Dear Tim,
Thanks again for sorting that out.
I've just downloaded the source code from CVS and successfully built
Artemis. I would really like to get involved with coding, but although
I'm a keen programmer and know some Java, I've never worked on a big
project.
One feature that I'd love is the ability to switch between a view of
genomic DNA and the mRNA transcript of a gene (for checking/storing
intron spanning primers for expression analysis on cDNA.) Can you give
me any pointers at all on how to add this?
If you think this is a bit hard for a newcomer, are there any smaller
projects that you think I could take on? How could I add a new format
for writing to? It would be nice to export beautified diagrams showing
the lengths of introns and exons and locations of features. I'd go for a
format like SVG.
Best wishes,
Rupert
Tim Carver wrote:
Hi Rupert
You are right it looks like PRIMARY is a new keyword in RefSeq. I have added
this to the code and the changes have been committed. I have also updated
the development version that can be found on the Artemis home page.
Regards
Tim
On 6/8/07 22:17, "Rupert Millard" <[EMAIL PROTECTED]> wrote:
Hi,
I am a great fan of Artemis, having used it since I started working in a
lab in May. I think I may have discovered a bug though (in version 9) -
Artemis is not properly loading some mRNA transcripts in GenBank format
from Entrez Gene such as the one at
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_001353.5
The "opened" sequence begins 'nrnmarynnnnnrnnsnnnsnannnnnnnnnnnrnmaryn'.
After removing the following section from the GenBank entry, the file
opens properly:
PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
1-623 BC040210.1 660-1282
624-628 CB119749.1 440-444
629-1179 BC040210.1 1288-1838
1180-1384 M86609.1 1003-1207
There is something about this first line which makes Artemis to try to
treat it as bases - I noticed the following correspondence between the
section I removed and the gobbledegook:
PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN
: :::: : : : :: : :::: : :: : : :::: : ::
nrnmarynnnnnrnnsnnnsnannnnnnnnnnnrnmarynndnntnnnnrnnrnmarynsnan
I hope someone can fix this. I looked at the source code, but don't know
where to begin!
Best wishes,
Rupert Millard
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