marcin p. joachimiak
marcin p. joachimiak
This is a hierarchical representation of huTF-classification, but also including binding site information. This would enable new kinds of enrichment analysis where one could test against a (large) collection of...
currently the return of the 'ancestors' method does not return parent nodes in consistent order.
Turns out that in the latest merge the new strain:bacdive_ nodes do not have any medium: edges: grep strain:bacdive_ merged-kg_nodes.tsv | wc 18537 139009 1890855 We do have a number...
My transform.py was as below, however the disbiome transform happened anyway - I imagine there may be something hardcoded for that one. Not a critical issue but good to have...
GTDB downloads: https://gtdb.ecogenomic.org/downloads After GTDB ingest revisit Madin et al: # - GTDB # link: https://github.com/bacteria-archaea-traits/bacteria-archaea-traits/blob/master/output/condensed_traits_GTDB.csv #- # url: https://github.com/bacteria-archaea-traits/bacteria-archaea-traits/blob/master/output/condensed_traits_GTDB.csv?raw=true # local_name: condensed_traits_GTDB.csv # - NCBI # link: https://github.com/bacteria-archaea-traits/bacteria-archaea-traits/tree/master/output
Traceback (most recent call last): File "/global/common/software/nersc/pe/conda-envs/23.10.0/python-3.10/nersc-python/lib/python3.10/multiprocessing/pool.py", line 131, in worker put((job, i, result)) File "/global/common/software/nersc/pe/conda-envs/23.10.0/python-3.10/nersc-python/lib/python3.10/multiprocessing/queues.py", line 377, in put self._writer.send_bytes(obj) File "/global/common/software/nersc/pe/conda-envs/23.10.0/python-3.10/nersc-python/lib/python3.10/multiprocessing/connection.py", line 200, in send_bytes self._send_bytes(m[offset:offset + size])...
https://figshare.com/articles/dataset/International_Journal_of_Systematic_and_Evolutionary_Microbiology_IJSEM_phenotypic_database/4272392?file=6994457