Commit 6f04fc8f authored by Ayse Berceste Dincer's avatar Ayse Berceste Dincer
Browse files

Curated hierarchies

parent f812c010
File added
%% Cell type:code id: tags:
``` python
import numpy as np
import pandas as pd
```
%% Cell type:code id: tags:
``` python
HIERARCHY = pd.read_table('GO_CC_Hierarchy_FINAL_ONLY_V7.tsv', index_col = 0)
print("All pathways ", HIERARCHY.shape)
nonobsolete_sets = [s for s in np.arange(HIERARCHY.iloc[:, 0].values.shape[0]) if 'OBSOLETE' not in HIERARCHY.iloc[:, 0].values[s]]
HIERARCHY = HIERARCHY.iloc[nonobsolete_sets]
print("All pathways, obsoletes excluded ", HIERARCHY.shape)
for i in range(HIERARCHY.shape[1]):
print("Layer ", i + 1)
print(len(np.unique(HIERARCHY.iloc[:, i].values.astype(str))))
```
%% Cell type:code id: tags:
``` python
HIERARCHY = pd.read_table('GO_MF_Hierarchy_FINAL_ONLY_V7.tsv', index_col = 0)
print("All pathways ", HIERARCHY.shape)
nonobsolete_sets = [s for s in np.arange(HIERARCHY.iloc[:, 0].values.shape[0]) if 'OBSOLETE' not in HIERARCHY.iloc[:, 0].values[s]]
HIERARCHY = HIERARCHY.iloc[nonobsolete_sets]
print("All pathways, obsoletes excluded ", HIERARCHY.shape)
for i in range(HIERARCHY.shape[1]):
print("Layer ", i + 1)
print(len(np.unique(HIERARCHY.iloc[:, i].values.astype(str))))
```
%% Cell type:code id: tags:
``` python
```
%% Cell type:code id: tags:
``` python
```
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