Problem with CGmapMethInBins

[guoweilong]

Problem with CGmapMethInBins

[guoweilong]

Hi @doncarlos999 ,

Thanks for your feedback. It seems to be a bug in code. And we just update the source code for this program.
Can you update the source code from https://github.com/guoweilong/cgmaptools/blob/master/src/CGmapMethInBins.py
for your local version, and see if the output is improved to right version?

We'll formally release the updated version if it runs well on your data set. And looking forward for your feedback.

Best,
Weilong

[doncarlos999]

Hi @guoweilong ,
Thanks so much for helping with this and for your quick response.

The updated source code has fixed the truncation problem but all but the last line are na.

➜  25bp_bdg  19-04-29 10:02 wc -l 25bin.tsv            
10564 25bin.tsv
➜  25bp_bdg  19-04-29 10:02 grep na 25bin.tsv | wc -l 
10563
➜  25bp_bdg  19-04-29 10:02 tail -n 4 25bin.tsv      
chr1    264001  264025  na
chr1    264026  264050  na
chr1    264051  264075  na
chr1    264076  264100  0.0473

➜  25bp_bdg  19-04-29 10:01 wc -l 25CGbin.tsv       
10560 25CGbin.tsv
➜  25bp_bdg  19-04-29 10:01 grep na 25CGbin.tsv | wc -l
10559
➜  25bp_bdg  19-04-29 10:01 tail -n 4 25CGbin.tsv      
chr1    263901  263925  na
chr1    263926  263950  na
chr1    263951  263975  na
chr1    263976  264000  0.3076

[guoweilong]

Hi @doncarlos999 ,

This function will scan from 1st base to the last base.
Thus, some region without enough coverage, will output "NA".
From my side, all the last lines are NOT "NA". So is this what you mean?

Best,
Weilong

[doncarlos999]

Did you try to run it on the file I attached in my first post?
If so can you attach the results with the same command that I am running?
cgmaptools mbin -i head_chr1.CGmap.txt -c 1 -B 25 -C CG > 25CGbin.tsv

I set the coverage to minimum 1 base. You can see in this file that there are many bases with more than 1 coverage but they are not being picked up in the scan.

Thanks
Carl

[guoweilong]

Hi Carl,

I just modified the code again, and commit the changes to github. Could you see if the new code works well for your data?

Looking forward to your feedback!

Best,
Weilong

[doncarlos999]

Hi @guoweilong

This has solved the issue. It now outputs the correct bins.

Thanks a lot for the assistance