Thumper: One of the types of stills used to accomplish the second distillation of American whiskey. It effectively removes impurities and concentrates the alcohol even further. “Low wines” go in; “high wines” come out. Thumpers differ from doublers in that the low wines enter a thumper as vapors that are bubbled through water, causing the stills to make a thumping sound; a doubler makes no distinctive noise since the low wines enter in condensed, liquid form.
Use two test genomes/proteomes previously classified w/2020-gtdb-smash
GB_GCA_002691795.1_protein.faa.gz
RS_GCF_003143755.1_protein.faa.gz
ran a gather against gtdb-genus in protein-11, dayhoff-19 and hp-33. Picked top 3 matches for each alpha-ksize (sometimes were same genomes) --> nine genomes to use as a reference set.
gtdb-nine reference set:
GCA_000384615
GCA_002387605
GCA_003210055
GCA_003210115
GCA_003282145
GCF_900111025
GCF_900112595
GCF_900114265
GCF_900141715
Built sbt.zip gtdb-nine index for each alpha-ksize (including dna at k 21,31,51) + ran search containment to verify that we get matches.
[x] init generate-index pipeline for generating user db's
[x] enable csv input for better sig/file naming
[x] add testing environment file and disable conda in testing
[x] Actually add test_snakemake.py
[x] make nice test data!
Use two test genomes/proteomes previously classified w/2020-gtdb-smash
ran a gather against gtdb-genus in protein-11, dayhoff-19 and hp-33. Picked top 3 matches for each alpha-ksize (sometimes were same genomes) --> nine genomes to use as a reference set.
gtdb-nine reference set:
Built
sbt.zip
gtdb-nine index for each alpha-ksize (including dna at k 21,31,51) + ran search containment to verify that we get matches.[x] init generate-index pipeline for generating user db's
[x] enable csv input for better sig/file naming
[x] add testing environment file and disable conda in testing
[x] get search-containment tests working
[x] init makefile for easier testing