[Bioperl-l] bp_genbank2gff3.pl error on last line ("//")

John Anderson genehack at genehack.org
Sun Jul 25 16:05:33 EDT 2010


On Jul 25, 2010, at 3:52 PM, David Breimann wrote:

> Thank you guys. I'm quite new to all this github stuff, so in order to view to use to updated version should I first update my clone of bioperl-live (git pull?) then go through the whole build and install again?

Or you could just change the one line in the script yourself; that was the only change. 

> Second, I have just noticed that bp_genbank2gff3.pl returns an error when given a circular genome with a feature that spans the "end" of the genome (e.g., assume the genome size is 1000np and a feature spans join(900..1000,1..100). 

Could you send me (not the list, just me) an input file that produces this problem? 

> Finally, is it possible to tell bp_genbank2gff3.pl to extract the features only (no sequences)? Currently I use the -y flag then delete the fasta file.

It looks like the '-n' option should do that, but it currently throws a few more errors of the same general type as you were seeing before -- let me look at those... 

j.




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