Closed miseminger closed 5 months ago
@miseminger tested with Dask version 2021.10.0. Will update to the current version and check that it still works.
Please replace the minimal use of pandas with dask in
bin/merge_indices.py
andbin/merge_logfiles.py
scripts and test it on the latest dask version 2023.10.1-py11-ol9_cv1
Latest Dask version (2024.2.1) depends on Pandas 2.2.1; can we update Pandas in environment.yml
?
new scripts are:
gvf2indexandlog.py
: takes one GVF, creates two TSVs: one index, one logfile.merge_indices.py
: reads all index files fromgvf2indexandlog.py
, as well as an optional original mutation index, and merges them into a new index using Dask.merge_logfiles.py
: reads all log files fromgvf2indexandlog.py
, as well as a log header file, and an optional original mutation index, and merges them into a new log using Dask. It also prints out the number of mutations in the log that have 5 or more corresponding lineages.the old script,
update_index_and_logfile.py
, is obsolete after the addition of these three scripts, and can be deleted.also important to note: the mutation index columns have changed since we last made an index. The new columns are:
['pos', 'mutation', 'hgvs_aa_mutation', 'hgvs_nt_mutation', 'gene', 'protein_name', 'alias', 'hgvs_alias', 'alias_protein', 'Pokay_annotation', 'lineages']