Issues using parameters in CLI

[jamesoccean1]

Thank you for creating this great tool!

I am having trouble using parameters that are available in the API version of coolbox in the CLI version.
For example, in API mode, one can use cmap, depth_ratio, and resolution as parameters:

dhic = DotHiC(test_hic, cmap="RdYlBu_r", depth_ratio=.5, resolution=10000)
frame = XAxis() + dhic
frame.plot("chr9:4000000-6000000")

However, the parameters do not work in CLI mode. I tried a couple of ways, one example with "resolution" below, using add. But I have also tried --resolution. But it is not recognized.

coolbox add XAxis -
add HiCMat "/YM1_inter_30_0.mcool" -
add resolution=10000 -
add Title "young hic" -
set_genome mm10 -
goto "chr1:4770000-6230000" -
plot /Users/jamesoccean/Desktop/sen_lab/hic_analysis/chr1_4770000-6230000_output_cool_adj.pdf

[Nanguage]

Hi, thanks for feedback! Did you tried to specify the parameter like this: add HiCMat "/YM1_inter_30_0.mcool" resolution=10000 ?

[jamesoccean1]

Hi, thanks for the response! I just tried:

coolbox add XAxis - \
add HiCMat "/YM1_inter_30_0.mcool" resolution=10000 - \
add Title "young hic" - \
set_genome mm10 - \
goto "chr1:4770000-6230000" - \
plot /hic_analysis/chr1_4770000-6230000_output_cool_adj.pdf

But received the following error:

exception ignored in: <function Track.__del__ at 0x142e68280>
Traceback (most recent call last):
  File "/Users/jamesoccean/miniforge3/envs/coolbox_env_3.9/lib/python3.9/site-packages/coolbox/core/track/base.py", line 97, in __del__
    name = self.properties['name']
AttributeError: 'Cool' object has no attribute 'properties'
[ERROR:cli.py:334 -                 plot()] Error when execute the generated source code:

------------------------
from coolbox.api import *
def fetch_top_frame():
    frame = Frame()
    frame += XAxis()
    frame += HiCMat('/YM1_inter_30_0.mcool', 'resolution=10000')
    frame += Title('young hic')
    return frame
    
top_frame = fetch_top_frame()
frame = top_frame

fig = frame.plot('chr1:4770000-6230000')
fig.savefig('/hic_analysis/chr1_4770000-6230000_output_cool_adj.pdf')

------------------------


Traceback (most recent call last):
  File "/Users/jamesoccean/miniforge3/envs/coolbox_env_3.9/bin/coolbox", line 6, in <module>
    fire.Fire(CLI)
  File "/Users/jamesoccean/miniforge3/envs/coolbox_env_3.9/lib/python3.9/site-packages/fire/core.py", line 143, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/Users/jamesoccean/miniforge3/envs/coolbox_env_3.9/lib/python3.9/site-packages/fire/core.py", line 477, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/Users/jamesoccean/miniforge3/envs/coolbox_env_3.9/lib/python3.9/site-packages/fire/core.py", line 693, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/Users/jamesoccean/miniforge3/envs/coolbox_env_3.9/lib/python3.9/site-packages/coolbox/cli.py", line 345, in plot
    raise e
  File "/Users/jamesoccean/miniforge3/envs/coolbox_env_3.9/lib/python3.9/site-packages/coolbox/cli.py", line 332, in plot
    eval(code)
  File "coolbox_cli_source", line 9, in <module>
  File "coolbox_cli_source", line 5, in fetch_top_frame
    import runpy
  File "/Users/jamesoccean/miniforge3/envs/coolbox_env_3.9/lib/python3.9/site-packages/coolbox/core/track/hicmat/hicmat.py", line 22, in HiCMat
    return Cool(file_or_hicmat, *args, **kwargs)
TypeError: __init__() takes 2 positional arguments but 3 were given

[zqbake]

have you tried this:

HiCMat "/YM1_inter_30_0.mcool" --resolution 10000 -\

or

HiCMat "/YM1_inter_30_0.mcool" - \
add Feature --resolution 10000 - \