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

[Sharvari Gujja]

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> 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 / 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>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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>>>
>>>       
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>
>
>
>