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Metagenomics
metagenedb
Commits
4a09070c
Commit
4a09070c
authored
Nov 19, 2019
by
Kenzo-Hugo Hillion
♻
Browse files
fix handling of taxonomy and way it is skipped
parent
220b598c
Changes
2
Hide whitespace changes
Inline
Side-by-side
backend/scripts/populate_db/import_igc_data.py
View file @
4a09070c
...
...
@@ -55,6 +55,8 @@ class ImportIGCGenes(object):
"""
phylum
=
gene_dict
.
pop
(
self
.
PHYLUM_COL
)
genus
=
gene_dict
.
pop
(
self
.
GENUS_COL
)
if
self
.
skip_tax
:
return
gene_dict
resp_dict
=
{}
if
genus
!=
unknown_val
:
resp_dict
=
self
.
metagenedb_taxonomy_api
.
get_all
(
params
=
{
'name'
:
genus
,
'rank'
:
'genus'
})
...
...
@@ -81,10 +83,7 @@ class ImportIGCGenes(object):
gene_dict
[
'gene_name'
]
=
gene_dict
[
'gene_id'
]
gene_dict
[
'gene_id'
]
=
slugify
(
gene_dict
[
'gene_id'
])
gene_dict
[
'functions'
]
=
gene_dict
.
pop
(
'kegg_ko'
)
if
gene_dict
.
get
(
'taxonomy'
,
None
)
==
'unknown'
or
self
.
skip_tax
:
gene_dict
.
pop
(
'taxonomy'
)
else
:
gene_dict
=
self
.
_select_taxonomy
(
gene_dict
)
gene_dict
=
self
.
_select_taxonomy
(
gene_dict
)
if
self
.
skip_functions
or
'unknown'
in
gene_dict
[
'functions'
]:
gene_dict
.
pop
(
'functions'
)
return
gene_dict
...
...
backend/scripts/populate_db/test_import_igc_data.py
View file @
4a09070c
...
...
@@ -76,23 +76,10 @@ class TestCleanGene(TestCase):
self
.
gene_dict
=
{
'gene_id'
:
'gene.01'
,
'length'
:
135
,
'taxonomy'
:
'Taxo'
,
'kegg_ko'
:
[
'K00001'
]
}
def
test_clean_gene
(
self
):
expected_gene_dict
=
{
'gene_id'
:
'gene-01'
,
'gene_name'
:
'gene.01'
,
'length'
:
135
,
'taxonomy'
:
'Taxo'
,
'functions'
:
[
'K00001'
]
}
test_gene_dict
=
self
.
import_igc_genes
.
_clean_gene
(
self
.
gene_dict
)
self
.
assertDictEqual
(
test_gene_dict
,
expected_gene_dict
)
def
test_clean_gene_skip_taxo
(
self
):
self
.
import_igc_genes
.
skip_tax
=
True
expected_gene_dict
=
{
'gene_id'
:
'gene-01'
,
'gene_name'
:
'gene.01'
,
...
...
@@ -108,7 +95,6 @@ class TestCleanGene(TestCase):
'gene_id'
:
'gene-01'
,
'gene_name'
:
'gene.01'
,
'length'
:
135
,
'taxonomy'
:
'Taxo'
,
}
test_gene_dict
=
self
.
import_igc_genes
.
_clean_gene
(
self
.
gene_dict
)
self
.
assertDictEqual
(
test_gene_dict
,
expected_gene_dict
)
...
...
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