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David Hoksza
bh19-rare-diseases
Commits
6b25414c
Commit
6b25414c
authored
Dec 03, 2019
by
David Hoksza
Browse files
enable passing parameters file; fixing minerva variants
parent
d92ab358
Changes
3
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Inline
Side-by-side
assemble.sh
View file @
6b25414c
#!/usr/bin/env bash
# Load parameters either from parameters.sh, or from a file provided as the first parameter of the script
if
[[
$1
==
""
]]
;
then
source
parameters.sh
else
source
$1
fi
# ------------------------- PARAMETERS TO SET -------------------------
source
parameters.sh
# ------------------------- PARAMETERS TO SET -------------------------
ASSOCIATIONS_DIR
=
associations/
...
...
associations/minerva_variants.py
View file @
6b25414c
...
...
@@ -4,6 +4,7 @@ import json
import
argparse
from
typing
import
List
,
Dict
,
Set
import
requests
import
copy
def
get_dbsnp
(
ids
:
List
[
str
])
->
List
[
Dict
]:
...
...
@@ -119,7 +120,7 @@ def get_dbsnp(ids: List[str]) -> List[Dict]:
"position"
:
position
,
"original_dna"
:
original_dna
,
"alternative_dna"
:
alternative_dna
,
"name"
:
name
,
"
gene_
name"
:
name
,
"description"
:
description
,
"color"
:
color
,
"contig"
:
contig
,
...
...
@@ -158,13 +159,18 @@ def get_minerva_format(db_snps: List[Dict]) -> str:
if
len
(
db_snps
)
==
0
:
return
out
out
+=
"#NAME=DISEASE_ASSOCIATED_VARIANTS
\n
"
out
+=
"#TYPE=GENETIC_VARIANT
\n
"
out
+=
"#GENOME_TYPE=UCSC
\n
"
out
+=
"#GENOME_VERSION=hg19
\n
"
out
+=
"
\t
"
.
join
(
db_snps
[
0
].
keys
())
+
"
\n
"
keys
=
list
(
db_snps
[
0
].
keys
())
keys
.
remove
(
'variant_identifier'
)
out
+=
"
\t
"
.
join
(
keys
)
+
"
\n
"
for
snp
in
db_snps
:
out
+=
"
\t
"
.
join
(
snp
.
values
())
+
"
\n
"
snp_cp
=
copy
.
deepcopy
(
snp
)
del
snp_cp
[
'variant_identifier'
]
out
+=
"
\t
"
.
join
(
snp_cp
.
values
())
+
"
\n
"
return
out
...
...
parameters.sh
View file @
6b25414c
...
...
@@ -12,8 +12,8 @@ USE_OPENTARGETS=1
OPENTARGETS_CNT_THRESHOLD
=
50
OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD
=
"0.3"
ENRICH_MAX_AREAS_PER_MAP
=
1
MAX_AREAS_PER_PATHWAY_DB
=
1
ENRICH_MAX_AREAS_PER_MAP
=
5
MAX_AREAS_PER_PATHWAY_DB
=
5
BUILD_MAP_GENERATOR
=
0
#1 for building it
STOP_AFTER_STAGE
=
-1
\ No newline at end of file
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