User: roussine
roussine • 10
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Posts by roussine
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Comment:
C: Newick trees analysis software
... Thank you indeed for valuable help. -- It all just works. ...
written 10 months ago by
roussine • 10
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Comment:
C: Newick trees analysis software
... Thank you - while I was fiddling with data, python3 returns:
Traceback (most recent call last):
File "br_lens+n_supp.py", line 1, in
from ete3 import Tree
ImportError: No module named 'ete3'
ete3 is installed however at /usr/local/bin/ete3
Please let me know what am I missi ...
written 10 months ago by
roussine • 10
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Comment:
C: Newick trees analysis software
... It's Python 3.4.3 (default, Nov 12 2018, 22:25:49) on BioLinix 8.
And yes - there is an arrow:
print(f'Tree = {sys.argv[1]}')
^
The code above doesn't show correctly: the arrow points to the last single quotation. ...
written 10 months ago by
roussine • 10
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Comment:
C: Newick trees analysis software
... Dear jrj.healey - great thanks for assistance and getting into this.
I tried the script, python returns this:
SyntaxError: invalid syntax
$ python3 br_lens+n_supp.py tree.tre [ 3:21PM]
File "br_lens+n_supp.py", line 6
print(f'Tree = {sys.argv[1]}')
Might be ve ...
written 10 months ago by
roussine • 10
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Comment:
C: Newick trees analysis software
... Ok, example in-outs are like this.
Input would be a standard newick:
((logi|XP_009052348.1:0.30900,(dapu|EFX67985.1:0.40918,dare|NP_001007771.1:0.18921)0.580:0.08422)0.826:0.09733,cate|ELT98251.1:0.29370,(lian|XP_013420576.1:0.18354,((ocbi|XP_014783723.1:0.22136,(neve|XP_001634838.1:1.09355,(s ...
written 10 months ago by
roussine • 10
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Comment:
C: Newick trees analysis software
... Dear jrj.healey – my need for this case is rather simple: to basically parse newick and extract numerical values of branch lengths and node support. I will then do basic statistics to assess trees and bin them further. This is a constitutive step of our phylogenomic approach to analyse orthology gro ...
written 10 months ago by
roussine • 10
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Comment:
C: Newick trees analysis software
... Michael – thanks indeed for your involvement. I will go through your suggestions in nearest time. ...
written 10 months ago by
roussine • 10
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2
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472
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Comment:
C: Newick trees analysis software
... Michael – thanks for your response.
The need is just a text output per each text tree: all branch lengths (or average), all node supports (or average). The values not need be in one file. Extracting these values from trees is now the step that would require ad hoc scripting if a nice pipelinable sof ...
written 10 months ago by
roussine • 10
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... Hello everyone-
please take a min to answer in case you might know. My need is to output basic parameters of text newick trees: branch lengths and node supports (all possibly with average values or other basic statistics, but it is not a priority). Is there a nice pipelinable soft around to do so? ...
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... Alex - thanx indeed for this advice ...
written 23 months ago by
roussine • 10
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