Can't locate object method "contains" via package "Bio::SeqFeature::Generic"

ProfessionalFarmer commented 8 years ago

Hi, I have try to run on test data. FEELnc_filter.pl and FEELnc_codpot.pl. But FEELnc_classifier.pl encountered a error.

Command: FEELnc_classifier.pl -i feelnc_codpot_out/candidate_lncRNA.gtf.lncRNA.gtf -a annotation_chr38.gtf > candidate_lncRNA_classes.txt

Error: window : 10000 - max window : 100000 - lncrna : feelnc_codpot_out/candidate_lncRNA.gtf.lncRNA.gtf - mrna : annotation_chr38.gtf - biotype: 0 Can't locate object method "contains" via package "Bio::SeqFeature::Generic" at /usr/local/share/perl/5.18.2/Bio/SeqFeature/Generic.pm line 865, line 1114.

It seems that script can load Bio::SeqFeature::Generic, but can not locate method contains. The error line:

864 } else { 865 if ( !$self->contains($feat) ) { 866 $self->throw("$feat is not contained within parent feature, and expansion is not valid"); 867 } 868 }

$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' 1.006924

$ perl -version This is perl 5, version 18, subversion 2 (v5.18.2) built for x86_64-linux-gnu-thread-multi (with 41 registered patches, see perl -V for more detail)

How can I fix this error? Could you have a check.

Many thanks.

ProfessionalFarmer commented 8 years ago

Sorry about this issue. I clean up my PERL5LIB variable. It works fine. So please close this issue.

vwucher commented 8 years ago

No problem. Happy this work fine !

ProfessionalFarmer commented 8 years ago

Hi, I am coming again.

is Parralell::ForkManager a spelling mistake?

I think Parallel::ForkManager is the right word in requirements section (https://github.com/tderrien/FEELnc#requirements).

tderrien commented 8 years ago

Hello,

Indeed, good catch! Best

Thomas

tderrien / FEELnc

Can't locate object method "contains" via package "Bio::SeqFeature::Generic" #6