jordanlab/tagore

The script presents a simple way to visualize features on human chromosome ideograms

tagore's Issues

Legend

Hi, thank you for developing this tool, super useful. Just wondering if it's possible to add legend function? Thanks!

apply this to other genomes

Hi,
I was wondering if is it possible to optimize this amazing tool for other genomes. not only on the human genome.
Best,
PF

Chose combo of X vs. XX vs. XY based on bed

I think the X vs. XX vs. XY plotting will need to be controlled by the input bed, and possibly throw a warning (but probably not error out) if XXY karyotype is implied.

pip --user install

Hello,

I did:

pip install tagore --user

This puts tagore in ~/.local/bin.

Running it I got a following error:

Could not open /usr/lib/tagore-data/base.svg.p.  Please reinstall tagore
Traceback (most recent call last):
  File "/home/darked89/.local/bin/tagore", line 242, in <module>
    raise base_e
  File "/home/darked89/.local/bin/tagore", line 239, in <module>
    BASE = open(BASE_PATH, 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/usr/lib/tagore-data/base.svg.p'

But I do have the missing file in my home dir installation:
$HOME/.local/lib/tagore-data/base.svg.p

IMHO it is a bug since not on all systems we have root/sudo and moving bed files back and forth can be quite cumbersome.

Hope it helps,

Darek Kedra

EDIT
BTW, the system wide install puts the file in question here: /usr/local/lib/tagore-data/base.svg.p

google colab installation

I installed tagore & librsvg2 on google colab and got:
Could not open /usr/lib/tagore-data/base.svg.p. Please reinstall tagore
Traceback (most recent call last):
File "/usr/local/bin/tagore", line 242, in
raise base_e
File "/usr/local/bin/tagore", line 239, in
BASE = open(BASE_PATH, 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/usr/lib/tagore-data/base.svg.p'.
Folder /usr/lib/tagore-data/ does not exist.
Reinstallation doesn't help.

add legend and remove chromsomes?

Thanks for this library.
I'd be interested in using the tagore to create some graphics.
I'd like to add legends for the color.
Also, if I'm not interested in say certain chromosome (say ChrX), I'd like to remove that.

Are these two things possible?

Thanks.

rsvg issue

getting:
Could not find rsvg in PATH.

I have libsvg installed, it seems to want to call rsvg-convert instead of just rsvg

any suggestions?

thanks,