Robert C. Edgar has developed a great program Usearch (https://drive5.com/usearch/download.html) However, the 32 bit version has limitations, the 64 bit version costs almost $ 1500 (
usearch -otutab_merge otutable1.txt,otutable2.txt,otutable3.txt -output otutable_merged.txt
This command is able to combine OTU tables. But due to the large amount of data, the 32-bit version cannot do this.
What does this command do? Here's an example
Table1
Sample 1
species1 0
species2 3
Table2
Sample 2
species1 1
species3 2
Output tab-delimited table
Sample1 Samlpe2
species1 0 1
species2 3 0
species3 0 2
Can you please tell me if there are analogs without limitation? I'm sure that python can do this, but maybe there are ready-made solutions.
1 answer
I wrote a simple and not elegant script (for 8 samples), maybe it will help someone.
$python3
import pandas as pd
import numpy as np
df1 = pd.read_csv("BVP1.txt", sep='\t')
df2 = pd.read_csv("BVP2.txt", sep='\t')
df3 = pd.read_csv("BVP3.txt", sep='\t')
df4 = pd.read_csv("BVP4.txt", sep='\t')
df5 = pd.read_csv("BVP5.txt", sep='\t')
df6 = pd.read_csv("BVP6.txt", sep='\t')
df7 = pd.read_csv("BVP7.txt", sep='\t')
df8 = pd.read_csv("BVP8.txt", sep='\t')
Mergedf = pd.merge(df1, df2, how = 'outer')
Mergedf2 = pd.merge(Mergedf, df3, how = 'outer')
Mergedf3 = pd.merge(Mergedf2, df4, how = 'outer')
Mergedf4 = pd.merge(Mergedf3, df5, how = 'outer')
Mergedf5 = pd.merge(Mergedf4, df6, how = 'outer')
Mergedf6 = pd.merge(Mergedf5, df7, how = 'outer')
Mergedf7 = pd.merge(Mergedf6, df8, how = 'outer')
Mergedf7.to_csv('Merged_BVP.txt', sep ='\t')
Log in to answer this question.
Hi,
Did you hear about
vsearch? (please see the link)As it appears stated in the github repository:
Although I don't know if the tool has the command that you're looking for. I was looking into their workflow in their wiki and I think they processed the samples in a slightly different way.
In any case, you may consider using this tool in the future, since it is open source and the 64-bit is free.
I hope this helps,
António
Many thanks, António for the answer!
I looked at the output of --help and did not find a similar command usearch -otutab_merge