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

Brian King kingb@doubletwist.com
Thu, 29 Nov 2001 14:39:12 -0800


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Ewan,
 
Sorry to take so long to get back to you on the AGAVE module.  We would like
to have it included in bioperl.  The reason the module only processes one
sequence is that we expect people to want to view the output in the
GenomicViewer.  The viewer only displays one sequence and its annotations.
If you think processing multiple sequences is more important we can change
it. 
 
Regards,
Brian King
DoubleTwist Inc.
 
============================================================================
=====
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. 



-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
< birney@ebi.ac.uk <mailto:birney@ebi.ac.uk> >. 
-----------------------------------------------------------------


 

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<DIV><FONT face=Arial size=2><SPAN 
class=465212322-29112001></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=Arial size=2><SPAN 
class=465212322-29112001>Ewan,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN 
class=465212322-29112001></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=Arial size=2><SPAN class=465212322-29112001>Sorry to take so 
long to get back to you on the AGAVE module.&nbsp; We would like to have it 
included in bioperl.&nbsp; The reason the module only processes one sequence is 
that we expect people to want to view the output in the GenomicViewer.&nbsp; The 
viewer only displays one sequence and its annotations.&nbsp; If you think 
processing multiple sequences is more important we can change 
it.&nbsp;</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN 
class=465212322-29112001></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=Arial size=2><SPAN 
class=465212322-29112001>Regards,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=465212322-29112001>Brian 
King</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=465212322-29112001>DoubleTwist 
Inc.</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN 
class=465212322-29112001></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=Arial size=2><SPAN 
class=465212322-29112001>=================================================================================</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2>Hanning -<BR><BR>thanks for the tools. Some 
comments -<BR><BR><BR>(a) would you guys like to check this in directly with 
bioperl or do you<BR>want to keep it a separate download?<BR><BR><BR>(b) 
traditionally in the bioperl SeqIO system one is transforming a set of 
<BR>sequences to a set of sequences. the agave write_seq is focused 
on<BR>building a file per sequence inside the agave.pm module in the 
current<BR>working directory <BR><BR>(eg, the line)<BR><BR> my $output = new 
IO::File("&gt;" . $self-&gt;{'file'} . '.' . $seq-&gt;display_id<BR>. 
'.dtx');<BR><BR><BR>which is pretty un-bioperl SeqIO. <BR><BR><BR>Can you not 
concatonate agave documents? In which case, should perhaps<BR>agave be extended 
to allow concatonation?<BR><BR><BR>(if not, guys - I guess this is like 
write_seq on the GCG module. What<BR>should we do here?)<BR><BR><BR>(c) DBLinks. 
This line is a little messy as well - <BR><BR>&nbsp; if( 
$annotation-&gt;each_DBLink ){<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; my $dblink = 
($annotation-&gt;each_DBLink) [0] ;<BR><BR><BR>I would have thought you would 
have wanted to loop through the DBLinks <BR><BR><BR>(which you do in the db_id 
line for the DBlinks on xrefs. Hmmmmm. I guess<BR>I am getting confused 
here)<BR><BR><BR><BR>Anyway - many thanks for the tool. 
<BR><BR><BR><BR>-----------------------------------------------------------------<BR>Ewan 
Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420<BR>&lt;<A 
href="mailto:birney@ebi.ac.uk">birney@ebi.ac.uk</A>&gt;. 
<BR>-----------------------------------------------------------------<BR><BR></FONT></DIV>
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