Hi Scott

No there is no way to do that other than editing an exiting template. Users
tend to open the sequence file from the interface and export the template.

If you wanted to get this running with a sequence file you could use a
wrapper script to take a copy of a dummy template and makes the changes,
something like this (with the attached template):



DIR=`dirname $seq`
FILE=`basename $seq`

echo "opening $DIR/$FILE"

sed "s|SEQDIR|$DIR|" /Users/tjc/Desktop/example1.template > ./tmp
sed "s|SEQFILE|$FILE|" ./tmp > ./new.template
rm -f ./tmp

java -jar dnaplotter.jar -t ./new.template


On 2/21/11 2:54 PM, "Scott Markel" <scott.mar...@accelrys.com> wrote:

> Tim,
> Thank you for confirming that sequence files can't be read directly.
> Is there a common or frequently-used way of creating a template from a
> sequence file *without* launching DnaPlotter?  I'd like the user's first
> view to be the circular plot.
> Scott
> -----Original Message-----
> From: Tim Carver [mailto:t...@sanger.ac.uk]
> Sent: Monday, 21 February 2011 1:32 AM
> To: Scott Markel; artemis-users@sanger.ac.uk
> Subject: Re: [Artemis-users] launching DnaPlotter with a sequence file
> Hi Scott
> Yes it is template driven, so there is no -f option. You can manually create
> a template or export a template out from a DNAPlotter session. Example
> templates can be found in the online manual page:
> http://www.sanger.ac.uk/resources/software/dnaplotter/#t_3
> The template then restores the track information that gets saved to the
> template.
> Regards
> Tim
> On 2/18/11 6:40 PM, "Scott Markel" <scott.mar...@accelrys.com> wrote:
>> I'd like to launch DnaPlotter with a sequence file name.  Best I can tell by
>> looking at main() in uk.ac.sanger.artemis.circular.DNADraw, DnaPlotter either
>> reads a template file (indicated by using "-t") or launches a wizard,
>> allowing
>> navigation to a sequence file or template.  I'm looking for a "-f" kind of
>> option, where I can indicate the EMBL or GenBank file I want to display.
>> An alternate, two-step approach would be to create a template from the
>> sequence file automatically, e.g., some sort of command-line converter (no
>> user interaction like browsing), and then launch with that template.
>> I checked the mailing list archives but didn't see anything germane.
>> Apologies in advance if I'm missing something obvious.
>> Scott
>> Scott Markel, Ph.D.
>> Principal Bioinformatics Architect  email:  smar...@accelrys.com
>> Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
>> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
>> San Diego, CA 92121                 fax:    +1 858 799 5222
>> USA                                 web:    http://www.accelrys.com
>> http://www.linkedin.com/in/smarkel
>> Secretary, Board of Directors:
>>     International Society for Computational Biology
>> Chair: ISCB Publications Committee
>> Associate Editor: PLoS Computational Biology
>> Editorial Board: Briefings in Bioinformatics
>> _______________________________________________
>> Artemis-users mailing list
>> Artemis-users@sanger.ac.uk
>> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users

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