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DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

Home Page: https://pmbio.github.io/pycoMeth/

License: GNU General Public License v3.0

Python 93.93% Shell 0.40% Jinja 5.67%

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drownedmala helrick lucmeister55

pycometh's Issues

Cannot install pycometh

Hi,

I am trying to install pycometh in a Docker image but I can't get it to install. As a minimal example, try this dockerfile
`
FROM condaforge/mambaforge

RUN mamba install -c aleg -c plotly -c bioconda -c anaconda pycometh
`

This gives the following error:

[2/2] RUN mamba install -c aleg -c plotly -c bioconda -c anaconda pycometh:
#6 7.760
#6 7.760 Looking for: ['pycometh']
#6 7.760
#6 7.760
#6 7.760 Pinned packages:
#6 7.760 - python 3.10.*
#6 7.760
#6 7.760
#6 7.760 Encountered problems while solving:
#6 7.760 - nothing provides openssl >=1.0.2p,<1.0.3a needed by python-3.6.7-hd21baee_1002

openssl is part of anaconda channel, so not sure why this can't be installed.

Any advice appreciated!

Cannot import dependencies required for static image export

Hi, an error was appeared when I run 'pycoMeth Comp_Report'：
'Cannot import dependencies required for static image export'. I noticed that this error occurred when I installed the software and ran the ‘pycoMeth -h’ command.

Can you help me? Thank you !

Plans to make pycoMeth compatible with Modkit bedMethyl format?

Hello,

Because of the improvements in modified basecalling accuracy Nanopolish states that it does not support R10 flowcells on its GitHub. It also seems that Oxford Nanopore is investing in this new tool suite called Modkit for analysis of base modification. I was wondering if there are any plans for pycoMeth to start supporting the bedMethyl files created by the pileup function from modkit? Alternatively, do you know of a way to convert the bedMethyl files from modkit into the MetH5 format from Nanopolish so that they are compatible with pycoMeth?

I really like the ease of use and great features included in pycoMeth. It would be great to be able to easily integrate it with the new R10 data pre-processed using modkit.

Installation failed

Hi @here I am trying to install this package using pip and conda but I have been having a series of errors, is there a possibility of getting any other ways to install it?

Cannot access pycoMeth documentation

Dear Rene,

I cannot access the pycoMeth documentation.
Best,
Madalina

AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

Dear pycoMeth developer(s),

I am trying using pycometh Meth_Comp to do methylation differential analysis. My command was pycometh Meth_Comp -i 1.m5 2.m5 3.m5 4.m5 5.m5 -f reference.fa -b output.bed.

It reported error as the following:

Cannot import dependencies required for static image export
## Checking options and input files ##
## Opening H5 files ##
	Starting asynchronous file parsing
	Launching 4 worker processes
Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

CRITICAL: Error in worker thread
Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

CRITICAL: Error in worker thread
Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'


Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

CRITICAL: Error in worker thread
Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'

Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
	No valid p-Value could be computed
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
	Results summary
CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
    label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
  File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
    interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'

CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
Exception ignored in: <function Pool.__del__ at 0x2b1a490240d0>
Traceback (most recent call last):
  File "/home/zhany0s/miniconda3/lib/python3.8/multiprocessing/pool.py", line 268, in __del__
    self._change_notifier.put(None)
  File "/home/zhany0s/miniconda3/lib/python3.8/multiprocessing/queues.py", line 368, in put
    self._writer.send_bytes(obj)
  File "/home/zhany0s/miniconda3/lib/python3.8/multiprocessing/connection.py", line 200, in send_bytes
    self._send_bytes(m[offset:offset + size])
  File "/home/zhany0s/miniconda3/lib/python3.8/multiprocessing/connection.py", line 411, in _send_bytes
    self._send(header + buf)
  File "/home/zhany0s/miniconda3/lib/python3.8/multiprocessing/connection.py", line 368, in _send
    n = write(self._handle, buf)
OSError: [Errno 9] Bad file descriptor

I thought it was because of no valid p-values can be used, so I adjusted --pvalue_threshold but it seemed not help. Would you please let me know what should I do to get it work?

Thank you very much in advance.

Yingzi

OSError: Unable to open file

Hi,
I'm running command "pycometh Meth_Seg" and encountering an error:

OSError: Unable to open file (unable to open file: name = '[/NAS/wg_hl/pancancer/OSCC/Methylation/f5c_meth/pycoMeth/MetH5/OSCC1/OSCC1_methylate.m5,', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0).

But my file is existing. I don't know how to solve this issue, can you help me?

Support BED instead of MetH5 as input format?

Hi,
I am interested in using Meth_Comp for DMR analysis and I already have per-site methylation calling results for 2 samples, they are in BED format with chromosome, start position, end position, and methylation frequency for each site.

Is it possible to use BED file instead of MetH5 in this case? Any hints for the implementation? Thanks.

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