4.2.4. iolib

This module contains functions that parses tabular files used to store orthologs or pair values, and to format output such as making PHYLIP matrices.

created:June 2018
last modified:August 2019
iolib.phylip(species, distances)

Make the distance matrix for the wanted species in PHYLIP format. The resulting matrix is returned as a single string object.

Warning

If not all species are present in distances, a KeyError exception is raised.

iolib.read_orthos(name)

Read the orthologs from a TSV file and return a set of the orthologs names (from all species) and a mapping of the ortholog names to their orthology group.

The orthologs file is described in the documentation.

iolib.read_values(orthos, groups, sp_left, sp_right, name)

Read the value file at name and return a dict of dict of group ids to species name to Hi-C value.

The values file is described in the documentation.

Note

Extract only the values where all four genes are present in orthos.