cjfields
commented
8 years ago Original Redmine Comment Author Name: Jason Stajich Original Date: 2011-03-11T20:27:08Z
Possible that Chris can take a look at the Unflattener code?
Open cjfields opened 8 years ago
cjfields
commented
8 years ago Original Redmine Comment Author Name: Jason Stajich Original Date: 2011-03-11T20:27:08Z
Possible that Chris can take a look at the Unflattener code?
Author Name: liyankai empty (liyankai empty) Original Redmine Issue: 3144, https://redmine.open-bio.org/issues/3144 Original Date: 2010-10-07 Original Assignee: Chris Mungall
Dear Sir,
we are using bp_genbank2gff3.pl to load genbank file into chado. However, the script keeps giving an error message as shown below, it seems to us that the script can not handle “Trans-spliced gene”, which is gene rps12 in the genbank file (ftp://ftp.ncbi.nih.gov/genomes/Chloroplasts/plastids/plastids/ NC_002762.gbk). Would you please tell us how we can get pass this.
Thank you very much for your prompt response.
best,
yankai.
NC_002762 Unflattening error: Details: ——————- EXCEPTION: Bio::Root::Exception ——————- MSG: PROBLEM, SEVERITY==1 inconsistent strands. Trans-spliced gene? Range: [67272,67385] [125870,126092] [126633,126664] STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368 STACK: Bio::SeqFeature::Tools::Unflattener::problem /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:952 STACK: Bio::SeqFeature::Tools::Unflattener::_check_order_is_consistent /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:2750 STACK: Bio::SeqFeature::Tools::Unflattener::infer_mRNA_from_CDS /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:2641 STACK: Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:1529 STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:915 STACK: /usr/local/bin/bp_genbank2gff3.pl:411 —————————————————————————————-