Python3: How to split the tuple generated by the .groupby function in pandas
My Code
data = pd.read_csv('input_file', header = None, delimiter="\t", names = ['chr', 'sTSS', 'eTSS', 'gene', 'clust1', 'clust2'])
dup_clust2 = data.groupby('clust2').filter(lambda x: len(x) > 1)
for element in dup_clust2.groupby('clust2'):
print(element)
Input: <tab separated="" file="">
chr2 166760255 166760255 Cse1l_tss10 52 5426
chr2 166760282 166760282 Cse1l_tss9 52 5426
chr2 166885599 166886548 IRF8 150.18 5431
chr2 166885925 166885925 Znfx1_tss1 52 5433
Output: <tab separated="" file="">
(5426, chr sTSS eTSS gene clust1 clust2
0 chr2 166760255 166760255 Cse1l_tss10 52.0 5426
1 chr2 166760282 166760282 Cse1l_tss9 52.0 5426)
Required Output:<tab separated="" file=""> split tuple in two lines
(0 chr2 166760255 166760255 Cse1l_tss10 52.0 5426)
(1 chr2 166760282 166760282 Cse1l_tss9 52.0 5426)
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Arup Ghosh
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written
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tinkuhim007 •
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written
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tinkuhim007 •
2 answers
Any particular reason to keep tabs?
import pandas as pd
data = pd.read_csv("file.txt", header = None, delimiter="\t", names = ['chr', 'sTSS', 'eTSS', 'gene', 'clust1', 'clust2'])
dup_clust2 = data.groupby('clust2').filter(lambda x: len(x) > 1).to_records().tolist()
for t in dup_clust2:
print(t)
#print with tabs
#out="\t".join(map(str,t))
#print(out)
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Arup Ghosh
The output of .groupby() function is tuple but the values of such tuple are dataframe, so we have to access their values using keys. I have just tried one solution using the same approach, it might help you.
import pandas as pd
data = pd.read_csv('input.txt', header = None, delimiter="\t", names = ['chr', 'sTSS', 'eTSS', 'gene', 'clust1', 'clust2'])
dup_clust2 = data.groupby('clust2').filter(lambda x: len(x) > 1)
userDict = {}
for element in dup_clust2.groupby('clust2'):
for key in element[1]:
index = 0
for i in element[1][key]:
if(not index in userDict):
userDict[index] = []
userDict[index].append(i)
index = index + 1
for key in userDict:
print(userDict[key])
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Nitin Narwade
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Hello tinkuhim007!
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Thread now has answers, but was not a bioinformatics question in the first place so should have been closed at the time.
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