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Fix Scoary-2 integration. #101

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Jul 2, 2024
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Fix Scoary-2 integration. #101

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1 change: 1 addition & 0 deletions docs/CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@ to [Common Changelog](https://common-changelog.org)

### Fixed

- Fix Scoary-2 integration. ([#101](https://github.com/metagenlab/zDB/pull/101)) (Niklaus Johner)
- Fix search_bar results view when all loci miss any gene annotation. ([#99](https://github.com/metagenlab/zDB/pull/99)) (Niklaus Johner)
- Fix locusx view error for loci with homologs without any gene annotation. ([#99](https://github.com/metagenlab/zDB/pull/99)) (Niklaus Johner)
- Fix extract_contigs view error for contigs without any gene annotation. ([#99](https://github.com/metagenlab/zDB/pull/99)) (Niklaus Johner)
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4 changes: 4 additions & 0 deletions webapp/views/gwas.py
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Expand Up @@ -9,6 +9,7 @@
from ete3 import Tree
from lib.ete_phylo import EteTree, MatchingColorColumn, ValueColoredColumn
from scoary import scoary
from scoary.permutations import CONFINT_CACHE

from views.analysis_view_metadata import GwasMetadata
from views.mixins import (AmrViewMixin, CogViewMixin, KoViewMixin,
Expand Down Expand Up @@ -160,6 +161,9 @@ def run_gwas(self, phenotype, qval_threshold, max_genes):
tree = Tree(self.db.get_reference_phylogeny())
tree.write(format=8, outfile=tree_path)

# Reset the db connection as it otherwise leads to issues with
# using an SQL object that was created in a separate thread.
CONFINT_CACHE.con, CONFINT_CACHE.cur = CONFINT_CACHE.get_cur()
scoary(genotype_path,
phenotype_path,
os.path.join(tmp, "out"),
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