Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix dataset reading and pearson correlation is 0 #31

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Fix dataset reading and pearson correlation is 0 #31

wants to merge 2 commits into from

Conversation

ghuls
Copy link

@ghuls ghuls commented May 28, 2020

No description provided.

ghuls added 2 commits May 28, 2020 11:07
@ghuls
Fix reading datasets from base_list if defined without '/' in the names.
269aaa5 
Fix reading datasets from base_list if defined without '/' in the names
by using os.path.basename instead of trying to get the basename ourself
in a hacky way.

Fixes the following error when filenames listed  in datalist don't
contain slashes:

  File "./NGSCheckMate/ncm.py", line 254, in createDataSetFromList
    file = link[link.rindex("/")+1:]
ValueError: substring not found
@ghuls
Allow Pearson correlation to be zero.
d1f5c80 
Allow Pearson correlation to be zero.

Fixes the following error:

  File "./NGSCheckMate/ncm.py", line 59, in pearson_def
    return diffprod / math.sqrt(xdiff2 * ydiff2)
ZeroDivisionError: float division by zero
@SPPearce SPPearce mentioned this pull request Jul 6, 2023
Merged
@kbarrr
Copy link

kbarrr commented Mar 10, 2024

Hi, i even with the new version got this error "ZeroDivisionError: float division by zero"

this is the code i run:
python ncm.py -B -l M1M2.txt -bed SNP_GRCh38_hg38_wChr.bed -O M1M2_results

WARNNING : NCM_HOME is not defined yet. Therefore, program will try to search ncm.conf file from the current directory
1.6
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
Set max per-file depth to 8000
/home/seisbio/mambaforge/envs/ngscheckmate-env/bin/samtools mpileup -uf GCA_000001405.29_GRCh38.p14_genomic.fna -l SNP_GRCh38_hg38_wChr.bed M2_dedup_filtrado_sorted.bam | /home/seisbio/mambaforge/envs/ngscheckmate-env/bin/bcftools call -c > M1M2_results/M2_dedup_filtrado_sorted.vcf
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 1 samples in 1 input files
Set max per-file depth to 8000
Generate Data Set from M1M2_results
using this bed file : SNP_GRCh38_hg38_wChr.bed
Traceback (most recent call last):
File "ncm.py", line 1453, in
createDataSetFromDir(base_dir,bedFile)
File "ncm.py", line 222, in createDataSetFromDir
real_depth[file] = depth[file] / float(real_count[file])
ZeroDivisionError: float division by zero

PLEASE HELP!!!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@ghuls @kbarrr