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[aaron@higgins scaffolder-annotation-locator (master)]$ git reset --hard 0fb5fb6 | |
HEAD is now at 0fb5fb6 Merge branch 'develop' | |
[aaron@higgins scaffolder-annotation-locator (master)]$ rvm use 1.9.3-p0 | |
Using /Users/aaron/.rvm/gems/ruby-1.9.3-p0 | |
[aaron@higgins scaffolder-annotation-locator (master)]$ sed -i '' 's/~> 1.0/= 1.1.3/' Gemfile | |
[aaron@higgins scaffolder-annotation-locator (master)]$ bundle update | |
Fetching gem metadata from http://rubygems.org/...... | |
Fetching gem metadata from http://rubygems.org/.. | |
Using rake (0.9.2.2) | |
Using rack (1.4.1) | |
Installing bcat (0.6.2) | |
Installing ffi (1.0.11) with native extensions | |
Installing childprocess (0.3.2) | |
Using builder (3.0.0) | |
Installing diff-lcs (1.1.3) | |
Using json (1.7.0) | |
Installing gherkin (2.4.21) with native extensions | |
Installing term-ansicolor (1.0.7) | |
Installing cucumber (0.10.7) | |
Installing rdiscount (1.6.8) with native extensions | |
Installing rspec-core (2.10.0) | |
Installing rspec-expectations (2.10.0) | |
Installing rspec-mocks (2.10.0) | |
Installing rspec (2.10.0) | |
Installing aruba (0.4.5) | |
Installing bio (1.4.2) | |
Using bundler (1.1.3) | |
Installing git (1.2.5) | |
Using rdoc (3.12) | |
Installing jeweler (1.8.3) | |
Using psych (1.3.2) | |
Installing scaffolder (0.4.4) | |
Installing scaffolder-test-helpers (0.3.0) | |
Installing yard (0.8.1) | |
Your bundle is updated! Use `bundle show [gemname]` to see where a bundled gem is installed. | |
[aaron@higgins scaffolder-annotation-locator (master)]$ bundle exec rake | |
/Users/aaron/.rvm/rubies/ruby-1.9.3-p0/bin/ruby -S rspec spec/scaffolder/annotation_locator_spec.rb spec/scaffolder/gff_record_helper_spec.rb | |
...............F..................F..................FF..................F.............. | |
Failures: | |
1) Scaffolder::AnnotationLocator relocating a single contig start trimmed with a single annotation | |
Failure/Error: described_class.new(@scaffold_file.path, @sequence_file.path, | |
Errno::ENOENT: | |
No such file or directory - /var/folders/yv/c2r06v597n5bdpw_bf8qcmb80000gp/T/gff20120504-25126-1nv380s | |
# ./lib/scaffolder/annotation_locator.rb:58:in `read' | |
# ./lib/scaffolder/annotation_locator.rb:58:in `records' | |
# ./lib/scaffolder/annotation_locator.rb:18:in `block in initialize' | |
# ./lib/scaffolder/annotation_locator.rb:15:in `initialize' | |
# ./spec/scaffolder/annotation_locator_spec.rb:7:in `new' | |
# ./spec/scaffolder/annotation_locator_spec.rb:7:in `relocate' | |
# ./spec/scaffolder/annotation_locator_spec.rb:64:in `block (4 levels) in <top (required)>' | |
# ./spec/scaffolder/annotation_locator_spec.rb:72:in `block (4 levels) in <top (required)>' | |
2) Scaffolder::AnnotationLocator relocating a single contig reversed with an insert before an annotation | |
Failure/Error: described_class.new(@scaffold_file.path, @sequence_file.path, | |
Errno::ENOENT: | |
No such file or directory - /var/folders/yv/c2r06v597n5bdpw_bf8qcmb80000gp/T/gff20120504-25126-f9ozw6 | |
# ./lib/scaffolder/annotation_locator.rb:58:in `read' | |
# ./lib/scaffolder/annotation_locator.rb:58:in `records' | |
# ./lib/scaffolder/annotation_locator.rb:18:in `block in initialize' | |
# ./lib/scaffolder/annotation_locator.rb:15:in `initialize' | |
# ./spec/scaffolder/annotation_locator_spec.rb:7:in `new' | |
# ./spec/scaffolder/annotation_locator_spec.rb:7:in `relocate' | |
# ./spec/scaffolder/annotation_locator_spec.rb:135:in `block (4 levels) in <top (required)>' | |
# ./spec/scaffolder/annotation_locator_spec.rb:142:in `block (4 levels) in <top (required)>' | |
3) Scaffolder::AnnotationLocator relocating two contigs where the two annotations are unordered annotations | |
Failure/Error: described_class.new(@scaffold_file.path, @sequence_file.path, | |
Errno::ENOENT: | |
No such file or directory - /var/folders/yv/c2r06v597n5bdpw_bf8qcmb80000gp/T/gff20120504-25126-1nzqvio | |
# ./lib/scaffolder/annotation_locator.rb:58:in `read' | |
# ./lib/scaffolder/annotation_locator.rb:58:in `records' | |
# ./lib/scaffolder/annotation_locator.rb:18:in `block in initialize' | |
# ./lib/scaffolder/annotation_locator.rb:15:in `initialize' | |
# ./spec/scaffolder/annotation_locator_spec.rb:7:in `new' | |
# ./spec/scaffolder/annotation_locator_spec.rb:7:in `relocate' | |
# ./spec/scaffolder/annotation_locator_spec.rb:213:in `block (4 levels) in <top (required)>' | |
# ./spec/scaffolder/annotation_locator_spec.rb:225:in `block (4 levels) in <top (required)>' | |
4) Scaffolder::AnnotationLocator relocating two contigs where the first of the two contigs is start trimmed | |
Failure/Error: described_class.new(@scaffold_file.path, @sequence_file.path, | |
Errno::ENOENT: | |
No such file or directory - /var/folders/yv/c2r06v597n5bdpw_bf8qcmb80000gp/T/gff20120504-25126-1dkz69t | |
# ./lib/scaffolder/annotation_locator.rb:58:in `read' | |
# ./lib/scaffolder/annotation_locator.rb:58:in `records' | |
# ./lib/scaffolder/annotation_locator.rb:18:in `block in initialize' | |
# ./lib/scaffolder/annotation_locator.rb:15:in `initialize' | |
# ./spec/scaffolder/annotation_locator_spec.rb:7:in `new' | |
# ./spec/scaffolder/annotation_locator_spec.rb:7:in `relocate' | |
# ./spec/scaffolder/annotation_locator_spec.rb:235:in `block (4 levels) in <top (required)>' | |
# ./spec/scaffolder/annotation_locator_spec.rb:238:in `block (4 levels) in <top (required)>' | |
5) Scaffolder::AnnotationLocator relocating two contigs separated by an unresolved region | |
Failure/Error: described_class.new(@scaffold_file.path, @sequence_file.path, | |
Errno::ENOENT: | |
No such file or directory - /var/folders/yv/c2r06v597n5bdpw_bf8qcmb80000gp/T/gff20120504-25126-d5issp | |
# ./lib/scaffolder/annotation_locator.rb:58:in `read' | |
# ./lib/scaffolder/annotation_locator.rb:58:in `records' | |
# ./lib/scaffolder/annotation_locator.rb:18:in `block in initialize' | |
# ./lib/scaffolder/annotation_locator.rb:15:in `initialize' | |
# ./spec/scaffolder/annotation_locator_spec.rb:7:in `new' | |
# ./spec/scaffolder/annotation_locator_spec.rb:7:in `relocate' | |
# ./spec/scaffolder/annotation_locator_spec.rb:282:in `block (4 levels) in <top (required)>' | |
# ./spec/scaffolder/annotation_locator_spec.rb:292:in `block (4 levels) in <top (required)>' | |
Finished in 2.09 seconds | |
88 examples, 5 failures | |
Failed examples: | |
rspec ./spec/scaffolder/annotation_locator_spec.rb:72 # Scaffolder::AnnotationLocator relocating a single contig start trimmed with a single annotation | |
rspec ./spec/scaffolder/annotation_locator_spec.rb:142 # Scaffolder::AnnotationLocator relocating a single contig reversed with an insert before an annotation | |
rspec ./spec/scaffolder/annotation_locator_spec.rb:225 # Scaffolder::AnnotationLocator relocating two contigs where the two annotations are unordered annotations | |
rspec ./spec/scaffolder/annotation_locator_spec.rb:238 # Scaffolder::AnnotationLocator relocating two contigs where the first of the two contigs is start trimmed | |
rspec ./spec/scaffolder/annotation_locator_spec.rb:292 # Scaffolder::AnnotationLocator relocating two contigs separated by an unresolved region | |
rake aborted! | |
/Users/aaron/.rvm/rubies/ruby-1.9.3-p0/bin/ruby -S rspec spec/scaffolder/annotation_locator_spec.rb spec/scaffolder/gff_record_helper_spec.rb failed | |
Tasks: TOP => default => spec | |
(See full trace by running task with --trace) | |
[aaron@higgins scaffolder-annotation-locator (master)]$ bundle exec rake features | |
/Users/aaron/.rvm/rubies/ruby-1.9.3-p0/bin/ruby -S bundle exec cucumber | |
Feature: Parsing contigs with inserts | |
In order to include inserts in a scaffold | |
A user can use scaffold-annotation-locator | |
to update annotation coordinates with respect to contigs with inserts | |
Scenario: An annotation before an insert in a contig # features/inserts.feature:6 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
inserts: | |
- | |
source: insert1 | |
open: 14 | |
close: 15 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> insert1 | |
TTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 4 13 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 4 13 . + 1 ID=gene1 | |
""" | |
Scenario: An annotation after an insert in a contig # features/inserts.feature:37 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
inserts: | |
- | |
source: insert1 | |
open: 1 | |
close: 3 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> insert1 | |
TTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 4 13 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 5 14 . + 1 ID=gene1 | |
""" | |
Scenario: An annotation before an insert in a reversed contig # features/inserts.feature:68 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
reverse: true | |
inserts: | |
- | |
source: insert1 | |
open: 1 | |
close: 3 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> insert1 | |
TTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 4 13 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 8 17 . - 1 ID=gene1 | |
""" | |
Scenario: An annotation overlapping with an insert location # features/inserts.feature:100 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
inserts: | |
- | |
source: insert1 | |
open: 1 | |
close: 4 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> insert1 | |
TTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 4 13 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
""" | |
Feature: Locating annotations on single contig scaffold | |
In order to build a genome from multiple contigs | |
A user can use scaffold-annotation-locator | |
to update annotation coordinates with respect from multiple contigs | |
Scenario: Three annotations on three contigs # features/multiple-contigs.feature:6 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
- sequence: | |
source: contig2 | |
- sequence: | |
source: contig3 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> contig2 | |
AAAAAGGGGGCCCCCTTTTT | |
> contig3 | |
AAAAAGGGGGCCCCCTTTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 1 10 . + 1 ID=gene1 | |
contig2 . CDS 1 6 . + 1 ID=gene2 | |
contig3 . CDS 1 6 . + 1 ID=gene2 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 1 10 . + 1 ID=gene1 | |
scaffold . CDS 21 26 . + 1 ID=gene2 | |
scaffold . CDS 41 46 . + 1 ID=gene2 | |
""" | |
Scenario: Unordered Annotations on multiple contigs # features/multiple-contigs.feature:42 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
- sequence: | |
source: contig2 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> contig2 | |
AAAAAGGGGGCCCCCTTTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig2 . CDS 1 6 . + 1 ID=gene2 | |
contig1 . CDS 1 10 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 1 10 . + 1 ID=gene1 | |
scaffold . CDS 21 26 . + 1 ID=gene2 | |
""" | |
Scenario: Annotations on trimmed contigs # features/multiple-contigs.feature:72 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
stop: 17 | |
- sequence: | |
source: contig2 | |
start: 4 | |
stop: 9 | |
- sequence: | |
source: contig3 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> contig2 | |
AAAAAGGGGGCCCCCTTTTT | |
> contig3 | |
AAAAAGGGGGCCCCCTTTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 1 10 . + 1 ID=gene1 | |
contig2 . CDS 4 6 . + 1 ID=gene2 | |
contig3 . CDS 1 6 . + 1 ID=gene3 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 1 10 . + 1 ID=gene1 | |
scaffold . CDS 18 20 . + 1 ID=gene2 | |
scaffold . CDS 24 29 . + 1 ID=gene3 | |
""" | |
Scenario: Annotations on reversed and trimmed contigs # features/multiple-contigs.feature:111 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
stop: 17 | |
- sequence: | |
source: contig2 | |
start: 4 | |
stop: 9 | |
reverse: true | |
- sequence: | |
source: contig3 | |
reverse: true | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> contig2 | |
AAAAAGGGGGCCCCCTTTTT | |
> contig3 | |
AAAAAGGGGGCCCCCTTTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 1 10 . + 1 ID=gene1 | |
contig2 . CDS 4 6 . + 1 ID=gene2 | |
contig3 . CDS 1 6 . + 1 ID=gene3 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 1 10 . + 1 ID=gene1 | |
scaffold . CDS 21 23 . - 1 ID=gene2 | |
scaffold . CDS 38 43 . - 1 ID=gene3 | |
""" | |
Scenario: Annotations on two contigs separated by an unannotated contig # features/multiple-contigs.feature:152 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
- sequence: | |
source: contig2 | |
- sequence: | |
source: contig3 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> contig2 | |
AAAAAGGGGGCCCCCTTTTT | |
> contig3 | |
AAAAAGGGGGCCCCCTTTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 1 6 . + 1 ID=gene1 | |
contig3 . CDS 1 6 . + 1 ID=gene2 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 1 6 . + 1 ID=gene1 | |
scaffold . CDS 41 46 . + 1 ID=gene2 | |
""" | |
Scenario: Annotations on a single duplicated contig # features/multiple-contigs.feature:186 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
- sequence: | |
source: contig1 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 1 6 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 1 6 . + 1 ID=gene1 | |
scaffold . CDS 21 26 . + 1 ID=gene1 | |
""" | |
Scenario: Annotations on reversed and trimmed contigs with inserts # features/multiple-contigs.feature:213 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
stop: 6 | |
- sequence: | |
source: contig2 | |
reverse: true | |
inserts: | |
- | |
source: insert1 | |
open: 6 | |
close: 7 | |
- sequence: | |
source: contig3 | |
start: 3 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGG | |
> contig2 | |
AAAAAGGGGGC | |
> contig3 | |
AAAAAGGG | |
> insert1 | |
TTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 1 4 . + 1 ID=gene1 | |
contig1 . CDS 5 8 . + 1 ID=gene2 | |
contig2 . CDS 1 4 . + 1 ID=gene3 | |
contig2 . CDS 8 11 . + 1 ID=gene4 | |
contig3 . CDS 1 3 . + 1 ID=gene5 | |
contig3 . CDS 4 8 . + 1 ID=gene6 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 1 4 . + 1 ID=gene1 | |
scaffold . CDS 15 18 . - 1 ID=gene3 | |
scaffold . CDS 7 10 . - 1 ID=gene4 | |
scaffold . CDS 20 24 . + 1 ID=gene6 | |
""" | |
Feature: Locating annotations on single contig scaffold | |
In order to add gff3 annotations to a scaffold | |
A user can use scaffold-annotation-locator | |
to return the updated coordinates of scaffold annotations | |
Scenario: One annotation on a contig # features/single-contig.feature:6 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 4 13 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 4 13 . + 1 ID=gene1 | |
""" | |
Scenario: One annotation on a reversed contig # features/single-contig.feature:30 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
reverse: true | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 1 6 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 15 20 . - 1 ID=gene1 | |
""" | |
Scenario: An annotation in a start trimmed region of the sequence # features/single-contig.feature:55 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
start: 5 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> insert1 | |
TTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 4 13 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
""" | |
Scenario: An annotation inside a stop trimmed region of the sequence # features/single-contig.feature:81 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
stop: 12 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> insert1 | |
TTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 4 13 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
""" | |
Scenario: An annotation bordering a stop trimmed region of the sequence # features/single-contig.feature:107 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
stop: 13 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> insert1 | |
TTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 4 13 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 4 13 . + 1 ID=gene1 | |
""" | |
Scenario: An annotation bordering a start trimmed region of the sequence # features/single-contig.feature:134 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
start: 4 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 4 13 . + 1 ID=gene1 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 1 10 . + 1 ID=gene1 | |
""" | |
Feature: Parsing unresolved regions | |
In order to include unresolved regions in a scaffold | |
A user can use scaffold-annotation-locator | |
to update annotation coordinates with respect to unresolved regions | |
Scenario: Annotations on two contigs separated by an unresolved region # features/unresolved.feature:6 | |
Given a file named "scaf.yml" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
--- | |
- sequence: | |
source: contig1 | |
- unresolved: | |
length: 10 | |
- sequence: | |
source: contig2 | |
""" | |
Given a file named "seq.fna" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
> contig1 | |
AAAAAGGGGGCCCCCTTTTT | |
> contig2 | |
AAAAAGGGGGCCCCCTTTTT | |
""" | |
Given a file named "anno.gff" with: # aruba-0.4.5/lib/aruba/cucumber.rb:15 | |
""" | |
##gff-version 3 | |
contig1 . CDS 1 6 . + 1 ID=gene1 | |
contig2 . CDS 1 6 . + 1 ID=gene2 | |
""" | |
When I relocate the annotations using "scaf.yml", "seq.fna" and "anno.gff" # features/step_definitions/scaffolder-annotation-locator_steps.rb:1 | |
Then the result should be: # features/step_definitions/scaffolder-annotation-locator_steps.rb:11 | |
""" | |
##gff-version 3 | |
scaffold . CDS 1 6 . + 1 ID=gene1 | |
scaffold . CDS 31 36 . + 1 ID=gene2 | |
""" | |
18 scenarios (18 passed) | |
90 steps (90 passed) | |
0m0.974s | |
[aaron@higgins scaffolder-annotation-locator (master)]$ ruby -v | |
ruby 1.9.3p0 (2011-10-30 revision 33570) [x86_64-darwin11.3.0] | |
[aaron@higgins scaffolder-annotation-locator (master)]$ bundle -v | |
Bundler version 1.1.3 | |
[aaron@higgins scaffolder-annotation-locator (master)]$ ruby -v | |
ruby 1.9.3p0 (2011-10-30 revision 33570) [x86_64-darwin11.3.0] | |
[aaron@higgins scaffolder-annotation-locator (master)]$ |
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