VirtualMicrobes.post_analysis package¶
Submodules¶
VirtualMicrobes.post_analysis.lod module¶
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
- tf_connections (list of
-
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.
- 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: - gene (
-
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 :
- Reference individual for which to find homologs
- cell2 :
- 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.
virtual_cell.Cell.Cell
virtual_cell.Cell.Cell
Returns: Mapping from virtual_cell.Gene.TranscriptionFactor
to (maximum) binding overlap score.Return type: dict