Commit 27a551d2 authored by Ayse Berceste Dincer's avatar Ayse Berceste Dincer
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pipeline

parent 98356dbe
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%% 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.tsv', index_col = 0)
print("All pathways ", HIERARCHY.shape)
for i in range(HIERARCHY.shape[1]):
print("Layer ", i + 1)
print(len(np.unique(HIERARCHY.iloc[:, i].values.astype(str))))
```
%% Output
All pathways (910, 10)
Layer 1
1
Layer 2
3
Layer 3
238
Layer 4
175
Layer 5
181
Layer 6
211
Layer 7
128
Layer 8
86
Layer 9
56
Layer 10
26
%% Cell type:code id: tags:
``` python
HIERARCHY = pd.read_table('GO_MF_Hierarchy_FINAL.tsv', index_col = 0)
print("All pathways ", HIERARCHY.shape)
for i in range(HIERARCHY.shape[1]):
print("Layer ", i + 1)
print(len(np.unique(HIERARCHY.iloc[:, i].values.astype(str))))
```
%% Output
All pathways (1369, 12)
Layer 1
1
Layer 2
13
Layer 3
70
Layer 4
264
Layer 5
384
Layer 6
371
Layer 7
314
Layer 8
190
Layer 9
121
Layer 10
63
Layer 11
29
Layer 12
9
%% Cell type:code id: tags:
``` python
HIERARCHY = pd.read_table('GO_BP_Hierarchy_FINAL.tsv', index_col = 0)
print("All pathways ", HIERARCHY.shape)
for i in range(HIERARCHY.shape[1]):
print("Layer ", i + 1)
print(len(np.unique(HIERARCHY.iloc[:, i].values.astype(str))))
```
%% Output
All pathways (7058, 16)
Layer 1
1
Layer 2
23
Layer 3
167
Layer 4
649
Layer 5
1101
Layer 6
1647
Layer 7
1902
Layer 8
1841
Layer 9
1510
Layer 10
954
Layer 11
586
Layer 12
303
Layer 13
133
Layer 14
46
Layer 15
7
Layer 16
2
%% Cell type:code id: tags:
``` python
```
%% Cell type:code id: tags:
``` python
```
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%% Cell type:code id: tags:
``` python
import networkx as nx
import algorithm_helpers as