usage

[agyow]

Hello,

Do you have any documentation on usage? I have tried running the centurion.py script (and every other .py script in the folders) with no luck. Trying to run the centurion.py script also gives an error, indicating there may be inconsistencies or missing packages. I have been unable to resolve the errors.

Thanks for your help.

Ash

[NelleV]

Hello,
Do you have the full error message? That would be helpful in understanding what is happening.
Thanks,
Nelle

[agyow]

Hi Nelle, Sorry for the late reply. I have tried a few other things based on the suggestions of a couple of our bioinformaticians. Currently, here is the issue I'm running into and am unable to get passed: I'm trying to run Centurion on a Linux server, not in a physical Linux environment on my machine. My machine is a Windows. I've installed x-ming, and have tried to use that as a means of creating a GUI for generating the plots from Centurion. I can get xclock and xeyes to display, as well as R plots when I use x-ming, but when I try to run the script in the examples folder, I get an error "failure to get current screen resources". I am wondering if x-ming is a compatible program for displaying the plots, or if there is something else I should use. I can also have access to a physical Linux OS if need be, but our server has more computing resources. I am also moderately experienced with bioinformatics, but not super high in skill level, so perhaps I am just missing something. Could you tell me how you and your associates run Centurion? Thanks for your help. Best, Ashley Yow

…

On Tue, Dec 4, 2018 at 6:14 PM Nelle Varoquaux ***@***.***> wrote: Hello, Do you have the full error message? That would be helpful in understanding what is happening. Thanks, Nelle — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Arfxii_zcvspO9-cZ_AQAw0mHaq27Earks5u1wHsgaJpZM4ZBnK_> .

-- *Ashley Yow* PhD Student Dept. of Horticultural Science NCSU Plants for Human Health Institute 600 Laureate Way Kannapolis, NC 28081

[allaigle]

Dear Nelle,

I am also very interested in using centurion, but I found it quite obscure to run. I tested the example given here with some modifications:

#!/bin/env python
import numpy as np
from centurion.externals import iced
from centurion import centromeres_calls
import matplotlib
matplotlib.use('Agg')  # to fix the $DISPLAY bug
import matplotlib.pyplot as plt
from matplotlib import colors

# Load the sample data
counts, lengths = iced.datasets.load_sample_yeast()

# Apply centromere calling algorithm
centromeres = centromeres_calls.centromeres_calls(
    counts, lengths,
    resolution=10000)

# Normalize data
counts = iced.filter.filter_low_counts(counts, percentage=0.04)
counts = iced.normalization.ICE_normalization(counts)

# Remove the cis interactions for visualization
mask = iced.utils.get_intra_mask(lengths)
counts[mask] = np.nan

# Map the position of centromeres
centro = centromeres / 10000
centro[1:] += lengths.cumsum()[:-1]

# Save centromere positions to a TXT file
with open('centromere_positions.txt', 'w') as f:
    for position in centro:
        f.write("{}\n".format(position))

# Plot
fig, ax = plt.subplots()
cax = ax.matshow(counts, cmap="RdBu", norm=colors.LogNorm())

# Add horizontal and vertical lines
[ax.axhline(i, color="#000000", linestyle="--") for i in centro]
[ax.axvline(i, color="#000000", linestyle="--") for i in centro]

# Add colorbar
plt.colorbar(cax)

# Save the figure
plt.savefig('test.png', dpi=300, bbox_inches='tight')

Note: centromere_positions.txt gives me only the 5 numbers (in kb I guessed) of S. cerevisiae chromosomes.

But I still don't really get how to run the whole workflow (considering that I already have the _raw.matrix and _raw.bed files) and so to get the tables of the specific locations, etc.

Could you please give me some insights?
Best wishes,
Alice