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AliTVTeam / AliTV

Visualize whole genome alignments as linear maps
https://alitvteam.github.io/AliTV/d3/AliTV.html
MIT License
70 stars 11 forks source link

How to add multiple genomes? #103

Closed a113n closed 7 years ago

a113n commented 8 years ago

In the demo page [https://alitvteam.github.io/AliTV/d3/AliTV.html], it seems multiple genomes are supported. But when I try to supply multiple genomes via the --query or --reference parameters, it doesn't work properly. May I know how I could generate figures like the one in demo page?

iimog commented 8 years ago

Hi @a113n, you are totally right, AliTV is supposed to visualize multiple whole genomes (as shown in our demo). The visualization front end fully supports multiple genomes. In earlier versions of AliTV only pairwise comparisons were possible. The AliTV.pl in the bin/ folder is still the legacy script capable of only two genomes. We rewrote the whole script for generating the data in the required json format and are currently putting the finishing touches on it. We will update the script and the documentation as soon as it is ready (we are aiming for tomorrow). Sorry for the inconvenience - if you need your visualization now I can assist you in preparing the data manually (similar to the steps here: https://github.com/AliTVTeam/AliTV/blob/master/t/data/dataset001/process_testdata.sh). If you can wait another day we would be happy to have you as an early tester of our brand new perl script.

a113n commented 8 years ago

Sounds good! I shall wait for the next release then. Thanks for the great tool!

On Thu, Jun 16, 2016 at 8:17 PM, Markus Ankenbrand <notifications@github.com

wrote:

Hi @a113n https://github.com/a113n, you are totally right, AliTV is supposed to visualize multiple whole genomes (as shown in our demo). The visualization front end fully supports multiple genomes. In earlier versions of AliTV only pairwise comparisons were possible. The AliTV.pl in the bin/ folder is still the legacy script capable of only two genomes. We rewrote the whole script for generating the data in the required json format and are currently putting the finishing touches on it. We will update the script and the documentation as soon as it is ready (we are aiming for tomorrow). Sorry for the inconvenience - if you need your visualization now I can assist you in preparing the data manually (similar to the steps here: https://github.com/AliTVTeam/AliTV/blob/master/t/data/dataset001/process_testdata.sh). If you can wait another day we would be happy to have you as an early tester of our brand new perl script.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/AliTVTeam/AliTV/issues/103#issuecomment-226468329, or mute the thread https://github.com/notifications/unsubscribe/ADEGJ4FTKCFjMWk23aI1DOtxDK6CUVe7ks5qMT7KgaJpZM4I3QLy .

iimog commented 8 years ago

I just merged the new perl script into the repo as a git submodule. To update to the latest version I suggest removing the old AliTV folder and cloning again via

git clone --recursive https://github.com/AliTVTeam/AliTV

I also updated the README to explain the usage of the new script. There are still some rough edges and only basic documentation is available. We will continue to improve the documentation, the perl script and the visualization interface.

@a113n: I encourage you to start using the perl script right now. Tell us if you encounter a bug or if you have features that you would like to see. I'll gladly assist you in case of problems.

a113n commented 8 years ago

That's great! Will try that soon. Should I use AliTV_new.pl https://github.com/AliTVTeam/AliTV/blob/master/bin/AliTV_new.pl ?

On Sat, Jun 18, 2016 at 6:46 AM, Markus Ankenbrand <notifications@github.com

wrote:

I just merged the new perl script into the repo as a git submodule. To update to the latest version I suggest removing the old AliTV folder and cloning again via

git clone --recursive https://github.com/AliTVTeam/AliTV

I also updated the README to explain the usage of the new script. There are still some rough edges and only basic documentation is available. We will continue to improve the documentation, the perl script and the visualization interface.

@a113n https://github.com/a113n: I encourage you to start using the perl script right now. Tell us if you encounter a bug or if you have features that you would like to see. I'll gladly assist you in case of problems.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/AliTVTeam/AliTV/issues/103#issuecomment-226898976, or mute the thread https://github.com/notifications/unsubscribe/ADEGJwQQBFIXCfj7HSSP3TTYKURisPm_ks5qMyPigaJpZM4I3QLy .

greatfireball commented 8 years ago

Hey @a113n,

After recursive cloning of our repository via 

git clone --recursive https://github.com/AliTVTeam/AliTV

just enter the AliTV-perl-interface folder and run the script alitv.pl as explained in our new documentation. The file is you need to use is located here. It is not located inside the AliTV repository due to it is included as submodule (think GitHub should improve the submodule handling).

Please let us know, if you need further assistance.

iimog commented 7 years ago

The perl part has been further improved, it is available and documented here: https://github.com/AliTVTeam/AliTV-perl-interface