Andrea Talenti
Andrea Talenti
Hi, after finding the issue #3369 I've tried to run the autoindex on the GFA generated with the pangenome workflow, and add the `-R XG` option. The resulting XG/GBZ/MIN/DIST work...
After reinstalling in a fresh environment with: ``` conda create -n xpclr -c bioconda xpclr ``` Or by fixing line 11 to: ``` import h5py ``` I get a different...
Yes, the command line is the same as before. 1 is the number of the chromosome to process
Yes, sorry I'll give more details. My VCF is generated from alignning to a scaffold level assembly. Therefore I don't have a real chromosome coding. I though that that was...
Ok, so how should I proceed? Is there some specific flag i need to change for the conversion?
Sorry, I haven't heard from you for a while. I managed to run the analyses with the vcf as input. But was wondering whether it was possible to fix the...
Ok thank you I'll give it a go!
Ok, I've tried you code. I've changed ```samples = vcf["samples][:]``` to ```vcf_in["samples"][:]```, then ran the core on a toy dataset. However, I get the following error: ``` File "vcf2hdf5.py", line...
Ok I've did another attempt. The object ```samples``` is a numpy array. I can convert it to any unicode with ``` samples = samples.as_type("U32") ``` However, now I get the...
Ok, it doesn't give that error anymore. It gies an error for impossibility to write, but I guess the problem is here: ``` fh = h5py.File("test.hdf5", mode="r") ``` Should I...