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