Comments (2)
Hello,
This is surprising in deed.
I've been able to replicate the issue.
It seems there's a problem with gene ID matching between ppanggolin's internal IDs and the original IDs from the GBFF file. Because of this mismatch, ppanggolin is unable to correctly associate gene families with input genes, resulting in that none of the genes have a pangenome family.
I'll work on fixing this promptly.
Thanks for reporting the bug !
Best regards,
from ppanggolin.
The fix for this issue has been released in v2.1.0.
from ppanggolin.
Related Issues (20)
- MAFFT error when running ppanggolin MSA HOT 9
- Gene family count matrix related with representative gene family . HOT 4
- RGP borders not in regions_of_plasticity.tsv HOT 4
- Clarification about the contents of `gene_to_gene_family.tsv ` from projection HOT 5
- product_string HOT 2
- Getting MSAs for single-copy gene families when duplicates are tolerated HOT 3
- Reading the gbff file error HOT 4
- ppanggolin msa --partition core HOT 6
- Writing gene-related data failed HOT 3
- error while writing genome annotations HOT 1
- ppanggolin projection: ValueError: The region is already with a different spot. HOT 2
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- conda installs old version HOT 2
- ValueError: The gene family has not beed associated to a partition. HOT 6
- Non-deterministic clustering (possibly due to multi-threading)
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from ppanggolin.