Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
David Hoksza
bh19-rare-diseases
Commits
19c2f8b9
Commit
19c2f8b9
authored
Nov 21, 2019
by
David Hoksza
Browse files
python dependencies
parent
a185ce22
Changes
2
Hide whitespace changes
Inline
Side-by-side
README.md
View file @
19c2f8b9
...
...
@@ -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
...
...
assemble.sh
View file @
19c2f8b9
...
...
@@ -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
}
"
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment