[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
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<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> </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. 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. </SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=465212322-29112001></SPAN></FONT> </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> </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(">" . $self->{'file'} . '.' . $seq->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> if(
$annotation->each_DBLink ){<BR> my $dblink =
($annotation->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><<A
href="mailto:birney@ebi.ac.uk">birney@ebi.ac.uk</A>>.
<BR>-----------------------------------------------------------------<BR><BR></FONT></DIV>
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