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Merge pull request #127 from Sage-Bionetworks/jbeck/AG-1384/remove_du…
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…plicate_biodomains

Fix genes_biodomains transform to drop duplicate rows
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@jaclynbeck-sage
jaclynbeck-sage authored Mar 1, 2024
2 parents efe6eec + 80bcf1a commit 4f7e8e5
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Showing 4 changed files with 53 additions and 56 deletions.
2 changes: 1 addition & 1 deletion src/agoradatatools/etl/transform/genes_biodomains.py
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Expand Up @@ -53,7 +53,7 @@ def transform_genes_biodomains(datasets: dict) -> pd.DataFrame:
"""
genes_biodomains = datasets["genes_biodomains"]
interesting_columns = ["ensembl_gene_id", "biodomain", "go_terms"]
genes_biodomains = genes_biodomains[interesting_columns].dropna()
genes_biodomains = genes_biodomains[interesting_columns].dropna().drop_duplicates()

# Count the number of go_terms associated with each biodomain
n_biodomain_terms = count_grouped_total(
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74 changes: 37 additions & 37 deletions tests/test_assets/genes_biodomains/input/biodomains_test_input.csv
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@@ -1,37 +1,37 @@
biodomain,abbr,label,color,go_id,go_terms,ensembl_gene_id
Autophagy,Au,Autophagy [Au],#9931fd,GO:0006914,autophagy,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0016236,macroautophagy,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0000422,autophagy of mitochondrion,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0000423,mitophagy,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0035973,aggrephagy,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0038096,Fc-gamma receptor signaling pathway involved in phagocytosis,ENSG00000000938
Autophagy,Au,Autophagy [Au],#9931fd,GO:0050764,regulation of phagocytosis,ENSG00000000938
Autophagy,Au,Autophagy [Au],#9931fd,GO:0061912,selective autophagy,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0005776,autophagosome,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0000407,phagophore assembly site,ENSG00000161011
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0005743,mitochondrial inner membrane,ENSG00000000938
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0005758,mitochondrial intermembrane space,ENSG00000000938
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0098780,response to mitochondrial depolarisation,ENSG00000161011
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0005739,mitochondrion,ENSG00000161011
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0005739,mitochondrion,ENSG00000000938
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0000422,autophagy of mitochondrion,ENSG00000161011
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0010821,regulation of mitochondrion organization,ENSG00000161011
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0000423,mitophagy,ENSG00000161011
Synapse,Sy,Synapse [Sy],#329a33,GO:0045202,synapse,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:0050808,synapse organization,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:0045887,positive regulation of synaptic growth at neuromuscular junction,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:1900273,positive regulation of long-term synaptic potentiation,ENSG00000161011
Synapse,Sy,Synapse [Sy],#329a33,GO:0005102,signaling receptor binding,ENSG00000000938
Synapse,Sy,Synapse [Sy],#329a33,GO:0007213,G protein-coupled acetylcholine receptor signaling pathway,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:0007528,neuromuscular junction development,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:0045887,positive regulation of synaptic assembly at neuromuscular junction,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:0035255,ionotropic glutamate receptor binding,ENSG00000161011
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0005783,endoplasmic reticulum,ENSG00000161011
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0005796,Golgi lumen,ENSG00000188157
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0042254,ribosome biogenesis,ENSG00000290146
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0070475,rRNA base methylation,ENSG00000290146
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0070037,rRNA (pseudouridine) methyltransferase activity,ENSG00000290146
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0031625,ubiquitin protein ligase binding,ENSG00000161011
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0043130,ubiquitin binding,ENSG00000161011
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0016235,aggresome,ENSG00000161011
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0016235,aggresome,ENSG00000000938
biodomain,abbr,label,color,go_id,go_terms,n_symbol,symbol,ensembl_gene_id
Autophagy,Au,Autophagy [Au],#9931fd,GO:0006914,autophagy,152,SQSTM1,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0016236,macroautophagy,71,SQSTM1,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0000422,autophagy of mitochondrion,43,SQSTM1,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0000423,mitophagy,20,SQSTM1,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0035973,aggrephagy,6,SQSTM1,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0038096,Fc-gamma receptor signaling pathway involved in phagocytosis,21,FGR,ENSG00000000938
Autophagy,Au,Autophagy [Au],#9931fd,GO:0050764,regulation of phagocytosis,10,FGR,ENSG00000000938
Autophagy,Au,Autophagy [Au],#9931fd,GO:0061912,selective autophagy,14,SQSTM1,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0005776,autophagosome,73,SQSTM1,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0000407,phagophore assembly site,31,SQSTM1,ENSG00000161011
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0005743,mitochondrial inner membrane,484,FGR,ENSG00000000938
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0005758,mitochondrial intermembrane space,84,FGR,ENSG00000000938
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0098780,response to mitochondrial depolarisation,6,SQSTM1,ENSG00000161011
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0005739,mitochondrion,1380,SQSTM1,ENSG00000161011
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0005739,mitochondrion,1380,FGR,ENSG00000000938
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0000422,autophagy of mitochondrion,43,SQSTM1,ENSG00000161011
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0010821,regulation of mitochondrion organization,22,SQSTM1,ENSG00000161011
Mitochondrial Metabolism,MM,Mitochondrial Metabolism [MM],#97cb98,GO:0000423,mitophagy,20,SQSTM1,ENSG00000161011
Synapse,Sy,Synapse [Sy],#329a33,GO:0045202,synapse,475,AGRN,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:0050808,synapse organization,57,AGRN,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:0045887,positive regulation of synaptic growth at neuromuscular junction,1,AGRN,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:1900273,positive regulation of long-term synaptic potentiation,22,SQSTM1,ENSG00000161011
Synapse,Sy,Synapse [Sy],#329a33,GO:0005102,signaling receptor binding,362,FGR,ENSG00000000938
Synapse,Sy,Synapse [Sy],#329a33,GO:0007213,G protein-coupled acetylcholine receptor signaling pathway,15,AGRN,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:0007528,neuromuscular junction development,36,AGRN,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:0045887,positive regulation of synaptic assembly at neuromuscular junction,1,AGRN,ENSG00000188157
Synapse,Sy,Synapse [Sy],#329a33,GO:0035255,ionotropic glutamate receptor binding,23,SQSTM1,ENSG00000161011
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0005783,endoplasmic reticulum,1111,SQSTM1,ENSG00000161011
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0005796,Golgi lumen,104,AGRN,ENSG00000188157
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0042254,ribosome biogenesis,1,EMG1-C1S,ENSG00000290146
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0070475,rRNA base methylation,1,EMG1-C1S,ENSG00000290146
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0070037,rRNA (pseudouridine) methyltransferase activity,1,EMG1-C1S,ENSG00000290146
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0031625,ubiquitin protein ligase binding,310,SQSTM1,ENSG00000161011
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0043130,ubiquitin binding,97,SQSTM1,ENSG00000161011
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0016235,aggresome,35,SQSTM1,ENSG00000161011
Proteostasis,Pr,Proteostasis [Pr],#c8b269,GO:0016235,aggresome,35,FGR,ENSG00000000938
17 changes: 9 additions & 8 deletions tests/test_assets/genes_biodomains/input/biodomains_test_input_bad_but_should_pass.csv
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@@ -1,8 +1,9 @@
biodomain,abbr,label,color,go_id,go_terms,ensembl_gene_id
,Au,Autophagy [Au],#9931fd,GO:0006914,autophagy,ENSG00000161011
Autophagy,,Autophagy [Au],#9931fd,GO:0016236,macroautophagy,ENSG00000161011
Autophagy,Au,,#9931fd,GO:0000422,autophagy of mitochondrion,ENSG00000161011
Autophagy,Au,Autophagy [Au],,GO:0000423,mitophagy,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,,aggrephagy,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0038096,,ENSG00000000938
Autophagy,Au,Autophagy [Au],#9931fd,GO:0050764,regulation of phagocytosis,
biodomain,abbr,label,color,go_id,go_terms,n_symbol,symbol,ensembl_gene_id
,Au,Autophagy [Au],#9931fd,GO:0006914,autophagy,152,SQSTM1,ENSG00000161011
Autophagy,,Autophagy [Au],#9931fd,GO:0016236,macroautophagy,71,SQSTM1,ENSG00000161011
Autophagy,Au,,#9931fd,GO:0000422,autophagy of mitochondrion,43,SQSTM1,ENSG00000161011
Autophagy,Au,,#9931fd,GO:0000422,autophagy of mitochondrion,43,DUPLICATE,ENSG00000161011
Autophagy,Au,Autophagy [Au],,GO:0000423,mitophagy,20,SQSTM1,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,,aggrephagy,6,SQSTM1,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0038096,,,,ENSG00000000938
Autophagy,Au,Autophagy [Au],#9931fd,GO:0050764,regulation of phagocytosis,10,FGR,
16 changes: 6 additions & 10 deletions tests/test_assets/genes_biodomains/input/biodomains_test_input_bad_should_fail.csv
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@@ -1,10 +1,6 @@
biodomain,abbr,label,color,go_id,go_terms,ensembl_gene_id
,Au,Autophagy [Au],#9931fd,GO:0006914,autophagy,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0016236,,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0000422,autophagy of mitochondrion,
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biodomain,abbr,label,color,go_id,go_terms,n_symbol,symbol,ensembl_gene_id
,Au,Autophagy [Au],#9931fd,GO:0006914,autophagy,152,SQSTM1,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0016236,,71,SQSTM1,ENSG00000161011
Autophagy,Au,Autophagy [Au],#9931fd,GO:0000422,autophagy of mitochondrion,,,
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