merge_cutup_clustering.py

Usage

The usage and help documentation of merge_cutup_clustering.py can be seen by running merge_cutup_clustering.py -h:

usage: - [-h] cutup_clustering_result

With contigs cutup with cut_up_fasta.py as input, sees to that the consequtive
parts of the original contigs are merged. prints result to stdout. @author:
alneberg

positional arguments:
  cutup_clustering_result
                        Input cutup clustering result.

optional arguments:
  -h, --help            show this help message and exit

Example

An example of how to run merge_cutup_clustering.py:

merge_cutup_clustering.py concoct_output/clustering_gt1000.csv > concoct_output/clustering_merged.csv

This merges the clustering clustering_gt1000.csv created by concoct by looking at cluster assignments per contig part and assigning a concensus cluster for the original contig. The output clustering_merged.csv contains a header line and contig_id and cluster_id per line, separated by a comma.