Hello,
I was wondering if anyone with Perl experience could help me debug a miRWoods? I tried reaching out the authors via e-mail with no response, and issues on GitHub are turned off so I'd be super grateful if anyone could provide any insight.
When I run miRWoods I get the following error:
Use of uninitialized value $geneId in pattern match (m//) at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 819, <PHC> line 1. Use of uninitialized value $location in pattern match (m//) at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 826, <PHC> line 1. Use of uninitialized value $location in pattern match (m//) at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 831, <PHC> line 1. Use of uninitialized value $location in pattern match (m//) at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 836, <PHC> line 1. Use of uninitialized value $location in pattern match (m//) at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 841, <PHC> line 1. Use of uninitialized value $chrom in hash element at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 8018, <PHC> line 1. Use of uninitialized value $name in hash element at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 8019, <PHC> line 1. Use of uninitialized value $name in hash element at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 6587, <OAF> line 1. Use of uninitialized value $name in hash element at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 6608, <OAF> line 1. Use of uninitialized value $strand in hash element at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 7874, <OAF> line 1. Use of uninitialized value $name in hash element at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 7874, <OAF> line 1. Use of uninitialized value $name in hash element at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 7883, <OAF> line 1. Use of uninitialized value $name1 in hash element at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 8107, <OAF> line 1. Can't use an undefined value as an ARRAY reference at /home/ubuntu/prog/miRWoods/PerlModules/miRWoods.pm line 8107, <OAF> line 1. /home/ubuntu/prog/miRWoods/Scripts/evaluateHairpinsWithRF.pl finished
I gather from this error that $geneId hasn't been initialised with a value and so the program terminates. Am I to assume that all of the other errors are caused by $geneId being uninitialised or is it that all of the other uninitialised variable errors are independent and that all of these variables are uninitialised?
My inspection of the offending line in the file gives this chunk of code:
sub parseGeneId {
my($geneId) = @_;
my($name,$location) = $geneId =~ /(^.*?)\_(.*)$/;
return($name,$location); }
Am I reading into it correctly that it's searching for some kind of matching string(s)? Could it not being able to find the string be causing this error and it remains uninitialised? I note that it seems miRWoods was build using HG19 and I am using HG38 as I couldn't locate all of the files needed for HG19 (namely hg19_ensembl.gff3) (required files listed here) but I suppose any change between the versions regarding headers such as geneID could cause problems?
