Commit 19c2f8b9 authored by David Hoksza's avatar David Hoksza
Browse files

python dependencies

parent a185ce22
......@@ -9,6 +9,13 @@ Code and comments to [https://r3.pages.uni.lu/biocuration/resources/biohackathon
- R
- zip utility
Python needs to have packages decribed in `associations/requirement.txt` which can be installed
via
```commandline
pip3 install -r associations/requirement.txt
```
If the pipeline is run at clean Linux installation you might need to install the following libraries
(`sudo apt-get install` on Ubuntu) prior to running the code:
- libcurl
......
......@@ -8,8 +8,8 @@ DISGENET_CNT_THRESHOLD=50
DISGENET_ASSOCIATION_SCORE_THRESHOLD=0
OPENTARGETS_CNT_THRESHOLD=50
OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD=0.2
BUILD_MAP_GENERATOR=0 #1 for building it
STOP_AFTER_STAGE=-1
BUILD_MAP_GENERATOR=1 #0 for building it
STOP_AFTER_STAGE=1
# ------------------------- PARAMETERS TO SET -------------------------
ASSOCIATIONS_DIR=associations/
......@@ -19,20 +19,23 @@ ENRICHMENT_DIR=enrichment/
ENRICHMENT_CONFIG=${ENRICHMENT_DIR}/config.txt
MAP_GENERATOR_DIR=map_generator/
PYTHON_BIN=python3
PIP_BIN=pip3
ORPHANET_IDS_UNDERSCORE=${ORPHANET_IDS//,/_}
mkdir $RES_DIR
# -------------- 1. Extract genes and variants associated with a disease --------------
# Get associations from DisGeNET
disgenet_out_path=${RES_DIR}/01-disgenet-id_${ORPHANET_IDS_UNDERSCORE}-n_${DISGENET_CNT_THRESHOLD}-s_${DISGENET_ASSOCIATION_SCORE_THRESHOLD}.json
$PYTHON_BIN $ASSOCIATIONS_DIR/disgenet.py -o ${ORPHANET_IDS} -n ${DISGENET_CNT_THRESHOLD} -s ${DISGENET_ASSOCIATION_SCORE_THRESHOLD} > ${disgenet_out_path}
echo "Disgenet gene and variant associations stored in ${disgenet_out_path}"
# Get associations from OpenTargets
opentargets_out_path=${RES_DIR}/01-opentargets-id_${ORPHANET_IDS_UNDERSCORE}-n_${DISGENET_CNT_THRESHOLD}-s_${DISGENET_ASSOCIATION_SCORE_THRESHOLD}.json
$PYTHON_BIN $ASSOCIATIONS_DIR/opentargets.py -o ${ORPHANET_IDS} -n ${OPENTARGETS_CNT_THRESHOLD} -s ${OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD} > ${opentargets_out_path}
echo "Opentargets gene and variant associations stored in ${opentargets_out_path}"
# Merge with ClinVar
genes_variants_out_path=${RES_DIR}/02-genes_variants-id_${ORPHANET_IDS_UNDERSCORE}.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}
echo "Integration with ClinVar stored in ${genes_variants_out_path}"
......
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