[Biojava-l] Sequence start/end location

[Mark Schreiber]

Hi Ahmed -

For a first time contribution it would probably be easiest to post
something to the list and someone with a development account can check
it in for you.

Please make sure to add javadoc comments and a basic JUnit test for
any classes you make.

- Mark

On Sat, Jan 31, 2009 at 3:13 PM, Hamed, Ahmed A.
<ahmed.elmasri at gmail.com> wrote:
> Dear Mark,
> Thank you for your response. I would be happy to contribute my PTTParser if
> you point me to where/how to check it in. I am still new to the BioJava
> community and there is so much to learn.
> Best wishes,
> Ahmed
>
> On Fri, Jan 30, 2009 at 11:15 PM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
>>
>> Hi -
>>
>> Unfortunately your FASTA file won't contain any feature information
>> which could tell you the start and end. If you don't want to get the
>> info from the PTT file you might want to look at parsing the Genbank
>> file instead which will have the feature information.
>>
>> A PTT parser might not be a bad thing for BioJava though. If you write
>> one please consider adding it.
>>
>> - Mark
>>
>> On Sat, Jan 31, 2009 at 10:41 AM, Hamed, Ahmed A.
>> <ahmed.elmasri at gmail.com> wrote:
>> >
>> > Hello list,
>> > I am trying to get find the start and end location of a gene in a gene
>> > sequence. I am reading from a gene FASTA database file. Is there a
>> > built-in
>> > method that I can use? The alternative is really painful since I have to
>> > parse a ptt file and not exactly working for me.
>> > Thanks very much!
>> > Ahmed
>> > _______________________________________________
>> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
> --
> Ahmed Abdeen Hamed
> Scientific Informatics Project Leader
> Marine Biological Laboratory Woods Hole, MA
> --
> Ph.D. student, Complex Systems
> School of Informatics, Indiana University
>
>
>
>