[BioRuby] Multi Fasta Sequence file to Genbank conversion..

[Sharvari Gujja]

Hi Adam,

I am using bioruby version is 1.2.1. How can I upgrade to the new version?

Also,the final output file would contain  genbank format for each fasta 
sequence right? I am interested in getting a single genabank file for 
all the sequences.

Thanks
S


Adam Kraut wrote:
> Naohisa, thanks for clearing that up.  I knew there was a better way ;)
>
> Sharvari, which version of Bioruby have you installed?  Both examples 
> will print everything to stdout, which you can redirect to a single file.
>
> On Fri, Sep 5, 2008 at 10:22 AM, Sharvari Gujja <sgujja at broad.mit.edu 
> <mailto:sgujja at broad.mit.edu>> wrote:
>
>     Hi,
>
>     Thank you so much for the reply.
>
>     However, I get the following error on running this code:
>
>     *require 'bio'
>
>      Bio::FlatFile.open($<) do |ff|
>       ff.each do |e|
>         print e.to_biosequence.output(:genbank)
>       end
>      end*
>
>
>     undefined method `to_biosequence' for
>     #<Bio::FastaFormat:0x2a95cc4948> (NoMethodError)
>
>     And running this code gives me:
>
>     *include Bio
>
>
>     fasta = Alignment::MultiFastaFormat.new(File.open('my.fasta').read)
>     fasta.entries.each do |seq|
>      puts seq.to_seq.output(:genbank)
>     end*
>
>     uninitialized constant Alignment (NameError)...
>
>     I guess this is something to do with rubygems.
>
>     Also, I believe this would generate a genbank file for each
>     sequence in the multi-fasta file. Is there a way to get single
>     Genbank file for the multi-fasta sequence file?
>
>     Appreciate all the help.
>
>     Thanks
>     S
>
>
>     Naohisa GOTO wrote:
>
>         Hi,
>
>         On Thu, 4 Sep 2008 19:13:25 -0400
>         "Adam Kraut" <adamnkraut at gmail.com
>         <mailto:adamnkraut at gmail.com>> wrote:
>
>          
>
>             I've never used the genbank format, but in Bioruby you
>             could try:
>
>             include Bio
>
>             fasta =
>             Alignment::MultiFastaFormat.new(File.open('my.fasta').read)
>             fasta.entries.each do |seq|
>              puts seq.to_seq.output(:genbank)
>             end
>                
>
>
>         No need to use Bio::Alignment::MultiFastaFormat in this case.
>         Bio::FlatFile alone can do.
>
>         For example, to read from stdin and output to stdout,
>
>          require 'bio'
>          Bio::FlatFile.open($<) do |ff|
>            ff.each do |e|
>              print e.to_biosequence.output(:genbank)
>            end
>          end
>
>         Note that the output(:genbank) are new feature only in
>         the latest development version in the git repository.
>         http://github.com/bioruby/bioruby
>         (i.e. in BioRuby 1.2.1, above examples cannot be run.)
>
>         Naohisa Goto
>         ngoto at gen-info.osaka-u.ac.jp
>         <mailto:ngoto at gen-info.osaka-u.ac.jp> / ng at bioruby.org
>         <mailto:ng at bioruby.org>
>
>          
>
>             The only tricky part is perhaps is the to_seq call for a
>             Bio::Sequence
>             object which has different output format methods.
>             -Adam
>
>             On Thu, Sep 4, 2008 at 10:53 AM, Sharvari Gujja
>             <sgujja at broad.mit.edu <mailto:sgujja at broad.mit.edu>>wrote:
>
>                
>
>                 Hi,
>
>                 I am trying to convert a multi fasta sequence file
>                 (nucleotide/protein) to
>                 genbank format.Is there a way to do this using Bioruby?
>
>                 Appreciate any input/suggestions.
>
>                 Thanks
>                 S
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