VARNA Command Line Options

[Yann Ponty]

Received directly from Justin Ritz, posted with his approval
------------
Hi Dr. Ponty,

My name is Justin and I'm a graduate student working under Alain
Laederach at the Wadsworth Center in Albany, NY. I believe we've
exchanged e-mails once before. I'm currently attempting to write a
bash script to call VARNA through the command line and I'm having
trouble getting some of the options to work correctly.

I've been referencing the 'Features Description' page on the VARNA
website to identify the parameters I'm looking to use, which are
colorMap, colorMapStyle and flat. Basically I'm trying to preset
certain positions to be the same color no matter what structure I feed
it. Yet, every time I attempt to use the colorMap option, it does not
seem to want to recognize the list that I am giving it, is there a
particular form that VARNA wants this in? The bash format for a list
does not seem to be working.

Also, every time I try to use the '-flat' option it tells me that
there is a missing argument. The 'Features' page does not identify
possible values for this option. I thought the option itself would let
the program know, but it seems to want something along with it.

Also, when I call VARNA with the -x option (to list all possible
options), the colorMap and colorMapStyle options are not listed. I
currently have version 3.7 installed on my Mac, so I'm not quite sure
why these wouldn't show up on the list. Any advice you could give
would be greatly appreciated. Thank you in advance!

-Justin

[Yann Ponty]

Hi Justin,

Of course I remember you. Actually, you are a regular of my
"acknowledgement slide" on my VARNA presentations :)

First of all, the "flat" option expects a boolean (ie "true" or
"false"), as specified in the "specifications" page. It used to be not
so explicit, but I think it should be ok now.

For the colormap options, everything works fine on my version, but I
have to admit the features are neither very intuitive nor really
documented (Baaad practice!). The lists must be specified within a
String (see example below)
The latest "dev" version (VARNA-v3.7b.jar, not posted here) fixes the
documentation issue.

I also attach a large RNA "ROC.dbn" file at

https://docs.google.com/leaf?id=0B85BtrmsfxQIYzg1MjljNmItY2Y1Ny00OWRjLWExY2YtYzg1ZmU0ZTQ5NTM1&sort=name&layout=list&num=50

and a test command-line (it should be a single line) below. Please run
it to make sure everything is ok :

java -cp VARNAv3-7.jar fr.orsay.lri.varna.applications.VARNAcmd -i
ROC.dbn -colorMap
"1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9,1,2,3,4,5,6,7,8,9"
-colorMapCaption "Coolness" -colorMapStyle "green" -title "ROC rulez!"
-flat true -resolution 5 -o out.jpg

Btw, feel free to show it to Alain, I think he might like the VARNA
output ;) I think we should build an RNA font...

Best,

Yann

PS: Is it ok with you if I post our conversation on the Google group
(to avoids duplicates since this question might pop up periodically
until next release)?

[Yann Ponty]

BTW, here is the output, in the absence of color map:
https://docs.google.com/leaf?id=0B85BtrmsfxQIMmI4YjFjZDMtMDBmMi00YTNmLWE4ZTItNTVjOGJmMmUyMDNk&sort=name&layout=list&num=50

Best,

Yann

On 26 nov, 10:24, Yann Ponty <yann.po...@gmail.com> wrote:
> Hi Justin,
>
> Of course I remember you. Actually, you are a regular of my
> "acknowledgement slide" on my VARNA presentations :)
>
> First of all, the "flat" option expects a boolean (ie "true" or
> "false"), as specified in the "specifications" page. It used to be not
> so explicit, but I think it should be ok now.
>
> For the colormap options, everything works fine on my version, but I
> have to admit the features are neither very intuitive nor really
> documented (Baaad practice!). The lists must be specified within a
> String (see example below)
> The latest "dev" version (VARNA-v3.7b.jar, not posted here) fixes the
> documentation issue.
>
> I also attach a large RNA "ROC.dbn" file at
>

>  https://docs.google.com/leaf?id=0B85BtrmsfxQIYzg1MjljNmItY2Y1Ny00OWRj...

[Yann Ponty]

Ah thank you so much Yann! When I read on the website that it needed a
list my brain automatically went to the bash version of a list. I
never thought to enter the list as a string! I will definitely show
this to Alain, this structure is really cool!

By all means, feel free to post the conversation any where you like.
This definitely helped me out and if it can help other people out, all
the better. Thank you as well for the latest version of VARNA, I will
make sure not to expose it in a website. I just wanted to let you know
that I've been using VARNA over the past couple version updates and it
just gets better and better. Thank you again!

-Justin

On 26 nov, 10:24, Yann Ponty <yann.po...@gmail.com> wrote:

> Hi Justin,
>
> Of course I remember you. Actually, you are a regular of my
> "acknowledgement slide" on my VARNA presentations :)
>
> First of all, the "flat" option expects a boolean (ie "true" or
> "false"), as specified in the "specifications" page. It used to be not
> so explicit, but I think it should be ok now.
>
> For the colormap options, everything works fine on my version, but I
> have to admit the features are neither very intuitive nor really
> documented (Baaad practice!). The lists must be specified within a
> String (see example below)
> The latest "dev" version (VARNA-v3.7b.jar, not posted here) fixes the
> documentation issue.
>
> I also attach a large RNA "ROC.dbn" file at
>

>  https://docs.google.com/leaf?id=0B85BtrmsfxQIYzg1MjljNmItY2Y1Ny00OWRj...