Comments (4)
Hi,
I have now added support for haploid data, which should automatically detect haploid genotypes in the vcf.
-Simon
from genomics_general.
thanks :)
from genomics_general.
Hi,
I've been trying to run the popgenWindows.py
script on a haploid geno file, but it seems there is an issue when invoking the genomics.py
script. The error I always get is:
Process Process-1:
Traceback (most recent call last):
File "/anaconda2/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/anaconda2/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "popgenWindows.py", line 32, in stats_wrapper
Aln = genomics.genoToAlignment(window.seqDict(), sampleData, genoFormat = genoFormat)
File "software/genomics_general/genomics_general-master/genomics.py", line 626, in genoToAlignment
if ploidy is not None: assert len(seqList) == ploidy, "Sample ploidy doesn't match genotype"
AssertionError: Sample ploidy doesn't match genotype
Not sure if the problem is my geno file (sample attached) or the script itself. At any rate I am not getting any calculation.
The command I used is:
python popgenWindows.py-w 10000 -p pops -g all_trans.geno -o all_trans.geno -f haplo
Cheers,
Javi
sample.geno.txt
from genomics_general.
I got this running after specifying the haploid individuals via "--haploid sample,sample2,sample3,..."
from genomics_general.
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