Class: Bio::GFF::Record
Overview
Represents a single line of a GFF-formatted file. See Bio::GFF for more information.
Direct Known Subclasses
Instance Attribute Summary collapse
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#attributes ⇒ Object
List of tag=value pairs (e.g. to store name of the feature: ID=my_id).
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#comment ⇒ Object
Comments for the GFF record.
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#end ⇒ Object
End position of feature on reference sequence.
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#feature ⇒ Object
Name of the feature.
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#frame ⇒ Object
For features of type ‘exon’: indicates where feature begins in the reading frame.
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#score ⇒ Object
Score of annotation (e.g. e-value for BLAST search).
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#seqname ⇒ Object
Name of the reference sequence.
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#source ⇒ Object
Name of the source of the feature (e.g. program that did prediction).
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#start ⇒ Object
Start position of feature on reference sequence.
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#strand ⇒ Object
Strand that feature is located on.
Instance Method Summary collapse
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#comments ⇒ Object
“comments” is deprecated.
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#comments=(str) ⇒ Object
“comments=” is deprecated.
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#initialize(str) ⇒ Record
constructor
Creates a Bio::GFF::Record object.
Constructor Details
#initialize(str) ⇒ Record
Creates a Bio::GFF::Record object. Is typically not called directly, but is called automatically when creating a Bio::GFF object.
Arguments:
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str: a tab-delimited line in GFF format
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# File 'lib/bio/db/gff.rb', line 125 def initialize(str) @comment = str.chomp[/#.*/] return if /^#/.match(str) @seqname, @source, @feature, @start, @end, @score, @strand, @frame, attributes, = str.chomp.split("\t") @attributes = parse_attributes(attributes) if attributes end |
Instance Attribute Details
#attributes ⇒ Object
List of tag=value pairs (e.g. to store name of the feature: ID=my_id)
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# File 'lib/bio/db/gff.rb', line 103 def attributes @attributes end |
#comment ⇒ Object
Comments for the GFF record
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# File 'lib/bio/db/gff.rb', line 106 def comment @comment end |
#end ⇒ Object
End position of feature on reference sequence
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# File 'lib/bio/db/gff.rb', line 91 def end @end end |
#feature ⇒ Object
Name of the feature
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# File 'lib/bio/db/gff.rb', line 85 def feature @feature end |
#frame ⇒ Object
For features of type ‘exon’: indicates where feature begins in the reading frame
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# File 'lib/bio/db/gff.rb', line 100 def frame @frame end |
#score ⇒ Object
Score of annotation (e.g. e-value for BLAST search)
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# File 'lib/bio/db/gff.rb', line 94 def score @score end |
#seqname ⇒ Object
Name of the reference sequence
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# File 'lib/bio/db/gff.rb', line 79 def seqname @seqname end |
#source ⇒ Object
Name of the source of the feature (e.g. program that did prediction)
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# File 'lib/bio/db/gff.rb', line 82 def source @source end |
#start ⇒ Object
Start position of feature on reference sequence
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# File 'lib/bio/db/gff.rb', line 88 def start @start end |
#strand ⇒ Object
Strand that feature is located on
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# File 'lib/bio/db/gff.rb', line 97 def strand @strand end |
Instance Method Details
#comments ⇒ Object
“comments” is deprecated. Instead, use “comment”.
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# File 'lib/bio/db/gff.rb', line 109 def comments #warn "#{self.class.to_s}#comments is deprecated. Instead, use \"comment\"." if $VERBOSE self.comment end |
#comments=(str) ⇒ Object
“comments=” is deprecated. Instead, use “comment=”.
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# File 'lib/bio/db/gff.rb', line 115 def comments=(str) #warn "#{self.class.to_s}#comments= is deprecated. Instead, use \"comment=\"." if $VERBOSE self.comment = str end |