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David Hoksza
bh19-rare-diseases
Commits
5264ad15
Commit
5264ad15
authored
Dec 02, 2019
by
David Hoksza
Browse files
ability to turn off given resources in the pipeline
parent
82f3d173
Changes
3
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Inline
Side-by-side
assemble.sh
View file @
5264ad15
...
...
@@ -38,25 +38,36 @@ check_exit_code(){
log
()
{
echo
`
date
+
"%T"
`
:
$1
}
# Get associations from DisGeNET
log
"Querying DisGeNET..."
disgenet_out_path
=
${
RES_DIR
}
/01-disgenet-n_
${
DISGENET_CNT_THRESHOLD
}
-s_
${
DISGENET_ASSOCIATION_SCORE_THRESHOLD_STR
}
.json
$PYTHON_BIN
$ASSOCIATIONS_DIR
/disgenet.py
-o
${
ORPHANET_IDS
}
-n
${
DISGENET_CNT_THRESHOLD
}
-s
${
DISGENET_ASSOCIATION_SCORE_THRESHOLD
}
>
${
disgenet_out_path
}
check_exit_code
log
"DisGeNET gene and variant associations stored in
${
disgenet_out_path
}
"
# Get associations from OpenTargets
log
"Querying OpenTargets..."
opentargets_out_path
=
${
RES_DIR
}
/01-opentargets-n_
${
DISGENET_CNT_THRESHOLD
}
-s_
${
OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD_STR
}
.json
$PYTHON_BIN
$ASSOCIATIONS_DIR
/opentargets.py
-o
${
ORPHANET_IDS
}
-n
${
OPENTARGETS_CNT_THRESHOLD
}
-s
${
OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD
}
>
${
opentargets_out_path
}
check_exit_code
log
"Opentargets gene and variant associations stored in
${
opentargets_out_path
}
"
out_paths
=
""
if
[
${
USE_DISGENET
}
=
1
]
;
then
log
"Querying DisGeNET..."
disgenet_out_path
=
${
RES_DIR
}
/01-disgenet-n_
${
DISGENET_CNT_THRESHOLD
}
-s_
${
DISGENET_ASSOCIATION_SCORE_THRESHOLD_STR
}
.json
$PYTHON_BIN
$ASSOCIATIONS_DIR
/disgenet.py
-o
${
ORPHANET_IDS
}
-n
${
DISGENET_CNT_THRESHOLD
}
-s
${
DISGENET_ASSOCIATION_SCORE_THRESHOLD
}
>
${
disgenet_out_path
}
check_exit_code
log
"DisGeNET gene and variant associations stored in
${
disgenet_out_path
}
"
out_paths
=
"
${
out_paths
}
,
${
disgenet_out_path
}
"
fi
if
[
${
USE_OPENTARGETS
}
=
1
]
;
then
# Get associations from OpenTargets
log
"Querying OpenTargets..."
opentargets_out_path
=
${
RES_DIR
}
/01-opentargets-n_
${
DISGENET_CNT_THRESHOLD
}
-s_
${
OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD_STR
}
.json
$PYTHON_BIN
$ASSOCIATIONS_DIR
/opentargets.py
-o
${
ORPHANET_IDS
}
-n
${
OPENTARGETS_CNT_THRESHOLD
}
-s
${
OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD
}
>
${
opentargets_out_path
}
check_exit_code
log
"Opentargets gene and variant associations stored in
${
opentargets_out_path
}
"
out_paths
=
"
${
out_paths
}
,
${
opentargets_out_path
}
"
fi
# Merge with ClinVar
log
"Merging with ClinVar..."
genes_variants_out_path
=
${
RES_DIR
}
/02-genes_variants.log
$PYTHON_BIN
$ASSOCIATIONS_DIR
/merge_with_clinvar.py
-v
$disgenet_out_path
,
$opentargets_out_path
-c
${
ASSOCIATIONS_DATA_DIR
}
/OrphaHPO_clinvar_variants_summary.tsv
-oid
${
ORPHANET_IDS
}
>
${
genes_variants_out_path
}
out_paths
=
${
out_paths
#,
}
$PYTHON_BIN
$ASSOCIATIONS_DIR
/merge_with_clinvar.py
-v
$out_paths
-c
${
ASSOCIATIONS_DATA_DIR
}
/OrphaHPO_clinvar_variants_summary.tsv
-oid
${
ORPHANET_IDS
}
>
${
genes_variants_out_path
}
check_exit_code
log
"Integration with ClinVar stored in
${
genes_variants_out_path
}
"
...
...
associations/extend_network/get_extended_network.R
View file @
5264ad15
...
...
@@ -61,7 +61,7 @@ if (dbsource == "stringdb" | dbsource == "text_mining") {
filters
=
'hgnc_symbol'
,
values
=
input
,
mart
=
ensembl
)
biomartCacheClear
()
ensprotein_idest
<-
subset
(
ensprotein_idest
,
ensembl_peptide_id
!=
""
)
message
(
paste0
(
"there are "
,
length
(
unique
(
ensprotein_idest
$
hgnc_symbol
))),
" genes in the input file with ensembl protein ids"
)
...
...
@@ -132,7 +132,7 @@ if (dbsource == "stringdb" | dbsource == "text_mining") {
filters
=
'ensembl_peptide_id'
,
values
=
protein_info
,
mart
=
ensembl
)
biomartCacheClear
()
protein_info_2ensp
<-
subset
(
protein_info_2ensp
,
hgnc_symbol
!=
""
)
ppi_network
<-
merge
(
ppi_network
,
protein_info_2ensp
,
by.x
=
"source"
,
by.y
=
"ensembl_peptide_id"
)
...
...
parameters.sh
View file @
5264ad15
#!/usr/bin/env bash
ORPHANET_IDS
=
"130"
#ORPHANET_IDS="851,404493,46348,85295"
#ORPHANET_IDS="33,67046,79327,79321,86309"
USE_DISGENET
=
1
DISGENET_CNT_THRESHOLD
=
50
DISGENET_ASSOCIATION_SCORE_THRESHOLD
=
"0"
USE_OPENTARGETS
=
1
OPENTARGETS_CNT_THRESHOLD
=
50
OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD
=
"0.3"
...
...
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