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David Hoksza
bh19-rare-diseases
Commits
240ebaae
Commit
240ebaae
authored
Dec 02, 2019
by
David Hoksza
Browse files
ability to pass parameters to enrichment analysis from the parameters script
parent
d41983b9
Changes
3
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assemble.sh
View file @
240ebaae
...
...
@@ -11,6 +11,7 @@ EXTEND_CONFIG=${EXTEND_DIR}/config.txt
RES_DIR
=
results
ENRICHMENT_DIR
=
enrichment/
ENRICHMENT_CONFIG
=
${
ENRICHMENT_DIR
}
/config.txt
ENRICHMENT_CONFIG_TMP
=
${
ENRICHMENT_CONFIG
}
.tmp
MAP_GENERATOR_DIR
=
map_generator/
PYTHON_BIN
=
python3
PIP_BIN
=
pip3
...
...
@@ -24,6 +25,9 @@ mkdir $RES_DIR
RES_DIR
=
$RES_DIR
/
${
ORPHANET_IDS_UNDERSCORE
}
mkdir
$RES_DIR
# First we copy the parameters into the result directory
cp
parameters.sh
${
RES_DIR
}
# Get associations from 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
}
...
...
@@ -69,11 +73,21 @@ if [ ${STOP_AFTER_STAGE} = 1 ]; then
fi
# ------------------------------ 2. Obtain pathways ------------------------------
echo
"Retrieving enriched pathways"
Rscript
--vanilla
${
ENRICHMENT_DIR
}
/enrich_maps.R
${
genes_out_path
}
${
ENRICHMENT_CONFIG
}
tr
'\r'
'\n'
<
${
ENRICHMENT_CONFIG
}
>
${
ENRICHMENT_CONFIG_TMP
}
#update paremters file
sed
-E
-i
"s/(max_areas_per_map)(.*)/
\1\t
${
ENRICH_MAX_AREAS_PER_MAP
}
/g"
${
ENRICHMENT_CONFIG_TMP
}
sed
-E
-i
"s/(max_areas_per_pathway_db)(.*)/
\1\t
${
MAX_AREAS_PER_PATHWAY_DB
}
/g"
${
ENRICHMENT_CONFIG_TMP
}
Rscript
--vanilla
${
ENRICHMENT_DIR
}
/enrich_maps.R
${
genes_out_path
}
${
ENRICHMENT_CONFIG_TMP
}
enriched_maps_out_path
=
$RES_DIR
/05-enriched_disease_maps.txt
enriched_paths_out_path
=
$RES_DIR
/05-enriched_pathways.txt
mv
enriched_disease_maps.txt
${
enriched_maps_out_path
}
mv
enriched_pathways.txt
${
enriched_paths_out_path
}
rm
${
ENRICHMENT_CONFIG_TMP
}
echo
"Enriched pathways obtained"
...
...
enrichment/config.txt
deleted
100644 → 0
View file @
d41983b9
type resource value parameter max_areas_per_map 5 parameter max_areas_per_pathway_db 5 map https://pdmap.uni.lu/minerva/api/ map https://progeria.uni.lu/minerva/api/ pathway_db WikiPathways_2019_Human pathway_db Panther_2016
\ No newline at end of file
parameters.sh
View file @
240ebaae
...
...
@@ -4,7 +4,12 @@ ORPHANET_IDS="130"
DISGENET_CNT_THRESHOLD
=
50
DISGENET_ASSOCIATION_SCORE_THRESHOLD
=
"0"
OPENTARGETS_CNT_THRESHOLD
=
50
OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD
=
"0.3"
ENRICH_MAX_AREAS_PER_MAP
=
1
MAX_AREAS_PER_PATHWAY_DB
=
1
BUILD_MAP_GENERATOR
=
0
#1 for building it
STOP_AFTER_STAGE
=
-1
\ No newline at end of file
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