IndexError: arrays used as indices must be of integer (or boolean) type

[nafusco22]

Hello,

I am trying to run locator on a .vcf file. I keep running into the error below. I have tried adjusting the chromosome codes in the VCF to be numeric only to solve this problem. No matter what I change I keep getting this error. I am not sure if this has to do with the format of my files or the installation of the program.

I am attempting to run this line:

python locator.py --vcf 403_VCF_locator_4.vcf.gz --sample_data Locator_XY.txt --out Locator_403

And get this error:
WARNING:tensorflow:period argument is deprecated. Please use save_freq to specify the frequency in number of batches seen.
Traceback (most recent call last):
File "/gpfs/ycga/home/naf35/install/locator/scripts/locator.py", line 381, in
train,test,traingen,testgen,trainlocs,testlocs,pred,predgen=split_train_test(ac,locs)
File "/gpfs/ycga/home/naf35/install/locator/scripts/locator.py", line 219, in split_train_test
predgen=np.transpose(ac[:,pred])
IndexError: arrays used as indices must be of integer (or boolean) type

The files I used are attached. Your assistance is much appreciated.
403_VCF_locator_6.vcf.gz
Locator_XY.txt
e

-Nicole Fusco

[cjbattey]

Hi Nicole,

Sorry for the late reply. The error is because there aren't any unknown locations in the --sample_data coordinates file. You can pick a set of samples to predict by replacing their locations with NA. E.g. Here's an edited version of your file set up to predict the first 15 samples.

Locator_XY.txt

Run with:

locator.py --vcf ~/Downloads/403_VCF_locator_6.vcf.gz --sample_data ~/Downloads/Locator_XY.txt --out ~/Desktop/test

CJ