search

pierrepo / PBxplore

A suite of tools to explore protein structures with Protein Blocks :snake:
https://pbxplore.readthedocs.org/en/latest/
MIT License
28 stars 17 forks source link

Weblogos are only available in PDF format #73

Closed jbarnoud closed 8 years ago

jbarnoud commented 8 years ago

PBstat only produce weblogo in PDF format while the weblogo program can produce a large variety of formats. A --logo-format option would allow to choose the file format to produce.

While PDF is the best format for logos in most case, it is difficult to embed in other documents (including ipython notbooks).

HubLot commented 8 years ago

+1 !

pierrepo commented 8 years ago

I would like to minimize the number of possible options in PBxplore. Adding an option to choose a logo format implies the implementation of tests that the format provided is correct. We did not implement such a thing for Neq and PBs map (matplotlib can generate many ouput formats too). I suggest we produce WebLogo in png format with a good resolution, as we do for Neq and PBs map. This will certainly covers 99% of user cases.

jbarnoud commented 8 years ago

On 17/09/15 16:38, Pierre Poulain wrote:

I would like to minimize the number of possible options in PBxplore. Adding an option to choose a logo format implies the implementation of tests that the format provided is correct. We did not implement such a thing for Neq and PBs map (matplotlib can generate many ouput formats too). I suggest we produce WebLogo in png format with a good resolution, as we do for Neq and PBs map. This will certainly covers 99% of user cases.

— Reply to this email directly or view it on GitHub https://github.com/pierrepo/PBxplore/issues/73#issuecomment-141106891.

Testing that the format is correct is built into argparse. In the PR, the test for the format is there; it is right in the definition of the --logo-format option.

I did not think about the other outputs. I think it is good to be able to choose the file format of the pictures. PNG is the most useful while we do explore, yet a lot of journals ask for EPS or PDF images. Also, vector graphics are better in a lot of situations. What we could have is a --image-format option that would control the output format of all the images. Then, the neq, the PB map, and the logos can be obtained in a large variety of formats with a single option added.

pierrepo commented 8 years ago

Grrr. OK for an --image-format option. But :

All good?

jbarnoud commented 8 years ago

Done. See #74