cafetutorial_report_analysis.py error #62
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Hello,
I believe you're seeing this error because one or more of the internal
nodes in your input tree has labels. To know for certain, I would need to
see your input tree. While CAFE itself can handle these internal labels,
unfortunately this version of the report_analysis script cannot.
To fix, either remove the internal labels from your input tree and re-run
CAFE, or just do a find/replace of the labels in the report file to replace
it with an empty string.
Hope that helps!
-Gregg
…On Fri, Jul 12, 2019 at 2:23 AM haojingshao ***@***.***> wrote:
Hi Hahn,
I have some problems running the tutorial scripts
(cafetutorial_report_analysis.py).
python python_scripts/cafetutorial_report_analysis.py -i
reports/report_run1.cafe -o summary
CAFE Report File Analysis
07.12.2019 | 04:15:26
------------------------------
Parsing format information...
Traceback (most recent call last):
File "python_scripts/cafetutorial_report_analysis.py", line 321, in
tinfo, newtree = cafecore.treeParseNew(labeled_tree,2);
File "/Users/uqhshao/Downloads/cafe_tutorial/python_scripts/cafecore.py",
line 195, in treeParseNew
if new_tree[-1] == ")":
IndexError: string index out of range
AND
python python_scripts/cafetutorial_report_analysis.py -i report.txt.cafe
-o summary
CAFE Report File Analysis
07.12.2019 | 04:15:13
------------------------------
Parsing format information...
------------------------------
Initializing output structures...
------------------------------
Counting changes per branch...
[*-------------------------------------------------] 0.067%
complete.Traceback (most recent call last):
File "python_scripts/cafetutorial_report_analysis.py", line 371, in
results_main, node_fams_main = cra(inlines_main, results_main,
node_fams_main, linestart_main, ancfilename, sorted_nodes, 1);
File "python_scripts/cafetutorial_report_analysis.py", line 192, in cra
curcount = int(tlinfo[tlnode][4]);
ValueError: invalid literal for int() with base 10: '5.8_11'
Do
report.txt.cafe.txt
<https://github.com/hahnlab/CAFE/files/3385208/report.txt.cafe.txt>
you have some ideas about this error?
Thanks,
Haojing
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Hello,
The report analysis script should be included in the tutorial files here:
https://hahnlab.github.io/CAFE/manual.html
Click on the 'Tutorial files' link to download.
Let me know if you still can't find it.
-Gregg
…On Sat, Jul 13, 2019 at 4:17 AM Lordhooze ***@***.***> wrote:
hi,
I am new to CAFE
would you please tell me where is the python script
"cafetutorial_report_analysis.py"
I can not find it
many thanks
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Hi,
Please see
#47
regards,
HJ
Lordhooze <notifications@github.com> 于2019年7月13日周六 下午6:17写道：
… hi,
I am new to CAFE
would you please tell me where is the python script
"cafetutorial_report_analysis.py"
I can not find it
many thanks
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Hi HJ, Are you saying you can't get to the tutorial files at https://iu.app.box.com/v/cafetutorial-files ? They should be available. |
|
Thank you very much, i got the script. |
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Hi, |
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Can I get the tutorial files at https://iu.app.box.com/v/cafetutorial-files? I can not open this site? Many thanks! |
|
Hi benfulton, zhilin |
|
I also can't get the tutorial files at https://iu.app.box.com/v/cafetutorial-files. Could someone share them?Many thanks! |
|
I also can't get the tutorial files at https://iu.app.box.com/v/cafetutorial-files. Could someone share them?Thanks! |
|
I think these files are now located here: https://github.com/hahnlab/cafe_tutorial |
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Hi Hahn,
I have some problems running the tutorial scripts (cafetutorial_report_analysis.py).
python python_scripts/cafetutorial_report_analysis.py -i reports/report_run1.cafe -o summary
Parsing format information...
Traceback (most recent call last):
File "python_scripts/cafetutorial_report_analysis.py", line 321, in
tinfo, newtree = cafecore.treeParseNew(labeled_tree,2);
File "/Users/uqhshao/Downloads/cafe_tutorial/python_scripts/cafecore.py", line 195, in treeParseNew
if new_tree[-1] == ")":
IndexError: string index out of range
AND
python python_scripts/cafetutorial_report_analysis.py -i report.txt.cafe -o summary
Parsing format information...
Initializing output structures...
Counting changes per branch...
[*-------------------------------------------------] 0.067% complete.Traceback (most recent call last):
File "python_scripts/cafetutorial_report_analysis.py", line 371, in
results_main, node_fams_main = cra(inlines_main, results_main, node_fams_main, linestart_main, ancfilename, sorted_nodes, 1);
File "python_scripts/cafetutorial_report_analysis.py", line 192, in cra
curcount = int(tlinfo[tlnode][4]);
ValueError: invalid literal for int() with base 10: '5.8_11'
Do
report.txt.cafe.txt
you have some ideas about this error?
Thanks,
Haojing
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