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 RD) 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 ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] artemis inside other software
Hi Bernd Thank you for your message. There are command line options for running Artemis and setting various display parameters, e.g. you can open sequences and feature tables from different files from the command line. The options are documented in the user manual. There is no programmer manual for Artemis but the majority of the code is well documented. If you download the software from the Artemis home page or from GitHub you can use the 'Makefile' to generate javadocs. Regards Tim On 2/20/11 8:26 AM, Bernd Jagla bernd.ja...@pasteur.fr wrote: Hi, I just got aware of the Artemis project and am quite excited about it. I am using KNIME (knime.org) a workflow management software that is also JAVA based and develop functionality for using KNIME on NGS and HCA related problems. My questions would be: is it possible to integrate ARTEMIS with other software? Is there an API? Is there a way control what it is displaying from outside the Artemis application (like e.g. IGV)? Can you please give me some pointers on where to start looking for further instructions (beyond the manual) like some introductions for programmers... Please let me know if you have any other suggestions/comments on this project. Kind regards, Bernd ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] launching DnaPlotter with a sequence file
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): #!/bin/sh seq=$1 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 Tim 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 RD) 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 example1.template Description: Binary data ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] launching DnaPlotter with a sequence file
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 RD) 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 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
