I have two text-files containing the abundances of genes in samples. However, one of the files measures the abundance of a greater variety of genes than the other, and therefore cannot be completely concatenated. Thus, I'm trying to concatenate the lines from the larger file that share an identical gene index as lines from the smaller file, such that:
>df1
Sample1 Sample2 Sample3
Gene1 0.001 0.002 0.003
Gene2 0.001 0.002 0.003
Gene3 0.001 0.002 0.003
>df2
Sample4 Sample5 Sample6
Gene1 0.001 0.002 0.003
Gene1.1 0.001 0.002 0.003
Gene2 0.001 0.002 0.003
Gene2.1 0.001 0.002 0.003
Gene3 0.001 0.002 0.003
>df1and2
Sample1 Sample2 Sample3 Sample4 Sample5 Sample6
Gene1 0.001 0.002 0.003. 0.001 0.002 0.003
Gene2 0.001 0.002 0.003 0.001 0.002 0.003
Gene3 0.001 0.002 0.003 0.001 0.002 0.003
Suggestions in Python or Bash are both welcome. Thank you!
•
written
by
Hau Tak Leighton •
In general this is called an inner join, which is easy using the pandas library in Python.
import pandas as pd
df1and2 = df1.merge(df2, how='inner', left_index=True, right_index=True)
Thanks for your response! However, when I tried it with my text files, I get an error stating: AttributeError: 'str' object has no attribute 'merge', even though they are in a very similar format to my example. What could be causing this problem?
'str' object has no attribute 'merge'
It appears you are trying to merge file names rather than dataframes. You have to read in those files first such that dataframes are named df1 and df2 and then it should work.
Thanks for your advice!
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I've removed tags such as
genetics,genesandbioinformatics. The last tag makes no sense - EVERY QUESTION here is related to bioinformatics.