Unicode Error in MacOSX about pgxpop

[alavertu]

Hi @sharmaa9,

Can you try pointing the --vcf path to the vcf and not the tabix index file?

Would be the following command instead:

python bin/PGxPOP.py --vcf /Users/sharmaa9/Desktop/PGx/PGXPOP/PGxPOP/test_vcf.vcf.gz -g CYP2D6 --phased --build grch38 -o test_new.txt

[sharmaa9]

Thanks for your response.
So I try that and i get this error-

File "/Users/sharmaa9/Desktop/PGx/PGXPOP/PGxPOP/PGxPOP/bin/DawgToys.py", line 320, in fetch_genotypes
records = tb.query("%s" % chr, position-1, position+1)
tabix.TabixError: query failed

Thanks,
Anu

[alavertu]

Hi Anu,

Sorry to hear that didn't work. Can you give me a little more information?

What do the top few lines of your VCF look like after the column header? I'd like to see how chromosome names are formatted, as this sometimes differs among VCFs.

Have you successfully tabix query'd this file outside of PGxPOP?

Are all the chromosomes present in the file?

[sharmaa9]

Thanks Alan,

Really appreciate your help. Actually, I am trying this with your example data file "VcfReaderTest-phasing.vcf". I bgzipped it and then tabixed it and now running PGxPOP on it.

[alavertu]

Hi Anu,

Sorry, that test file doesn't contain CYP2D6. Can you try running:

python bin/PGxPOP.py --vcf /Users/sharmaa9/Desktop/PGx/PGXPOP/PGxPOP/test_vcf.vcf.gz -g DPYD --phased --build grch38 -o test_new.txt

[sharmaa9]

Hi Adam,

Got it! Its working! :) thanks so much for your help! Really appreciate your time.
And thanks for coding this tool. Also, I am just starting in this field so I might bug you again in near future with queries.

Best,
Anu

[alavertu]

Glad to hear its working and welcome to the field, it's a good one :)