[BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58,0.58.2.1
Naohisa Goto
ngoto at dev.open-bio.org
Wed Feb 13 10:28:20 UTC 2008
Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv17175/lib/bio
Modified Files:
Tag: BRANCH-biohackathon2008
sequence.rb
Log Message:
Added a new class method Bio::Sequence.read(str).
Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58
retrieving revision 0.58.2.1
diff -C2 -d -r0.58 -r0.58.2.1
*** sequence.rb 5 Apr 2007 23:35:39 -0000 0.58
--- sequence.rb 13 Feb 2008 10:28:16 -0000 0.58.2.1
***************
*** 334,337 ****
--- 334,356 ----
@moltype = AA
end
+
+ # Create a new Bio::Sequence object from a formatted string
+ # (GenBank, EMBL, fasta format, etc.)
+ #
+ # s = Bio::Sequence.read(str)
+ # ---
+ # *Arguments*:
+ # * (required) _str_: string
+ # * (optional) _format_: format specification (class or nil)
+ # *Returns*:: Bio::Sequence object
+ def self.read(str, format = nil)
+ if format then
+ klass = format
+ else
+ klass = Bio::FlatFile::AutoDetect.default.guess(str)
+ end
+ obj = klass.new(str)
+ obj.to_biosequence
+ end
end # Sequence
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