Enveomics collection

A toolbox for microbial genomics and metagenomics

AAsubs.log2ratio.rb

Estimates the log2-ratio of different amino acids in homologous sites using an AAsubs file (see BlastPairwise.AAsubs.pl). It provides the point estimation (.obs file), the bootstrap of the estimation (.boot file) and the null model based on label-permutation (.null file).

    See source code, Artistic license 2.0.

§ References

    Konstantinidis et al, 2009, AEM; Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

AAsubs.log2ratio.rb --input in_file [opts]

§ Arguments

Input*
 --input in_file  Input file in AAsubs format. It's a tab-delimited table where each line corresponds to a substitution, the first column corresponds to the compared protein IDs, the second and third columns correspond to the AA on each protein, and the fourth column indicates the length of the protein (not used by this script.
Obs file
 --obs-file out_file  Output file with the log2-ratios per amino acid. By default, 'Input value'.obs.
Bootstrap file
 --bootstrap-file out_file  Output file with the bootstrap results of log2-ratios per amino acid. By default, 'Input value'.boot.
Null file
 --null-file out_file  Output file with the permutation results of log2-ratios per amino acid. By default, 'Input value'.null.
Overwrite
 --overwrite   Overwrite existing files. By default, skip steps if the files already exist.
Bootstraps
 --bootstraps integer  Number of bootstraps to run.
Permutations
 --permutations integer  Number of permutations to run.
Quiet
 --quiet   Run quietly (no STDERR output).
* Mandatory.