Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
add error message for setting recursion limit on revision, to mitigate issue where some users may not have permissions to change their stack size / recursion limit
DISCUSSION
one of the users got this error on make system_test
File "/Users/immlerlab/Documents/TE/TE_Density/transposon/revise_annotation.py", line 65, in init
resource.setrlimit(resource.RLIMIT_STACK, (1000, -1))
ValueError: not allowed to raise maximum limit
make: *** [system_test] Error 1
I can't reproduce but this change logs the error and attempts to continue
It could still fail later when it attempts the revision but I figure it's worth a shot
TESTING
you can add a ValueError in the try block to see the log, so far I'm not sure how to reproduce,
but this will exercise the update
make system_clean
make system_test
...
2023-06-11 23:52:26 GOKU ReviseAnno[110652] ERROR could not raise recursion limit using 'resource' module, are you using Windows? revision may fail
2023-06-11 23:52:26 GOKU ReviseAnno[110652] WARNING got this ValueError in __init__: testing
...
DISCUSSION
one of the users got this error on
make system_testI can't reproduce but this change logs the error and attempts to continue
It could still fail later when it attempts the revision but I figure it's worth a shot
TESTING
you can add a ValueError in the try block to see the log, so far I'm not sure how to reproduce, but this will exercise the update