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PauBadiaMPauBadiaM
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Updated db names
1 parent e3e3af7 commit 825baf4

2 files changed

Lines changed: 32 additions & 32 deletions

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‎src/gretapy/config.py‎

Lines changed: 29 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@
2020
"metric": None,
2121
},
2222
# Literature
23-
"Human Protein Atlas (HPA)": {
23+
"HPA": {
2424
"fname": "hg38_tfm_hpa.tsv.gz",
2525
"metric": "TF Markers",
2626
},
@@ -79,30 +79,30 @@
7979
},
8080
"eQTL Catalogue": {
8181
"fname": "hg38_c2g_eqtlcatalogue.bed.gz",
82-
"metric": "CRE to gene links",
82+
"metric": "CRE to Gene",
8383
},
8484
# Predictive
8585
"Hallmarks": {
8686
"fname": "hg38_gst_hall.csv.gz",
87-
"metric": "Gene sets",
87+
"metric": "Gene Sets",
8888
},
8989
"KEGG": {
9090
"fname": "hg38_gst_kegg.csv.gz",
91-
"metric": "Gene sets",
91+
"metric": "Gene Sets",
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},
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"Reactome": {
9494
"fname": "hg38_gst_reac.csv.gz",
95-
"metric": "Gene sets",
95+
"metric": "Gene Sets",
9696
},
9797
"PROGENy": {
9898
"fname": "hg38_gst_prog.csv.gz",
99-
"metric": "Gene sets",
99+
"metric": "Gene Sets",
100100
},
101-
"gene ~ TFs": {
101+
"Gene ~ TFs": {
102102
"fname": None,
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"metric": "Omics",
104104
},
105-
"gene ~ CREs": {
105+
"Gene ~ CREs": {
106106
"fname": None,
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"metric": "Omics",
108108
},
@@ -121,7 +121,7 @@
121121
},
122122
"Boolean rules": {
123123
"fname": None,
124-
"metric": "Steady state simulation",
124+
"metric": "Steady State Simulation",
125125
},
126126
},
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"dts": {
@@ -150,7 +150,7 @@
150150
"Neuroblastoma cell",
151151
"Brain carcinoma cell",
152152
],
153-
"Human Protein Atlas (HPA)": [
153+
"HPA": [
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"Astrocytes",
155155
"Brain",
156156
"Neurons",
@@ -367,7 +367,7 @@
367367
"Macrophages cell",
368368
"T cell",
369369
],
370-
"Human Protein Atlas (HPA)": [
370+
"HPA": [
371371
"Breast cancer",
372372
"Breast glandular cells",
373373
"Glandular & Luminal cells",
@@ -575,7 +575,7 @@
575575
"Trophoblastic cell",
576576
"Stem cell",
577577
],
578-
"Human Protein Atlas (HPA)": [
578+
"HPA": [
579579
"Placenta",
580580
"Cytotrophoblasts",
581581
"Syncytiotrophoblasts",
@@ -756,7 +756,7 @@
756756
"Retinal cell",
757757
"Cornea",
758758
],
759-
"Human Protein Atlas (HPA)": [
759+
"HPA": [
760760
"Retina",
761761
"Retina & Testis",
762762
"Photoreceptor cells",
@@ -897,7 +897,7 @@
897897
"Fibroblast cell",
898898
"Macrophage cell",
899899
],
900-
"Human Protein Atlas (HPA)": [
900+
"HPA": [
901901
"Kidney",
902902
"Kidney & Intestine",
903903
"Kidney cancer",
@@ -1057,7 +1057,7 @@
10571057
"B cell",
10581058
"Natural killer cell",
10591059
],
1060-
"Human Protein Atlas (HPA)": [
1060+
"HPA": [
10611061
"Alveolar cells",
10621062
"Respiratory epithelial cells",
10631063
"Ciliated cells",
@@ -1319,7 +1319,7 @@
13191319
"Endothelium",
13201320
"Fibroblast cell",
13211321
],
1322-
"Human Protein Atlas (HPA)": [
1322+
"HPA": [
13231323
"Cardiomyocytes",
13241324
"Heart muscle",
13251325
"Smooth muscle cells",
@@ -1517,7 +1517,7 @@
15171517
"Acute lymphoblastic leukemia cell",
15181518
"Chronic myeloid leukemia cell",
15191519
],
1520-
"Human Protein Atlas (HPA)": [
1520+
"HPA": [
15211521
"B",
15221522
"T",
15231523
"NK",
@@ -1812,7 +1812,7 @@
18121812
"Macrophages cell",
18131813
"Gland cell",
18141814
],
1815-
"Human Protein Atlas (HPA)": [
1815+
"HPA": [
18161816
"Pituitary gland",
18171817
"Endocrine & Neural",
18181818
"Brain",
@@ -1974,7 +1974,7 @@
19741974
"Epidermis",
19751975
"Keratinocytes cell",
19761976
],
1977-
"Human Protein Atlas (HPA)": [
1977+
"HPA": [
19781978
"Fibroblasts",
19791979
"Connective tissue",
19801980
"Connective tissue cells",
@@ -2168,7 +2168,7 @@
21682168
"T cell",
21692169
"Immune",
21702170
],
2171-
"Human Protein Atlas (HPA)": [
2171+
"HPA": [
21722172
"Skin",
21732173
"Skin cancer",
21742174
"Suprabasal keratinocytes",
@@ -2464,21 +2464,21 @@
24642464
# Predictive
24652465
"Hallmarks": {
24662466
"fname": "mm10_gst_hall.csv.gz",
2467-
"metric": "Gene sets",
2467+
"metric": "Gene Sets",
24682468
},
24692469
"Reactome": {
24702470
"fname": "mm10_gst_reac.csv.gz",
2471-
"metric": "Gene sets",
2471+
"metric": "Gene Sets",
24722472
},
24732473
"PROGENy": {
24742474
"fname": "mm10_gst_prog.csv.gz",
2475-
"metric": "Gene sets",
2475+
"metric": "Gene Sets",
24762476
},
2477-
"gene ~ TFs": {
2477+
"Gene ~ TFs": {
24782478
"fname": None,
24792479
"metric": "Omics",
24802480
},
2481-
"gene ~ CREs": {
2481+
"Gene ~ CREs": {
24822482
"fname": None,
24832483
"metric": "Omics",
24842484
},
@@ -2497,7 +2497,7 @@
24972497
},
24982498
"Boolean rules": {
24992499
"fname": None,
2500-
"metric": "Steady state simulation",
2500+
"metric": "Steady State Simulation",
25012501
},
25022502
},
25032503
"dts": {
@@ -2610,10 +2610,10 @@
26102610
"Reference GRN": "Literature",
26112611
"TF Binding": "Genomic",
26122612
"CREs": "Genomic",
2613-
"CRE to gene links": "Genomic",
2614-
"Gene sets": "Predictive",
2613+
"CRE to Gene": "Genomic",
2614+
"Gene Sets": "Predictive",
26152615
"Omics": "Predictive",
26162616
"TF Scoring": "Mechanistic",
26172617
"Perturbation Forecasting": "Mechanistic",
2618-
"Steady state simulation": "Mechanistic",
2618+
"Steady State Simulation": "Mechanistic",
26192619
}

‎src/gretapy/tl/_eval.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -393,7 +393,7 @@ def _run_omics_metric(
393393
verbose: bool = True,
394394
) -> tuple | None:
395395
"""Run omics metric based on the specific type."""
396-
if db_name == "gene ~ TFs":
396+
if db_name == "Gene ~ TFs":
397397
return _omics(
398398
data=dataset,
399399
grn=grn,
@@ -403,7 +403,7 @@ def _run_omics_metric(
403403
mod_target="rna",
404404
verbose=verbose,
405405
)
406-
elif db_name == "gene ~ CREs" and is_mudata and has_cre:
406+
elif db_name == "Gene ~ CREs" and is_mudata and has_cre:
407407
return _omics(
408408
data=dataset,
409409
grn=grn,
@@ -423,7 +423,7 @@ def _run_omics_metric(
423423
mod_target="atac",
424424
verbose=verbose,
425425
)
426-
elif db_name in {"gene ~ CREs", "CRE ~ TFs"}:
426+
elif db_name in {"Gene ~ CREs", "CRE ~ TFs"}:
427427
_log(
428428
f"Skipping '{db_name}': requires MuData with ATAC and GRN with 'cre' column.",
429429
level="warning",

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