[BioRuby] Multi Fasta Sequence file to Genbank conversion..
Sharvari Gujja
sgujja at broad.mit.edu
Fri Sep 5 15:11:36 UTC 2008
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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