diff options
Diffstat (limited to 'examples/phylogenies/tree_reconciliation.py')
| -rw-r--r-- | examples/phylogenies/tree_reconciliation.py | 10 |
1 files changed, 5 insertions, 5 deletions
diff --git a/examples/phylogenies/tree_reconciliation.py b/examples/phylogenies/tree_reconciliation.py index 58122ec..e24f162 100644 --- a/examples/phylogenies/tree_reconciliation.py +++ b/examples/phylogenies/tree_reconciliation.py @@ -7,7 +7,7 @@ gene_tree_nw = '((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu_00 species_tree_nw = "((((Hsa, Ptr), Mmu), (Mms, Cfa)), Dme);" genetree = PhyloTree(gene_tree_nw) sptree = PhyloTree(species_tree_nw) -print genetree +print(genetree) # /-Dme_001 # /--------| # | \-Dme_002 @@ -32,14 +32,14 @@ print genetree recon_tree, events = genetree.reconcile(sptree) # a new "reconcilied tree" is returned. As well as the list of # inferred events. -print "Orthology and Paralogy relationships:" +print("Orthology and Paralogy relationships:") for ev in events: if ev.etype == "S": - print 'ORTHOLOGY RELATIONSHIP:', ','.join(ev.inparalogs), "<====>", ','.join(ev.orthologs) + print('ORTHOLOGY RELATIONSHIP:', ','.join(ev.inparalogs), "<====>", ','.join(ev.orthologs)) elif ev.etype == "D": - print 'PARALOGY RELATIONSHIP:', ','.join(ev.inparalogs), "<====>", ','.join(ev.outparalogs) + print('PARALOGY RELATIONSHIP:', ','.join(ev.inparalogs), "<====>", ','.join(ev.outparalogs)) # And we can explore the resulting reconciled tree -print recon_tree +print(recon_tree) # You will notice how the reconcilied tree is the same as the gene # tree with some added branches. They are inferred gene losses. # |