Problems running customize

[bozbezbozzel]

Hi all,

I detailed my issue here: roseorenbuch/arcasHLA-quant#10

it seems like this repo is slightly more active, so I'd like to highlight it as I'm still stumped on how to get this to work! Any push in the right direction is very much appreciated.

[abuendia]

Hi @bozbezbozzel - Since the problematic line is entirely from SeqIO could you please try the first call separately and let me know if the output is empty:

for record in SeqIO.parse(dummy_hla_fa, 'fasta'): print(record.id)

[bozbezbozzel]

Hi @abuendia I don't know why I never received a notification of your comment, so please forgive my very late reply. Indeed when I run this after the little code block in my original bug report:

$ python3
Python 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:21) 
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
$ from Bio import SeqIO
$ dummy_hla_fa = "/home/a.vliet/miniconda3/envs/arcas/share/arcas-hla-0.5.0-3/dat/ref/GRCh38.chr6.HLA.fasta"
$ dummy_HLA_dict = SeqIO.to_dict(SeqIO.parse(dummy_hla_fa, 'fasta')) 
$ dummy_HLA_dict
{}
$ for record in SeqIO.parse(dummy_hla_fa, 'fasta'): print(record.id)
... 
$

So SeqIO is not reading the file-- presumably it can't because it's not actually a fasta file but a git-lfs file that needs to be fetched. I think for now I will replace the fasta file with the file you have on your GitHub so I can try to run it.