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removed gene_gene_scores from check
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kataikko committed Oct 19, 2023
1 parent 9d33eb8 commit ec21191
Showing 4 changed files with 6 additions and 8 deletions.
3 changes: 1 addition & 2 deletions .gitignore
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@@ -4,9 +4,8 @@ config.yml
credentials.yml
.idea
pid-info.txt
db/source/*
db/scripts/function_times.tsv

db/scripts/function_times.tsv
db/source/

# Created by https://www.toptal.com/developers/gitignore/api/node,maven,python,pycharm,intellij,visualstudiocode,macos,windows,linux
2 changes: 1 addition & 1 deletion db/Docs.md
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@@ -247,7 +247,7 @@ Checks if files are in the ```source/processed/``` directory.
**Important Functions:** [base_setup()](#base_setup), [catlas_extention()](#catlas_extention), [bulk_extention()](#bulk_extention)

#### base_setup()
This Function Sets up the base network (Protein, Gene nodes, TF labels, Protein-Gene Links, STRING associations, Functional Terms, Overlap, TG-FT und Protein-FT links, Distance between OR and TG). Uses [start_driver()](#start_driver), [stop_driver()](#stop_driver), [setup_base_db()](#setup_base_db)
This Function Sets up the base network (Protein, Gene nodes, TF labels, Protein-Gene Links, STRING associations, Functional Terms, Overlap, TG-FT und Protein-FT links, Distance between OR and TG) from [ENSEMBL Mouse](https://ftp.ensembl.org/pub/current_tsv/mus_musculus/), [ENSEMBL Human](https://ftp.ensembl.org/pub/current_tsv/homo_sapiens/), [STRING Mouse](https://string-db.org/cgi/download?sessionId=bl9fRiGU0Q4X&species_text=Mus+musculus), [STRING Human](https://string-db.org/cgi/download?sessionId=bl9fRiGU0Q4X&species_text=Homo+sapiens), Baderlabs([Mouse](http://download.baderlab.org/EM_Genesets/current_release/Mouse/symbol/Mouse_GO_AllPathways_with_GO_iea_October_01_2023_symbol.gmt), [Human](http://download.baderlab.org/EM_Genesets/current_release/Human/symbol/Human_GO_AllPathways_with_GO_iea_October_01_2023_symbol.gmt)) and [KEGG](https://www.genome.jp/kegg/). Uses [start_driver()](#start_driver), [stop_driver()](#stop_driver), [setup_base_db()](#setup_base_db)

##### Input
- species (String): Representing Species (i.e. "Mus_Musculus", "Homo_Sapiens")
4 changes: 3 additions & 1 deletion db/Notes.md
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@@ -1,2 +1,4 @@

* If your storage fills up, after repeated transactions, you might want to look at the <NEO4J-HOME>/data/transactions/neo4j/ directory, and remove the "neostore.transaction.db." files.
* If your storage fills up, after repeated transactions, you might want to look at the <NEO4J-HOME>/data/transactions/neo4j/ directory, and remove the "neostore.transaction.db." files.

* source directory can be downloaded from: https://drive.google.com/drive/folders/1AKkq2YGMj5DoS3OsFg2zpvX4tEPtkMRX?usp=sharing
5 changes: 1 addition & 4 deletions db/scripts/utils.py
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@@ -104,7 +104,6 @@ def timing(i=None, **variables):
else:
writer.writerow([function.__name__, end_time - start_time])
return result

return timing


@@ -211,11 +210,9 @@ def check_for_files(mode: int):
elif mode == 1:
# STRING
return not (
os.path.exists("../source/processed/gene_gene_scores_mouse.csv")
and os.path.exists("../source/processed/genes_annotated_mouse.csv")
os.path.exists("../source/processed/genes_annotated_mouse.csv")
and os.path.exists("../source/processed/protein_protein_scores_mouse.csv")
and os.path.exists("../source/processed/proteins_annotated_mouse.csv")
and os.path.exists("../source/processed/gene_gene_scores_human.csv")
and os.path.exists("../source/processed/genes_annotated_human.csv")
and os.path.exists("../source/processed/protein_protein_scores_human.csv")
and os.path.exists("../source/processed/proteins_annotated_human.csv")

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