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hillerlab / REforge

Regulatory Element Forward Genomics to associate transcription factor binding site divergence in regulatory elements with phenotypic differences between species
MIT License
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How to get element sequences from ancestral node #9

Open aaannaw opened 1 week ago

aaannaw commented 1 week ago

Dear author, I noticed the element_sequences/el137_10000.fa file in the example directory include sequences in the ancestral node. However, I can not know how to get the sequences in the ancestral node, which are necessary?

I try to delete the labels for ancestral nodes in the tree_simulation.nwk file (Cgu,(((Tsw,Pty),Hcr),(Hgl,((Gca,Bsu),(Cho,(Fme,(Fda,(Fdm,(Fan,Fmi)))))))));. However I got the error:

Traceback (most recent call last):
  File "/home/REforge-master/REforge_branch_scoring.py", line 172, in <module>
    sys.exit(__score_branches())
  File "/home/REforge-master/REforge_branch_scoring.py", line 165, in __score_branches
    anc0filter=not args.no_ancestral_filter)
  File "/home/REforge-master/REforge_branch_scoring.py", line 69, in traverse_tree
    sequence = str(sequences[parent.name].seq).replace("-", "")
KeyError: 'Cgu-Tsw'

Could you give me any suggestions? Best wishes! Na Wan

aaannaw commented 1 week ago

Hi, I used PRANK to generate the ancestral sequences. However, I found for some CNE sequences and some branches, the stubb score can not be calculated. Why? Could you give me any explanation for the output?