[Biojava-l] [Biojava-dev] GSoC - BioJava File Parsers question

[Andreas Prlic]

Hi David,

If you take a look at the Sequence interface, this is the central
place to represents all sorts of sequences.
New parser should fit in with providing instances of objects that
implement Sequence. If this principle is kept up we are pretty close
to the SeqIO scenario from what I understand.

Andreas




On Wed, Mar 28, 2012 at 3:46 PM, David Felty <davfelty at gmail.com> wrote:
> Thanks for the info, the SeqIO modules are very helpful. In fact, it seems
> like they are quite similar to what this project asks for. Could this this
> type of implementation work for BioJava?
>
> David
>
> On Wed, Mar 28, 2012 at 6:09 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:
>
>> On Wed, Mar 28, 2012 at 10:05 PM, P. Troshin <to.petr at gmail.com> wrote:
>> > Well, they all widely used tools, and as a result of analysis they
>> > produce files. If you need to process these results further then you'd
>> > need to parse the result files. Hence the connection.
>> >
>> > Regards,
>> > Peter
>>
>> Indeed. It is quite common in Bioinformatics for file formats to
>> be named after the tool which introduced them - even if sometimes
>> they become much more widely used.
>>
>> And for GenBank and UniProt, people typically mean the GenBank
>> plain text 'flat file' format also used by DDBJ (there is a very similar
>> format used by EMBL with a common feature table), and for
>> UniProt that could refer to the old plain text 'SwissProt' file format
>> or the newer UniProt XML format. For background on these an
>> other sequence file file formats you might find these pages
>> helpful:
>>
>> http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats
>> http://biopython.org/wiki/SeqIO
>>
>> Peter C.
>>
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