Add number of dereplicated genomes to output of - dRep dereplicate

[paulzierep]

For MAGs it would be useful to know how many genomes were dereplicated for the representative genomes, since multiple occurrences of a similar genome would increase the probability of the MAG being biologically correct and not an artificial construct.
Could you maybe add the genome count to the output. Even better would be if you could add the names of all other genomes that were collapsed into the dereplicated set.

[MrOlm]

Thanks for the suggestion! You can already get this information pretty easily from the Cdb.csv file that dRep outputs. Here's a simple way to do it:

If you want to find, for each secondary cluster, how many genomes were collapsed together and what their names are
you can run the following in Python:

import pandas as pd

# Load the Cdb.csv file
df = pd.read_csv('~/Programs/drep/tests/test_solutions/ecoli_wd/data_tables/Cdb.csv')

# Group by secondary cluster
grouped = df.groupby('secondary_cluster')['genome'].apply(list).reset_index()

# Add genome count
grouped['genome_count'] = grouped['genome'].apply(len)

# Print the output
for idx, row in grouped.iterrows():
    print(f"Secondary Cluster {row['secondary_cluster']}:")
    print(f"  Genome count: {row['genome_count']}")
    print(f"  Genomes: {', '.join(row['genome'])}")
    print()

Example output:

Secondary Cluster 1_1:
  Genome count: 2
  Genomes: Enterococcus_faecalis_T2.fna, Enterococcus_faecalis_YI6-1.fna

Secondary Cluster 1_2:
  Genome count: 1
  Genomes: Enterococcus_faecalis_TX0104.fa

Secondary Cluster 2_0:
  Genome count: 1
  Genomes: Enterococcus_casseliflavus_EC20.fasta

Secondary Cluster 3_0:
  Genome count: 1
  Genomes: Escherichia_coli_Sakai.fna

If you prefer a quick one-liner from the command line (no Python needed), you can also do:

awk -F, 'NR>1 {a[$2]=a[$2]","$1} END {for (i in a) print i, gsub(",", "&", a[i])+1, a[i]}' ~/Programs/drep/tests/test_solutions/ecoli_wd/data_tables/Cdb.csv

Let me know if you have any questions.

Best,
Matt