cafetutorial_report_analysis.py error

[haojingshao]

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

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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

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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

[gwct]

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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#62?email_source=notifications&email_token=AC7RJCKOLYXM2RJRSCWPEEDP7APPZA5CNFSM4ICCUXRKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G6ZR2VQ>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AC7RJCLVBEMGGPBMVSWSKK3P7APPZANCNFSM4ICCUXRA> .

[gwct]

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

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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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#62?email_source=notifications&email_token=AC7RJCMP6KXGLWNDEGFUJRDP7GFTDA5CNFSM4ICCUXRKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZ3MULI#issuecomment-511101485>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AC7RJCJHD3IZNLIA3S6WZIDP7GFTDANCNFSM4ICCUXRA> .

[haojingshao]

Hi, Please see #47 regards, HJ Lordhooze <[email protected]> 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 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#62?email_source=notifications&email_token=AFYZEIQ43E5MOMI7X6DFJBTP7GFTDA5CNFSM4ICCUXRKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZ3MULI#issuecomment-511101485>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFYZEIT4VRGUK6G3RZGTY5DP7GFTDANCNFSM4ICCUXRA> .

[benfulton]

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.

[Lordhooze]

Thank you very much, i got the script.
jiaxiang hu
China Agriculture University

[U201412486]

Hi,
I can't get to the tutorial files at https://iu.app.box.com/v/cafetutorial-files. Can you help me?
Thanks,
sun,

[cassytha]

Can I get the tutorial files at https://iu.app.box.com/v/cafetutorial-files? I can not open this site? Many thanks!

Hui
[email protected]

[lingzl]

Hi benfulton,
I also can't get the tutorial files at https://iu.app.box.com/v/cafetutorial-files. Could you email me? My email is [email protected]. Many thanks!

zhilin

[wuxiaopei0509]

I also can't get the tutorial files at https://iu.app.box.com/v/cafetutorial-files. Could someone share them?Many thanks!

[yuanw-18]

I also can't get the tutorial files at https://iu.app.box.com/v/cafetutorial-files. Could someone share them?Thanks!
[email protected]

[gwct]

I think these files are now located here: https://github.com/hahnlab/cafe_tutorial