Normalizing Tree Support Values From [0-1] To [0-100]
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7.2 years ago
Pappu ★ 1.9k

I am trying to convert the tree support values like 0.555 to 55 in the tree file. For example:

(sp|P56726|SMO_MOUSE:0.00978,sp|P97698|SMO_RAT:0.00708,(sp|Q99835|SMO_HUMAN:0.03115,(sp|O42224|SMO_CHICK:0.13084,(sp|P91682|SMO_DROME:1.27659,(tr|Q90YY4|Q90YY4_DANRE:0.00055,tr|Q90X26|Q90X26_DANRE:0.00254)0.997:0.17060)0.982:0.11965)1.000:0.12313)0.990:0.03506);

0.99 will change to 99

(sp|P56726|SMO_MOUSE:0.00978,sp|P97698|SMO_RAT:0.00708,(sp|Q99835|SMO_HUMAN:0.03115,(sp|O42224|SMO_CHICK:0.13084,(sp|P91682|SMO_DROME:1.27659,(tr|Q90YY4|Q90YY4_DANRE:0.00055,tr|Q90X26|Q90X26_DANRE:0.00254)99:0.17060)0.982:0.11965)1.000:0.12313)99:0.03506);

Could you tell me about a good regular expression or software to do it?

Thanks.

python • 1.9k views
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8
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7.2 years ago

Here you go:

from ete2 import Tree

pappu_tree = "(sp|P56726|SMO_MOUSE:0.00978,sp|P97698|SMO_RAT:0.00708,(sp|Q99835|SMO_HUMAN:0.03115,(sp|O42224|SMO_CHICK:0.13084,(sp|P91682|SMO_DROME:1.27659,(tr|Q90YY4|Q90YY4_DANRE:0.00055,tr|Q90X26|Q90X26_DANRE:0.00254)0.997:0.17060)0.982:0.11965)1.000:0.12313)0.990:0.03506);"

t = Tree(pappu_tree)

for node in t.traverse():
    node.support *= 100.0

print t.write()

It will give you:

(sp|P56726|SMO_MOUSE:0.00978,sp|P97698|SMO_RAT:0.00708,(sp|Q99835|SMO_HUMAN:0.03115,(sp|O42224|SMO_CHICK:0.13084,(sp|P91682|SMO_DROME:1.27659,(tr|Q90YY4|Q90YY4_DANRE:0.00055,tr|Q90X26|Q90X26_DANRE:0.00254)99.7:0.1706)98.2:0.11965)100:0.12313)99:0.03506);
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1
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note that you don't need to use the internal _set_support() function. float conversion occurs transparently if you just use the 'node.support *= 100.0' syntax

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You're right. I updated my answer.

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