Issue using combine_CpG_sites.py with supplied example

[nickyph]

Hi @jsh58

Before tyring with my own data, I wanted to use DMRfinder with the supplied examples to make sure I understand the workflow. The sample data I used is

C1.cov C2.cov chrZ 100 0 1 chrZ 100 1 2 chrZ 120 1 2 chrZ 120 2 3 chrZ 200 0 4 chrZ 200 1 5 chrZ 300 3 3 chrZ 300 0 2 chrZ 401 2 6 chrZ 401 3 3 chrZ 450 3 5 chrZ 450 4 5 chrZ 600 5 2 chrZ 600 6 3 chrZ 625 4 2 chrZ 625 8 0 chrZ 650 5 1 chrZ 650 7 1 chrZ 700 3 2 chrZ 700 3 4

From Appendix A. Illustrative examples with combine_CpG_sites.py. I acknowledge that column 3 and 4 are missing. I created the C1.cov and C2.cov file by putting them in seperate .txt files and then running the following commands to make sure the file is tab-delimited.

$ cat C1.txt | tr ' ' '\t' > C1.cov
cat C2.txt | tr ' ' '\t' > C2.cov

When running combine_CpG_sites.py I run into the following error:

python combine_CpG_sites.py -o result_31aug C1.cov C2.cov path/combine_CpG_sites.py:59: DeprecationWarning: 'U' mode is deprecated f = open(filename, 'rU') Error! Poorly formatted record: chrZ 100 0 1

What I have tried is using my own data, .bed file data, or just the C1.txt/C2.txt, or the .cov's I made but then space-delimited, but to no avail. Reason for wanting to know is that for my own study I use ONT data and I have all the needed columns as mentioned in Extracting methylation counts which are:

chrom | chromosome name chromStart | 1-based position of the cytosine in the CpG chromEnd | chromStart + 1 percent | percent methylation at this site methylated | count of methylated cytosines unmethylated | count of unmethylated cytosines

So I do acknowlegde my starting point differs. Do you have any guesses on what the issue might be? I do apologize if I am missing something very obvious. This area of research is new to me so I am exploring for now :)

[jsh58]

The input files for combine_CpG_sites.py must be of the correct format, which is described in the README:

These headerless files must have six tab-delimited fields per line, with the first, second, fifth, and sixth columns being chromosome, position, methylated counts, and unmethylated counts, respectively