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GUDMAP_RBK
data_hub_scripts
Commits
109bf9a2
Commit
109bf9a2
authored
Feb 01, 2021
by
Gervaise Henry
🤠
Browse files
Change server query to dev
parent
80c522ff
Changes
1
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Inline
Side-by-side
scripts/split_study.sh
View file @
109bf9a2
...
...
@@ -42,7 +42,7 @@ main(){
fi
# query GUDMAP/RBK study RID for experiment RIDs
echo
"curl --location --request GET 'https://
www
.gudmap.org/ermrest/catalog/2/entity/RNASeq:Experiment/Sequencing_Type=mRNA-Seq/Study_RID="
${
rid
}
"'"
| bash
>
${
rid
}
\_
experimentRIDs.json
echo
"curl --location --request GET 'https://
dev
.gudmap.org/ermrest/catalog/2/entity/RNASeq:Experiment/Sequencing_Type=mRNA-Seq/Study_RID="
${
rid
}
"'"
| bash
>
${
rid
}
\_
experimentRIDs.json
# extract experiment RIDs
>
${
rid
}
\_
experimentRIDs.csv
python3 ./scripts/extract_RIDs.py
-f
${
rid
}
\_
experimentRIDs
...
...
@@ -53,7 +53,7 @@ main(){
do
# query GUDMAP/RBK experiment RIDs for replicate RIDs
>
temp
\_
${
expRID
}
\_
repRIDs.json
echo
"curl --location --request GET 'https://
www
.gudmap.org/ermrest/catalog/2/entity/RNASeq:Replicate/Experiment_RID="
${
expRID
}
"'"
| bash
>>
temp
\_
${
expRID
}
\_
repRIDs.json
echo
"curl --location --request GET 'https://
dev
.gudmap.org/ermrest/catalog/2/entity/RNASeq:Replicate/Experiment_RID="
${
expRID
}
"'"
| bash
>>
temp
\_
${
expRID
}
\_
repRIDs.json
# extract replicate RIDs
>
temp
\_
${
expRID
}
\_
repRIDs.csv
python3 ./scripts/extract_RIDs.py
-f
temp
\_
${
expRID
}
\_
repRIDs
...
...
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