[Bioperl-l] Re: [Biojava-l] about AGAVE

[Ewan Birney]

Hanning -

thanks for the tools. Some comments -


(a) would you guys like to check this in directly with bioperl or do you
want to keep it a separate download?


(b) traditionally in the bioperl SeqIO system one is transforming a set of 
sequences to a set of sequences. the agave write_seq is focused on
building a file per sequence inside the agave.pm module in the current
working directory 

(eg, the line)

 my $output = new IO::File(">" . $self->{'file'} . '.' . $seq->display_id
. '.dtx');


which is pretty un-bioperl SeqIO. 


Can you not concatonate agave documents? In which case, should perhaps
agave be extended to allow concatonation?


(if not, guys - I guess this is like write_seq on the GCG module. What
should we do here?)


(c) DBLinks. This line is a little messy as well - 

  if( $annotation->each_DBLink ){
      my $dblink = ($annotation->each_DBLink) [0] ;


I would have thought you would have wanted to loop through the DBLinks 


(which you do in the db_id line for the DBlinks on xrefs. Hmmmmm. I guess
I am getting confused here)



Anyway - many thanks for the tool. 



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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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