Scoary issues

Stop at "Calculating max number of contrasting pairs for each nominally significant gene: in the Ternimal

when we used scoary to analysis more then 10000 genomes, the analysis process end at "Calculating max number of contrasting pairs for each nominally significant gene" in Terminal, and only...

Xiangyang1984

Startcol error

1

==== Scoary started ==== Command: /Users/nondumisondhlovu/opt/anaconda3/bin/scoary -g gene_presence_absence.csv -t case.csv -s 15 Reading gene presence absence file CRITICAL: Traceback (most recent call last): File "/Users/nondumisondhlovu/opt/anaconda3/lib/python3.8/site-packages/scoary/methods.py", line 359, in Csv_to_dic_Roary header[startcol]...

GillNdhlovu

Convert vcf from parsnp to Scoary input

[parsnp.vcf.txt](https://github.com/AdmiralenOla/Scoary/files/8141166/parsnp.vcf.txt) Dear Author, I am trying to do a test GWAS using SNPs for 12 strains of Gallibacterium, fitting different antibiotic resistance binary vectors. If I understand correctly, Scoary can...

nicola-palmieri

Maximum recursion depth

4

As originally reported by @dutchscientist in #53 , Scoary currently throws a ``` RuntimeError: maximum recursion depth exceeded while calling a Python object ``` when attempting to perform pairwise comparisons...

AdmiralenOla

bug

IndexError: list index out of range

4

Hi, I'm new to using scoary and am running into an issue. Here is the full error that scoary gives me: `Traceback (most recent call last): File "/home/hcm59/miniconda3/envs/scoary/bin/scoary", line 8,...

hollygene

Support for non-binary traits

9

Dear @AdmiralenOla Under `Coming soon`, you list `Support for non-binary traits`. This could be of interest to me. What approach are you thinking of? (Simply binarizing continuous traits?) What use...

MrTomRod

help wanted

question

Question about --collapse

2

I have a very basic question about how the `--collapse` flag determines grouping. Does it collapse genotypes that have the *exact* same distribution across all the samples, or is some...

Antonia-Chalka

enhancement

Don't crash when newick file has node labels

2

Should be fairly simple to allow internal node labels in the newick file. Although this does not impact results, there is no reason for the program to crash.

AdmiralenOla

bug