Greetings All:
I've been trying to read pfam files to get the protein accessions for
each family. This almost works using Embl format readers, but the
(Stockholm) sequence format in the fifth or sixth family is causing an
exception:
[java] Exception in thread "main" rethrown as
org.biojava.
Bioperl works I think. I know that internall Pfam runs off a branched copy
of bioperl, but it was branched about 2 years ago (when I left the Pfam
group...) so no promises.
Bio::AlignIO is what you are looking for...
-
Ewan Birn
No, I don't think any of our current SeqIO code will handle
this format. Certainly, I'm amazed that the EmblLikeFormat
got as far as it did -- STOCKHOLM format really isn't much
like EMBL at all (even in the headers, there's the
extra #= stuff, to be confusing).
I don't know much about the HMMer
Thomas Down wrote:
> No, I don't think any of our current SeqIO code will handle
> this format. Certainly, I'm amazed that the EmblLikeFormat
> got as far as it did -- STOCKHOLM format really isn't much
> like EMBL at all (even in the headers, there's the
> extra #= stuff, to be confusing).
>
>
We'd like to add IO support for the AGAVE XML format
(http://www.agavexml.org) into the BioJava library. Creating the output
code in a SequenceFormat seems straightforward, but I'm confused about
input. AGAVE and BioJava have hierarchies of features and hierarchies of
sequences to represent ass
On Wed, Sep 12, 2001 at 12:32:36PM -0700, Brian King wrote:
>
> We'd like to add IO support for the AGAVE XML format
> (http://www.agavexml.org) into the BioJava library. Creating the output
> code in a SequenceFormat seems straightforward, but I'm confused about
> input. AGAVE and BioJava have
>>SeqIOListener interface works quite a lot like the SAX
>>ContentHandler: You do something like:
>>
>> startFeature(container)
>> startFeature(child1);
>> endFeature();
>> startFeature(child2);
>> endFeature();
>> endFeature();
Thanks.
hi biojava'ers,
i have discovered a small potential problem with the biojava 1.10 distribution that i thought you might like to have brought to your attention.
i have biojava installed on an imac running os-x. os-x apparently limits the filename sizes to shorter than those of a number of the files
