I can't find the compare_methylation.py script and I can't download the sample data

[lanyunxin]

--2023-07-25 20:11:51-- http://s3.climb.ac.uk/nanopolish_tutorial/methylation_example.tar.gz Resolving s3.climb.ac.uk (s3.climb.ac.uk)... 147.188.173.14 Connecting to s3.climb.ac.uk (s3.climb.ac.uk)|147.188.173.14|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://s3.climb.ac.uk/nanopolish_tutorial/methylation_example.tar.gz [following] --2023-07-25 20:11:51-- https://s3.climb.ac.uk/nanopolish_tutorial/methylation_example.tar.gz Connecting to s3.climb.ac.uk (s3.climb.ac.uk)|147.188.173.14|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2023-07-25 20:11:52 ERROR 404: Not Found.

[rdeborja]

The script and example data can be found in the following bundle:

warwick.s3.climb.ac.uk/nanopolish_tutorial/methylation_example.tar.gz

Issue reference: https://github.com/jts/nanopolish/issues/1069

[lanyunxin]

There is only sample data in this bundle, and there is no script, please check it again, trouble

[rdeborja]

Hi @lanyunxin,

I just re-downloaded and unarchived the file and the script is in the directory:

$ ls -lah methylation_example/compare_methylation.py
-rwxr-x--x  1 user  staff   2.9K 14 May  2018 methylation_example/compare_methylation.py
$ tree -L 1 methylation_example
methylation_example
├── albacore_output.fastq
├── bisulfite.ENCFF835NTC.example.tsv
├── compare_methylation.py
├── fast5_files
└── reference.fasta

[rdeborja]

Note that I used both wget and curl to download the file. Here are the specific commands I used to download and unarchive:

Using wget

$ wget warwick.s3.climb.ac.uk/nanopolish_tutorial/methylation_example.tar.gz
$ tar xvfz methylation_example.tar.gz

Using curl:

$ curl -O warwick.s3.climb.ac.uk/nanopolish_tutorial/methylation_example.tar.gz
$ tar xvfz methylation_example.tar.gz

[lanyunxin]

Can you send me the script directly as I really didn't find the script in the sample data

[rdeborja]

While the script should be in the root of the extracted methylation_example directory,
I have submitted a PR to include the compare_methylation.py script as part of nanpolish: https://github.com/jts/nanopolish/pull/1099