4.1.4. dist_all_pairs.py¶
Compute the scaled distance using all pairs of orthologs (the “standard way”). The result is one distance matrix for a full dataset.
The mode argument define what kind of value we want to keep while computing the distance:
- intersection: only the values present in all species are kept.
- atLeastTwo: keep the values present in at least two species.
- union: keep all values.
Note
It is intended to be used instead of dist_pairs_indep.py and bootstrap.py.
| created: | August 2019 |
|---|---|
| last modified: | August 2019 |
4.1.4.1. Usage¶
Compute the distance matrix using all pairs of genes.
usage: dist_all_pairs [-h] [-m {intersection,atLeastTwo,union}] [-p] [-v]
orthos outfile values [values ...]
4.1.4.1.1. Positional Arguments¶
| orthos | all the orthos, in TSV |
| outfile | the matrix filename |
| values | the values files, in (Gzipped) TSV |
4.1.4.1.2. Named Arguments¶
| -m, --mode | Possible choices: intersection, atLeastTwo, union the mode, that is, the kind of values we want to keep while computing the distance Default: “intersection” |
| -p, --progress | print a progress bar; need tqdm to be installed Default: False |
| -v, --verbose | be verbose Default: False |