Commit 0f5c1d69 authored by flothoni's avatar flothoni Committed by Mathieu Giraud
Browse files

fuse.py: update test to include diversity

link to #1941
parent 57f4918b
...@@ -156,9 +156,14 @@ class Diversity: ...@@ -156,9 +156,14 @@ class Diversity:
def __init__(self, data=None): def __init__(self, data=None):
self.d={} self.d={}
self.d["index_H_entropy"] = [data["index_H_entropy"]] if data == None:
self.d["index_E_equitability"] = [data["index_E_equitability"]] self.d["index_H_entropy"] = ["na"]
self.d["index_Ds_diversity"] = [data["index_Ds_diversity"]] self.d["index_E_equitability"] = ["na"]
self.d["index_Ds_diversity"] = ["na"]
else:
self.d["index_H_entropy"] = [data["index_H_entropy"]]
self.d["index_E_equitability"] = [data["index_E_equitability"]]
self.d["index_Ds_diversity"] = [data["index_Ds_diversity"]]
def __add__(self, other): def __add__(self, other):
self.d['index_H_entropy'].append( other.d['index_H_entropy'][0] ) self.d['index_H_entropy'].append( other.d['index_H_entropy'][0] )
...@@ -352,7 +357,10 @@ class ListWindows(VidjilJson): ...@@ -352,7 +357,10 @@ class ListWindows(VidjilJson):
self.d["clones"] = [] self.d["clones"] = []
self.check_version(file_path) self.check_version(file_path)
self.d["diversity"] = Diversity(self.d["diversity"]) if "diversity" in self.d.keys():
self.d["diversity"] = Diversity(self.d["diversity"])
else:
self.d["diversity"] = Diversity()
if 'distribution' not in self.d['reads'].d: if 'distribution' not in self.d['reads'].d:
self.d['reads'].d['distribution'] = {} self.d['reads'].d['distribution'] = {}
...@@ -642,6 +650,8 @@ lw1.d["timestamp"] = 'ts' ...@@ -642,6 +650,8 @@ lw1.d["timestamp"] = 'ts'
lw1.d["reads"] = json.loads('{"total": [30], "segmented": [25], "germline": {}, "distribution": {}}', object_hook=lw1.toPython) lw1.d["reads"] = json.loads('{"total": [30], "segmented": [25], "germline": {}, "distribution": {}}', object_hook=lw1.toPython)
lw1.d["clones"].append(w5) lw1.d["clones"].append(w5)
lw1.d["clones"].append(w6) lw1.d["clones"].append(w6)
lw1.d["diversity"] = Diversity()
w7 = Window(1) w7 = Window(1)
w7.d ={"id" : "aaa", "reads" : [8], "top" : 4 } w7.d ={"id" : "aaa", "reads" : [8], "top" : 4 }
...@@ -653,6 +663,7 @@ lw2.d["timestamp"] = 'ts' ...@@ -653,6 +663,7 @@ lw2.d["timestamp"] = 'ts'
lw2.d["reads"] = json.loads('{"total": [40], "segmented": [34], "germline": {}, "distribution": {}}', object_hook=lw1.toPython) lw2.d["reads"] = json.loads('{"total": [40], "segmented": [34], "germline": {}, "distribution": {}}', object_hook=lw1.toPython)
lw2.d["clones"].append(w7) lw2.d["clones"].append(w7)
lw2.d["clones"].append(w8) lw2.d["clones"].append(w8)
lw2.d["diversity"] = Diversity()
......
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