random_resampler.py

Construct supermatrices from randomly sampled genes.

random_resampler.py [OPTIONS] -i <input_directory>

Required arguments:

• -i, --input <input_dir> Path to input directory containing gene files in fasta format

Optional arguments:

• -if, --in_format <format> Format of the input single gene alignments
  • Options: fasta, phylip (names truncated at 10 characters), phylip-relaxed (names are not truncated), or nexus
  • Default: fasta
• -of, --out_format <format> Desired format of the output steps
  • Options: fasta, nexus, phylip (names truncated at 10 characters), or phylip-relaxed (names are not truncated)
  • Default: fasta
• -ci, --confidence_interval <0.N> Confidence interval to use to calculate the number of replicates required
  • Default: 0.95
• -ps, --percent_sampling <N> Percent sampling step size
  • Default: 20
  • The default 20% sampling results in a sampling series of 20%, 40%, 60%, and 80%
• -o, --output <out_dir> Path to user-defined output directory
  • Default: ./random_sample_iteration_out_<M.D.Y>_ps<percentage increment>_ci<confidence interval>
• -p, --prefix <prefix> Prefix of input files
  • Default: NONE
  • Example: path/to/input/prefix*
• -s, --suffix <suffix> Suffix of input files
  • Default: NONE
  • Example: path/to/input/*suffix
• -h, --help Show this help message and exit

Default random_resampler.py output:

• a directory ./random_resampler_out_<M.D.Y>ps<percentage> that contains:
  • a set of supermatrices made from the randomly sampled genes. Each matrix has a file name structured in the following way: <percentage of genes from total sampled>rep<replicate number>.<fas|phy|nex>
  • a set of files <percentage of genes from total sampled>_Percent.tsv where column headers correspond to replicate matrices created and the rows below are genes within a particular replicate matrix.
  • a set of files <percentage of genes from total sampled>_Percent.tgz that contain all replicates for the respective increment and the corresponding .tsv file.