Running CM construction

Quick Start

python nc_coreset.py -p <parameters.yaml> -n <mirnas.tsv> -o <outdir>

Full help text:

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usage: coreset.py [-h] -p <path> -n <path> -o <path> [--threads [int]] [--mgi [int]] [--dust [yes/no]] [--create_model [yes/no]] [--idtype [str]]

Build Covariance models of reference miRNAs from core set of orthologs.

Required Arguments:
  -p <path>, --parameters <path>
                        Path to the parameters file in yaml format
  -n <path>, --ncrna <path>
                        Path to tab separated file of reference miRNAs information
  -o <path>, --output <path>
                        Path for the output folder

Optional Arguments:
  --threads [int]       Number of CPU cores to use (Default: All available)
  --mgi [int]           Maximum number of gene insertions in the core species (Default: 3)
  --dust [yes/no]       Use BLASTn dust filter. Will not build models from repeat regions. (Default: yes)
  --create_model [yes/no]
                        set to "no" if you only want to create the alignment. (Default: yes)
  --idtype [str]        Choose the ID in the reference gff file that is compared to the IDs in the pairwise orthologs file (default:ID) Options: ID, Name, GeneID, gene_id