/sequence.fna" with:
+ And I overwrite "assembly/sequence.fna" with:
"""
>contig1
ATGCATGC
"""
- And I append to "assembly/annotations.gff" with:
+ And I overwrite "assembly/annotations.gff" with:
"""
##gff-version 3
contig2 . gene 5 7 . + 1 .
contig1 . gene 1 3 . + 1 .
contig1 . gene 5 7 . + 1 .
@@ -122,29 +122,29 @@
@disable-bundler
Scenario: Three unordered annotations on a single contig
Given I run the genomer command with the arguments "init project"
And I cd to "project"
- And I append to "Gemfile" with:
+ And I overwrite "Gemfile" with:
"""
gem 'genomer', :path => '../../../'
gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
"""
- And I append to "assembly/scaffold.yml" with:
+ And I overwrite "assembly/scaffold.yml" with:
"""
---
-
sequence:
source: contig1
"""
- And I append to "assembly/sequence.fna" with:
+ And I overwrite "assembly/sequence.fna" with:
"""
>contig1
ATGCATGCATGC
"""
- And I append to "assembly/annotations.gff" with:
+ And I overwrite "assembly/annotations.gff" with:
"""
##gff-version 3
contig1 . gene 9 11 . + 1 .
contig1 . gene 1 3 . + 1 .
contig1 . gene 5 7 . + 1 .
@@ -161,34 +161,34 @@
@disable-bundler
Scenario: Four unordered annotations on a two contigs
Given I run the genomer command with the arguments "init project"
And I cd to "project"
- And I append to "Gemfile" with:
+ And I overwrite "Gemfile" with:
"""
gem 'genomer', :path => '../../../'
gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
"""
- And I append to "assembly/scaffold.yml" with:
+ And I overwrite "assembly/scaffold.yml" with:
"""
---
-
sequence:
source: contig1
-
sequence:
source: contig2
"""
- And I append to "assembly/sequence.fna" with:
+ And I overwrite "assembly/sequence.fna" with:
"""
>contig1
ATGCATGC
>contig2
ATGCATGC
"""
- And I append to "assembly/annotations.gff" with:
+ And I overwrite "assembly/annotations.gff" with:
"""
##gff-version 3
contig2 . gene 5 7 . + 1 .
contig2 . gene 1 3 . + 1 .
contig1 . gene 1 3 . + 1 .
@@ -208,16 +208,16 @@
@disable-bundler
Scenario: Annotations on reversed and trimmed contigs with inserts
Given I run the genomer command with the arguments "init project"
And I cd to "project"
- And I append to "Gemfile" with:
+ And I overwrite "Gemfile" with:
"""
gem 'genomer', :path => '../../../'
gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
"""
- And I append to "assembly/scaffold.yml" with:
+ And I overwrite "assembly/scaffold.yml" with:
"""
---
- sequence:
source: contig1
stop: 6
@@ -232,21 +232,21 @@
- sequence:
source: contig3
start: 3
"""
- And I append to "assembly/sequence.fna" with:
+ And I overwrite "assembly/sequence.fna" with:
"""
> contig1
AAAAAGGG
> contig2
AAAAAGGGGGC
> contig3
AAAAAGGG
> insert1
TTT
"""
- And I append to "assembly/annotations.gff" with:
+ And I overwrite "assembly/annotations.gff" with:
"""
##gff-version 3
contig1 . gene 1 4 . + 1 ID=gene1
contig1 . gene 5 8 . + 1 ID=gene2
contig2 . gene 1 4 . + 1 ID=gene3