VirtualMicrobes.post_analysis package

Submodules

VirtualMicrobes.post_analysis.lod module

VirtualMicrobes.post_analysis.network_funcs module

Created on Feb 18, 2016

@author: thocu

VirtualMicrobes.post_analysis.network_funcs.prune_GRN(grn, log_dif_effect=0.5, rescue_regulated=True, iterative=True)[source]

VirtualMicrobes.post_analysis.network_properties module

Created on Feb 9, 2016

@author: thocu

class VirtualMicrobes.post_analysis.network_properties.PhyloGeneticAnalysis[source]

Bases: object

Analyze biological networks

VirtualMicrobes.post_analysis.network_properties.calculate_overlap(tf_connections, connections_of_homologous_tfs, closest_bound_homologs_dict)[source]

Calculate the overlap in bound genes between tf homologs.

Parameters:
  • tf_connections (list of virtual_cell.Gene.Gene) – Downstream connections of the reference TF
  • connections_of_homologous_tfs (list of sets of :class:`virtual_cell.Gene.Gene`s) – List of sets of downstream genes for each homolog of the reference TF
  • closest_bound_homologs_dict (dict of sets of :class:`virtual_cell.Gene.Gene`s) – Mapping of each original downstream gene of the reference TF to sets of homologs of these downstream genes.
Returns:

Tuple of fractions: [0]: Fraction of downstream genes who’s homologs are bound by a homolog of the reference TF. [1]: Fraction of new connections (averaged over tf homologs) per original connection of the reference TF.
Return type:

float,float
VirtualMicrobes.post_analysis.network_properties.find_homolog_distances(gene, genome, closest_homolog=False)[source]

Find homologs and their distance for a gene in a target genome.

Parameters:
  • gene (virtual_cell.GenomicElement.GenomicElement) – Reference gene for homology search.
  • genome (virtual_cell.Genome.Genome) – Genome in which to search for homologs.
  • closest_homolog (bool) – Flag to filter found homologs to those that have the shortest phylogenetic distance to the gene.
VirtualMicrobes.post_analysis.network_properties.find_homologs(gene, genome)[source]

For a gene, find all its homologs in a given genome.

This is a naive approach that uses a combination of the gene’s type and its virtual_cell.Identifier.Identifier attribute to detect common descent.

Parameters:
  • gene (virtual_cell.GenomicElement.GenomicElement) – Reference gene for homology search.
  • genome (virtual_cell.Genome.Genome) – Genome in which to search for homologs.
Returns:

The set of homologs of gene in the genome.
Return type:

set
VirtualMicrobes.post_analysis.network_properties.tf_binding_overlap(cell1, cell2, closest_homolog=False, no_phylogeny=False, verbose=False)[source]

Measure the overlap in target genes for tf homologs in phylogenetically related individuals.

cell1
: virtual_cell.Cell.Cell
Reference individual for which to find homologs
cell2
: virtual_cell.Cell.Cell
Homologs of TFs and downstream targets will be detected in this individual.
closest_homolog
: bool
Flag to filter found homologs to those that have the shortest phylogenetic distance to the gene.
verbose
: bool
Print messages about homologs found.
Returns:Mapping from virtual_cell.Gene.TranscriptionFactor to (maximum) binding overlap score.
Return type:dict

Module contents