extract_fasta_bins.py¶
Usage¶
The usage and help documentation of extract_fasta_bins.py
can be seen by
running extract_fasta_bins.py -h
:
usage: - [-h] [--output_path OUTPUT_PATH] fasta_file cluster_file
extract_fasta_bins.py Extract a fasta file for each cluster from a concoct
result file.
positional arguments:
fasta_file Input Fasta file.
cluster_file Concoct output cluster file
optional arguments:
-h, --help show this help message and exit
--output_path OUTPUT_PATH
Directory where files will be printed
Example¶
An example of how to run extract_fasta_bins.py
:
mkdir concoct_output/fasta_bins
extract_fasta_bins.py original_contigs.fa concoct_output/clustering_merged.csv --output_path concoct_output/fasta_bins
This creates a fasta file for each cluster assigned by concoct. The clusters assigned need not to be complete or uncontaminated and should be investigated closer with e.g. CheckM.