scripts.lorelei package¶

scripts.lorelei.constrained_aore_lore_topologies module¶

Script that browses scorpios corrected tree forest to build constrained AORe and LORe tree topologies.

Example::
$ python -m scripts.lorelei.constrained_aore_lore_topologies TODO

scripts.lorelei.constrained_aore_lore_topologies.check_aore_consistent_tree(subtree, outgroups, dup_sp)¶

Checks that groups in synteny-consistent trees look correct and use them to build the AORe tree.

Parameters

subtree (ete3.subtree) – AORe tree
outgroups (list of str) – list of outgroup species
dup_sp (list of str) – list of duplicated species

Returns

a tuple containing:

tree (ete3.Tree): resulting gene tree, None if the tree is fishy

outgr_gene (str) : one outgroup gene name, to identify the tree, None if the tree is fishy

Return type

tuple

scripts.lorelei.constrained_aore_lore_topologies.check_copy_number(tree, ref_species, sp_min=3, copy_max=2, sp_min_2copies=0, copy_in_ref=None, groups=None)¶

Checks the number of gene copies in an input tree.

Parameters

tree (ete3.Tree) – input tree
ref_species (list of str) – list of outgroup species
sp_min (int) – minimal number of species in the tree
copy_max (int) – maximal number of gene copies for any species in tree
sp_min_2copies (int) – minimal number of species with 2 gene copies
copy_in_ref (int) – number of gene copies expected in ref species
groups (list of str) – groups of species, if provided, sp_min_2copies has to be verified for all groups.

Returns

True if criteria are met, False otherwise

Return type

bool

scripts.lorelei.constrained_aore_lore_topologies.extract_subtrees(tree, ali, target_species, ref_species, treedir, outali, olore, oaore, species_groups, restrict_sp=None)¶

For a full gene tree, extracts subtrees and builds AORe and LORe gene tree topologies for them. Writes aore and lore trees to file in nhx format and corresponding multiple alignement in fasta.

Parameters

tree (str) – tree file in nhx format for the considered gene family
ali (str) – alignment fasta file for the considered gene family
target_species (list of str) – duplicated+outgroup species
ref_species (list of str) – outgroup(s) species
treedir (str) – directory with SCORPiOs constrained gene tree topologies
outali (str) – output directory for the alignment
olore (str) – output directory for the lore topology (should exist)
oaore (str) – output directory for the aore topology (should exist)
species_groups (list of str) – groups of species for the LORe topology
restrict_sp (list of str, optional) – restrict the set of duplicated species to this set

scripts.lorelei.constrained_aore_lore_topologies.get_scorpios_aore_tree(gene_list, treefile, outgroups, outgr_gene)¶

Loads the AORe gene tree built by SCORPiOs.

Parameters

gene_list (dict) – dict of gene_names (key) : species_names (value) to keep in the tree
treefile (str) – name of the input tree file
outgroups (list of str) – list of outgroup species to keep/add in tree
outgr_gene (str) – name of the outgroup gene

Returns

the loaded tree

Return type

ete3.Tree

scripts.lorelei.constrained_aore_lore_topologies.get_species_groups(speciestree, dup_anc, outgroups, restrict_sp=None, groups_by_anc=None)¶

Get the 2 species groups diverging at a given speciation point (dup_anc) + 1 group of outgroup species.

Parameters

speciestree (str) – filename for the newick species tree
dup_anc (str) – speciation point to consider
outgroups (list of str) – list of outgroup species to include in the outgroup group.
restrict_sp (list of str, optional) –
groups_by_anc (str) – ancestral name for the two species groups to extract, comma separated (overrules the dup_anc arg).

Returns

the 3 groups of species

Return type

list of str

scripts.lorelei.constrained_aore_lore_topologies.make_tree_from_groups(subtree_leaves, species_groups, groups_are_genes=False)¶

Builds a gene tree from groups of species or groups of genes.

Parameters

subtree_leaves (list of ete3.nodes) – all genes to place in the tree
species_groups (list of str) – species to group together (first group is outgroup)
groups_are_genes (bool, optional) – set to True if species_groups are groups of genes

Returns

resulting gene tree str : one outgroup gene name, to identify the tree

Return type

ete3.Tree

scripts.lorelei.fix_rideogram module¶

Fix RIdeogram karyotype figure by adding a legend and title to it.

Example:

$ python -m scripts.lorelei.fix_rideograms -i fig.svg -o out.svg -l AORe LOre [-c 2] [-t '']

scripts.lorelei.fix_rideogram.add_legend(input_svg, legend_svg, outfile)¶

Create a new svg by putting one svg on top of another.

Parameters

input_svg (str) – name for first svg file
legend_svg (str) – name for second svg file (will be drawn on top of first)
outfile (list) – name for the output figure file

scripts.lorelei.fix_rideogram.make_legend(outfilename, title, colors, labels)¶

Plots to file a matplotlib figure with only legend and title.

Parameters

outfilename (str) – name for the output figure file
title (str) – title for the figure
colors (list) – ordered list of colors for the legend
labels (list) – ordered list of labels for the legend

scripts.lorelei.homeologs_pairs_from_ancestor module¶

Loads gene tree classes and group them by ancestrally duplicated chromsome pairs.

An ancestral karyotype or a non-duplicated outgroup can be used as a proxy to the ancestral pre-duplication genome.

Example:

$ python -m scripts.lorelei.homeologs_pairs_from_ancestor.py TODO

scripts.lorelei.homeologs_pairs_from_ancestor.load_acc(input_file)¶

Loads accepted correction.

Parameters: input_file (str) – path to the input file.
Returns: all family ids (outgroup gene name) for which correction was accepted
Return type: set

scripts.lorelei.homeologs_pairs_from_ancestor.load_combin(input_file, genes)¶

Loads family SCORPiOs family combination file (get family correspondance across multiple outgr)

Parameters

input_file (str) – path to the family combination file
genes (set) – list of the genes of the outgroup used as reference

Returns

genes in the reference outgroup to genes in the non-reference outgroups

Return type

dict

scripts.lorelei.homeologs_pairs_from_ancestor.load_outgr_fam(input_file, ctrees=None)¶

Loads SCORPiOs teleost families file.

Parameters

input_file (str) – path to the input file
ctrees (set, optional) – list of families to load, by default everything is loaded.

Returns

for each family, identified by the outgroup gene (key, str), teleost genes (value, set)

Return type

dict

scripts.lorelei.homeologs_pairs_from_ancestor.load_pm(input_file, is_post_dup=False)¶

Loads predicted homeolog names for teleosts gene families.

Parameters: input_file (str) – path to the input file (output from the paralogy_map pipeline)
Returns: for each gene family (key, a set of teleost genes) its corresponding homoelog chromosome (value).
Return type: dict

scripts.lorelei.homeologs_pairs_from_ancestor.load_summary(input_file, accepted)¶

Loads SCORPiOs summary of synteny-sequence trees inconsistencies.

Parameters

input_file (str) – path to the input file
accepted (str) – path to the file with accepted correction (inconsistent trees which have been corrected are now consistent)

Returns

for each outgroup gene family identifier (key, str) wheter trees and synteny predictions are consistent or inconsistent (value, str).

Return type

dict

scripts.lorelei.homeologs_pairs_from_ancestor.outgroup_genes_to_homeologs(fam_outgr, fam_homeo)¶

Combines teleost genes in SCORPiOs families and paralogy map result to assign SCORPiOs families to homeologs.

Parameters

fam_outgr (dict) – for each gene family (name of the outgroup gene, str, key) the set of genes (value)
fam_homeo (dict) – for each gene family (set of genes, set, key) its homeolog (value)

Returns

for each gene family (name of the outgroup gene, str, key), its homeolog (value)

Return type

dict

scripts.lorelei.homeologs_pairs_from_ancestor.write_counter(counter, output_file)¶

Writes a dict object to file

Parameters

counter (dict) – input dict
output_file (str) – name of the output file

scripts.lorelei.homeologs_pairs_from_ancestor.write_output(d_homeo, ctrees, output_all, output_incons)¶

Write numbers of trees per homeologs

Parameters

d_homeo (dict) – family to homeologs correspondance
ctrees (dict) – family to synteny-sequence conflicts
output_all (str) – output file to write all considered families
output_incons (str) – output file to write sequence-synteny inconsistent families

scripts.lorelei.homeologs_tree_conflicts module¶

Barplots and hypergeomtric tests.

Example:

$ python -m scripts.lorelei.homeologs_tree_conflicts TODO

scripts.lorelei.homeologs_tree_conflicts.barplot(data, output, title='', xlabel='', ylabel='', avg=None, avg_lab='', highlight_over='', highlight_under='', sign_all=False, sign_up_only=False, sign_down_only=False)¶

Plots data as a barplot and highlight significant enrichment and/or depletion. Saves the plot to file.

Parameters

data (tuple of lists) – categorical input data, with each tuple containing, category, proportion of observed counts, enrichment or depletion, whether null hyp. is rejected, and adjusted p-values.
output (str) – output file name for the figure
title (str, optional) – title for the plot
xlabel (str, optional) – label for the x axis
ylabel (str, optional) – label for the y axis
avg (float, optional) – average over bars, plot as a dashed-line if given
avg_lab (str, optional) – label to give to the average line
highlight_under (str, optional) – color for bars under average
highlight_over (str, optional) – color for bars over average
sign_all (bool, optional) – highlight significant enrichment & depletion with stars
sign_up_only (bool, optional) – highlight significant enrichment with stars
sign_down_only (bool, optional) – highlight significant depletion with stars

scripts.lorelei.homeologs_tree_conflicts.hypergeom_enrich_depl(data_obs, data_tot, alpha=0.05, multitest_adjust='fdr_bh')¶

Hypergeometric tests for enrichment and depletion with multiple testing correction.

Parameters

data_obs (dict) – for each category, observed counts
data_tot (dict) – for each category, total number of objects
alpha (float) – significance level
multitest_adjust (str) – method to adjust pvalues for multiple testing

Returns

categories, corresponding proportion of observed counts, enrichment or depletion, whether null hyp. is rejected, and adjusted p-values.

Return type

tuple of lists

scripts.lorelei.homeologs_tree_conflicts.load_counts(input_file)¶

Loads input data for hypergeom test: each line is a count category pair, space-separated.

Parameters: input_file (str) – path to the input file
Returns: for each category (chromosomes), as keys, the count (value)
Return type: dict

scripts.lorelei.homeologs_tree_conflicts.plot_sign(ax, to_highlight=None)¶

Adds star for significant p-val on an existing barplot.

Parameters

ax (matplotlib.Axes) – matplotlib figure (axis object) to update
to_highlight (list of int) – x values for significant bars

scripts.lorelei.make_rideograms_inputs module¶

Writes files that can be read by RIdeograms to draw karyotype with overlaid features.

Example:

$ python -m scripts.make_rideograms_inputs TODO

scripts.lorelei.make_rideograms_inputs.features_to_ide(genome, features_file, karyo, output, to_load=None)¶

Writes the gene to gene family class to file, to use as input to RIdeogram.

Parameters

genome (scripts.synteny.mygenome.Genome) – genome of the species for which to extract classes
features_file (str) – path to the input file with gene family classes
karyo (list) – ordered set of chromosome
output (str) – name for the output file
to_load (list, optional) – load only genes of given classes

scripts.lorelei.make_rideograms_inputs.load_features(genome, features_file, to_load=None)¶

Loads a 3-columns tab-delimited file with gene_family_name, genes and gene_family class.

Parameters

genome (scripts.synteny.mygenome.Genome) – genome of the species for which to extract classes
features_file (str) – path to the input file with gene family classes
to_load (list, optional) – load only genes of given classes

Returns

for genes in the input genome (key) gives the gene family class (value)

Return type

dict

scripts.lorelei.make_rideograms_inputs.make_karyo(genesfile, output, fomt='bed', min_size=None)¶

Makes a karyotype file for drawing with RIdeograms from a bed file with genes coordinates.

Parameters

genesfile (str) – input file with genes coordinates
output (str) – output file name
fomt (str, optional) – input format .bed or dyogen format

Returns

a tuple containing:

genome (scripts.synteny.mygenome.Genome): genome of the species for which to extract classes

karyo (list): ordered set of chromosomes.

Return type

tuple

scripts.lorelei.make_rideograms_inputs.strip_chr_name(chr_name)¶

Tries to strip a chr name so that it can be converted to int for RIdeograms.

Parameters: chr_name (str) – chr name
Returns: stripped chr name
Return type: str

scripts.lorelei.write_ancgenes_treeclass module¶

Writes a 3-columns file for gene families, giving family_id, genes in the family and its class. Class can be for instance LORe or AORe, tree clustering, synteny consistency etc…

Example:

$ python -m scripts.lorelei.write_ancgenes_treeclust TODO

scripts.lorelei.write_ancgenes_treeclass.load_gene_list(input_summary, input_acc=None)¶

Loads a tab-delimited summary of tree classes.

Parameters

input_summary (str) – path to the two-columns tab-delimited input file, giving a family_id to tree class correspondance. The family_id should be the name of the corresponding tree file for write_ancgenes to work properly.
input_acc (str, optional) – if input is SCORPiOs-generated sequence-synteny inconsistent trees summary, provide here the summary of accepted correction. Indeed, gene trees that were initially found to be synteny-inconsistent but were later corrected should be defined as consistent.

Returns

for each gene family, the corresponding gene tree class

Return type

dict

scripts.lorelei.write_ancgenes_treeclass.write_ancgenes(clustered_genes, treedir, out_ancgenes, clusters_to_load=None)¶

Writes the output 3-columns file, tab-separated.

Parameters

clustered_genes (dict) – class of gene families
treedir (str) – path to the gene trees
out_ancgenes (str) – name of the output file
clusters_to_load (list, optional) – write only entries for these given family classes.

scripts.lorelei.write_ancgenes_treeclass.write_summary(summary_dict, output_file)¶

Writes a simpler 2-columns file with family_id and family class.

Parameters

summary_dict (dict) – class of gene families
output_file (str) – name of the output file