Given a dataframe:
Sample_Name SNP1 SNP2 SNP3
Sample 1 AA AC GC
Sample 2 GA AC CG
Sample 3 AA AA GG
How do I get:
Sample_Name SNP Value
Sample 1 SNP1 AA
Sample 1 SNP2 AC
Sample 1 SNP3 GC
Sample 2 SNP1 GA
Sample 2 SNP2 AC
Sample 2 SNP3 CG
...
I'm a beginner and I've been trying to find a way to do this but none of the options I've tried have been successful. Thanks to anyone who could help!
Like this?
import pandas as pd
df = pd.DataFrame(
[["AA", "AC", "GC"], ["GA", "AC", "CG"], ["AA", "AA", "GG"]],
index=["Sample 1", "Sample 2", "Sample 3"],
columns=["SNP1", "SNP2", "SNP3"],
)
print(df.stack())
Output:
Sample 1 SNP1 AA
SNP2 AC
SNP3 GC
Sample 2 SNP1 GA
SNP2 AC
SNP3 CG
Sample 3 SNP1 AA
SNP2 AA
SNP3 GG
dtype: object
Once you have this object, how can you subset / filter to find, say, all samples with SNP1 'AA'?
For this task there is no need to convert it. You can use:
df.index[df['SNP1'].str.match('AA')].tolist()
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Minor point: You're unpivoting the data (going from wide-form to long-form), not pivoting it.