error reporting

[martin-raden]

Hi @PatrickRWright,

I am currently "cleaning" error handling in the scripts..

Is there a reason why you use within homology_intaRNA.pl sometimes an explicit error file err.log via ERRORLOG and sometimes die which writes to STDERR?

If not, I would like to unify both towards die for an early abortion with according exit status, while the latter can be used upstream in the calling script to check whether all went fine or something was aborted..

That way, we can have a clean exit with reasonable error message anywhere within the scripting-mess.. ;)

Thanks for feedback,
Martin

[PatrickRWright]

Hi @martin-mann ,

the reason would be historic. Originally homology_intaRNA.pl was the "master" script. I never thought about/had time to clean this up. err.log is intended to catch and report errors in the scripts running hierarchically below CopraRNA2.pl so a somewhat useful error message can be provided. Having said that, the parts where die is invoked usually do not happen but the errors that print into the err.log sometimes do.

Best,
Patrick

[martin-raden]

even more reason to trigger a die rather than printing to a specific log file, since the err.log typically does not exit the script such that intermediate failures cause a lot of downstream errors due to missing files etc...

what do you think?

[PatrickRWright]

I'll leave that decision in your hands. Thanks!