subtree corresponding to ev.etype

[Arun Prasanna]

Hello,

I tried to extract the orthologs and paralogs based on get_my_evol_events(). One of my speciation node (#7, for example), i.e one inferred as ev.etype =="S" contains a paralog in a deeper node. The out_seq generates a list that includes all the species of node #7. Instead, is there a way to extract corresponding subtree of node #7 and further process it for split by duplication ?. Can anyone suggest a way to achieve this ?

Thanks in advance.

Arun

[Jaime Huerta Cepas]

yes, you can process the node labeled as "S" as a separate tree. For instance, you could use "node_7.write()" or "for descendant in node_7.traverse()"

Every node in a tree is another tree. 

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[Arun Prasanna]

Hi,

"for descendant in node_7.traverse():" It does return the corresponding subtree. But when I further want to process it "for get_my_evol_events"  to mark for duplication, I get error with node must have more than 1 child. I am still unable to detect deep paralog. 

For more clarity, please find attached an image, where I was able to obtain the circled subtree as an "S" type through "get_my_evol_events". However, it has a deep paralog. I intend to leave out one of them and pick the node with more species (leave out 850, retain 557, 7147) which is more of a python problem. 

for ev in events:
    if ev.etype == "S":
        print 'ORTHOLOGY RELATIONSHIP:', ','.join(ev.out_seqs)
        for descendant in ev.node.traverse():
            print "descendant is:", descendant      
            subevent = descendant.get_my_evol_events()
            for subev in subevent:
                if subev.etype =="D":
                      print "Deep Paralog event:", ','.join(subev.in_seqs), "<==>", ','.join(subev.out_seqs)

What is the reason for error? Please give your suggestions.

Thanks,

Arun

On Monday, September 12, 2016 at 10:40:03 AM UTC+2, Jaime wrote:

yes, you can process the node labeled as "S" as a separate tree. For instance, you could use "node_7.write()" or "for descendant in node_7.traverse()"

Every node in a tree is another tree. 

On 10 September 2016 at 14:12, Arun Prasanna <arunpra...@gmail.com> wrote:

Hello,

I tried to extract the orthologs and paralogs based on get_my_evol_events(). One of my speciation node (#7, for example), i.e one inferred as ev.etype =="S" contains a paralog in a deeper node. The out_seq generates a list that includes all the species of node #7. Instead, is there a way to extract corresponding subtree of node #7 and further process it for split by duplication ?. Can anyone suggest a way to achieve this ?

Thanks in advance.

Arun

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[Jaime Huerta Cepas]

Hi Arun, 

the deep paralogy relationship shown in your image (Ompol1->Cylto1) does not look as a paralogy to me. I would call it a many-to-one orthology relationship.

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