edgardomortiz / paralog-finder Goto Github PK

Hi Edgardo,

Thanks for improving upon HDplot. In giving the py script a try with unfiltered snps out of stacks:populations, the snp count dropped from 656k to 520k, from the populations.snps.vcf to the populations.depthBias. We should be adding metrics, not dropping snps at this point?

I would prefer to apply the py script to the vcf after filtering, but vcftools rightly drops the INFO fields after filtering operations. With vcftools' filtered output, HDplot_process_vcf.py hangs on the NS being equivalent to ".". Following up on this, I used stacks:populations to recalc the INFO fields on the vcf after having filtered for GQ, MAC, mindepth, and minmeandepth. Of 80k snps, the py script now drops 35. I'm not seeing a pattern to the drops, except maybe a low MAF. I'll attach one in transposed format.

So why is the py script dropping snps?

depthBias-drop.txt

Hello Edgardo,
I would like to let you know that ever since I upgraded to python 3.9 I have not been able to use your scripts.
Even when trying to get the help message using the command:

python HDplot_process_vcf.py -h

I get the following error:

File "/paralog-finder-1.0/HDplot_process_vcf.py", line 58
print 'skipped {} header lines'.format(header_lines)
^
SyntaxError: invalid syntax

Could you please let me know how to fix this?
Thank you very much!
Kind regards,
Marcos