Hi, I was doing some associations using gene abundance data from humann2 output, and got top results with hundreds of gene entries. By mapping them back to uniprot, I get the information on which species it come from and proteins they encode. Is there a way to clump all gene entries that encode the same proteins together? --for better annotation of the result.
A example of 4 gene entries from different organisms all encode for HTH cro/C1-type domain-containing protein. Thanks!
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xinyuanzhang22 •
If you have the 'Protein names' and 'Organism' columns in one table you can use Pandas.
df.groupby('Protein names')['Organism'].agg(lambda col: ','.join(col)).reset_index()
For this table:
class order
bird Falconiformes
bird Psittaciformes
mammal Carnivora
mammal Primates
mammal Carnivora
You will get something like this:
class order
bird Falconiformes,Psittaciformes
mammal Carnivora,Primates,Carnivora
Hi Thanks! Just that the protein names are usually not exactly the same, so it's a bit hard to do it for all proteins...
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