def validate_tree(tree_path, msa_path):
''' Tries to validate that the tree contains unique ids, that those ids exist in the MSA, and finally,
it links each leaf to its msa row.'''
# holds the link between the leaf accession and the row in that msa
leaf_information = {}
# first load the tree
tree = TreeNode(newick=tree_path, format=0)
# also load in the MSA
msa = AlignIO.read(msa_path,'fasta')
# next go through all of the leaves
for leaf in tree.get_leaves():
found = False
for alignment_row in msa:
if leaf.name in alignment_row.description:
if leaf.name not in leaf_information:
leaf_information[leaf.name] = alignment_row
found = True
break
else:
raise Exception("%s is found in the tree/MSA twice, accessions must be unique" % (leaf.name))
if not found:
raise Exception("%s is in the tree but not found in the MSA" % (leaf.name))
return (tree, msa, leaf_information)
elif arg.startswith("--paralogs="):
pz = arg.split("=")
paralogsStr = pz[1]
elif not arg.startswith('-'):
if graphfile1 == '':
graphfile1 = arg
elif graphfile2 == '':
graphfile2 = arg
# Map each species name to a leaf. This avoids using search_nodes, which is slow
# speciesTree is used in every mode, so we build it right here right now
speciesTree = None
if speciesTreeStr != '':
speciesTree = TreeNode(speciesTreeStr)
speciesLeavesList = speciesTree.get_leaves()
speciesLeaves = {}
for leaf in speciesLeavesList:
speciesLeaves[leaf.name] = leaf
class ConstraintGraph:
""" Given a set of genes, and and two set of tuples that represent orthology and paralogy relationships between genes,
builds a graph of orthologies, and a graph of paralogies. It then becomes possible to build a DS-tree that satisifies
all these constraints (or detect that it can't be done).
"""
def __init__(self, genes, orthology_relations, paralogy_relations, speciesTree = None, geneSpeciesMapping = None, treelessGeneSpeciesMapping = None):
"""Constructor. The 2 graphs are built here, as adjacency lists (self.orthologs and self.paralogs, two dicts with key = gene-string, value = neighbors as a set of gene-strings).
