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Merge branch 'master' into develop

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commit 2a892536373269843c5e63e19e8a64ef1ff76489 2 parents 89bcda9 + 3031e3f
@michaelbarton authored
View
8 features/table/cds_entries.feature
@@ -303,7 +303,7 @@ Feature: Producing cds annotation view from a scaffold
"""
@disable-bundler
- Scenario: A CDS entry with a single db_xref attribute
+ Scenario: A CDS entry with a single DBxref attribute
Given I successfully run `genomer init project`
And I cd to "project"
And I write to "assembly/scaffold.yml" with:
@@ -320,7 +320,7 @@ Feature: Producing cds annotation view from a scaffold
And I write to "assembly/annotations.gff" with:
"""
##gff-version 3
- contig1 . gene 1 3 . - 1 ID=gene1;db_xref=GO:000001
+ contig1 . gene 1 3 . - 1 ID=gene1;DBxref=GO:000001
"""
And I append to "Gemfile" with:
"""
@@ -340,7 +340,7 @@ Feature: Producing cds annotation view from a scaffold
"""
@disable-bundler
- Scenario: A CDS entry with multiple db_xref attributes
+ Scenario: A CDS entry with multiple DBxref attributes
Given I successfully run `genomer init project`
And I cd to "project"
And I write to "assembly/scaffold.yml" with:
@@ -357,7 +357,7 @@ Feature: Producing cds annotation view from a scaffold
And I write to "assembly/annotations.gff" with:
"""
##gff-version 3
- contig1 . gene 1 3 . - 1 ID=gene1;db_xref=GO:000001;db_xref=InterPro:IPR000111
+ contig1 . gene 1 3 . - 1 ID=gene1;DBxref=GO:000001;DBxref=InterPro:IPR000111
"""
And I append to "Gemfile" with:
"""
View
2  genomer-plugin-view.gemspec
@@ -6,7 +6,7 @@ Gem::Specification.new do |s|
s.name = "genomer-plugin-view"
s.version = GenomerViewPlugin::VERSION
s.platform = Gem::Platform::RUBY
- s.homepage = "http://github.com/michaelbarton/genomer-plugin-view"
+ s.homepage = "http://next.gs"
s.license = "MIT"
s.authors = ["Michael Barton"]
s.email = ["mail@michaelbarton.me.uk"]
View
2  lib/genomer-plugin-view/gff_record_helper.rb
@@ -2,7 +2,7 @@
module GenomerPluginView::GffRecordHelper
- DEFAULT_GFF_MAPPING = {'product' => 'product', 'Note' => 'note', 'db_xref' => 'db_xref'}
+ DEFAULT_GFF_MAPPING = {'product' => 'product', 'Note' => 'note', 'DBxref' => 'db_xref'}
GFF_TO_TABLE = {
'gene' => {
View
2  lib/genomer-plugin-view/version.rb
@@ -1,3 +1,3 @@
class GenomerViewPlugin
- VERSION = "0.0.5"
+ VERSION = "0.0.6"
end
View
8 man/genomer-view.ronn
@@ -68,6 +68,10 @@ begin with an upper case letter.
Used to populate the **Note** field for entries when the
`--generate_encoded_features` option is passed.
+ * `DBxref`: Used to link the annotation to other database references. This
+ field is added verbatim to generated output. Multiple entires of this
+ field may be used.
+
### GENOMER ATTRIBUTES
These attributes are specific to genomer and should begin with a lower case
@@ -99,10 +103,6 @@ section.
**product** attributes are present. See the next section for an explanation
of this.
- * `db_xref`: Used to link the annotation to other database references. This
- field is added to verbatim to generated output. Multiple entires of this
- field may be used.
-
### OVERLAP BETWEEN NAME, PRODUCT AND FUNCTION FIELD
The genbank annotation table **product** fields may contain either a short four
View
5 spec/genomer-view-plugin/gff_record_helper_spec.rb
@@ -203,20 +203,23 @@
['Name', 'gene'],
['ID', 'locus_tag']],
:tRNA => [
+ ['DBxref', 'db_xref'],
['product', 'product'],
['Note', 'note']],
:rRNA => [
['product', 'product'],
['Note', 'note']],
:miscRNA => [
+ ['DBxref', 'db_xref'],
['product', 'product'],
['Note', 'note']],
:tmRNA => [
+ ['DBxref', 'db_xref'],
['product', 'product'],
['Note', 'note']],
:CDS => [
['ec_number', 'EC_number'],
- ['db_xref', 'db_xref'],
+ ['DBxref', 'db_xref'],
['function', 'function'],
['product', 'product'],
['Note', 'note'],
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