Closed evanbiederstedt closed 5 years ago
I've tried this out with a paranoid gleam in my eye, and I believe this script gives the same results:
$ diff tmp_here/BRCA_00117-T_vs_BRCA_00117-N.netmhcpan_netmhc_combined.output.txt neoantigen-tmp3/BRCA_00117-T_vs_BRCA_00117-N.netmhcpan_netmhc_combined.output.txt
$ diff tmp_here/BRCA_00117-T_vs_BRCA_00117-N.all_neoantigen_predictions.txt neoantigen-tmp3/BRCA_00117-T_vs_BRCA_00117-N.all_neoantigen_predictions.txt
I've checked with python as well.
Naturally, I would prefer to have Chai review this, but he's on vacation; we can double-check when he's back.
This is meant to fix two warnings in pandas:
FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. DONE
FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order.
Here were the full warnings from a pipeline run:
The following should fix these. I'll slack you three the data to double-check.