mathii / gdc Goto Github PK

Hi, I ran the vcf2eigenstrat.py script, but I got the following error. This might sound a bit weird of me to ask, but am I supposed to clone the whole gdc to be able to run this? Is gdc a self defined module?

FYI, I am using Python 2.7.15.

Thank you.

Traceback (most recent call last):
  File "/home/wlim/exploring_vcf/vcf2eigenstrat.py", line 10, in <module>
    import sys, getopt, gdc, pdb
ImportError: No module named gdc

Hi,

I am trying to use your script eigenstrat2vcf.py however I am receiving the error:

Traceback (most recent call last):
File "/bin/mathii_gdc/gdc/eigenstrat2vcf.py", line 67, in
main(options)
File "/bin/mathii_gdc/gdc/eigenstrat2vcf.py", line 56, in main
for i,d in enumerate(data):
TypeError: iter() returned non-iterator of type 'unpacked_data'

And I am using the commands:

python3 -u /bin/mathii_gdc/gdc/eigenstrat2vcf.py -r v44.3_HO_public -i v44.3_HO_public.ind -p v44.3_HO_public_populations -s v44.3_HO_public.snp

I wondered if maybe I am using the incorrect version of Python (3.8.6) and the script is written for an earlier version or perhaps I am using the wrong syntax? I tried with python 2.7.12 but that failed too. Any help to correct this matter would be much appreciated.

Best wishes,

Dean

Hi!
I'm trying to use your vcf2eigenstrat.py script using the .ind file, which I assumed was a two column file with the individual's name and the pop name associated to it (pop_map-like), but it didn't work

python /home/buitracn/RADseq/tools/gdc/vcf2eigenstrat.py -v spis.296.all.filtered.markers.recode.vcf -i pop_map_spis296.ind -o spis296.all.loci.eigenstrat
[('-v', 'spis.296.all.filtered.markers.recode.vcf'), ('-i', 'pop_map_spis296.ind'), ('-o', 'spis296.all.loci.eigenstrat')] []
-v spis.296.all.filtered.markers.recode.vcf
-i pop_map_spis296.ind
-o spis296.all.loci.eigenstrat
found options:
{'indmap': 'pop_map_spis296.ind', 'indAsPop': False, 'ref': None, 'vcf': 'spis.296.all.filtered.markers.recode.vcf', 'out': 'spis296.all.loci.eigenstrat'}
Traceback (most recent call last):
File "/home/buitracn/RADseq/tools/gdc/vcf2eigenstrat.py", line 138, in
main(options)
File "/home/buitracn/RADseq/tools/gdc/vcf2eigenstrat.py", line 56, in main
pop_map[bits[0]]=bits[2]
IndexError: list index out of range

could you please define how should I format such file in order to work?

Thanks in advance,
Carol

Is there not a open2 function?

-bash-4.1$ python ../../script/vcf2eigenstrat.py -v BPS1206.Recali.gatk.vcf.snp.HQ -o test
[('-v', 'BPS1206.Recali.gatk.vcf.snp.HQ'), ('-o', 'test')] []
-v BPS1206.Recali.gatk.vcf.snp.HQ
-o test
found options:
{'indmap': None, 'indAsPop': False, 'ref': None, 'vcf': 'BPS1206.Recali.gatk.vcf.snp.HQ', 'out': 'test'}
Traceback (most recent call last):
File "../../script/vcf2eigenstrat.py", line 138, in
main(options)
File "../../script/vcf2eigenstrat.py", line 45, in main
vcf=gdc.open2(options["vcf"])
AttributeError: 'module' object has no attribute 'open2'