[Bioperl-l] latest bioperl commit

Hilmar Lapp hlapp at drycafe.net
Tue Feb 23 10:21:02 EST 2010

Thanks for your help Nathan - these sound like very useful additions!


On Feb 22, 2010, at 8:33 PM, Nathan Liles wrote:

> I just made a major commit to the bioperl svn. These changes all  
> affect the genbank2gff3.pl converter. The following is a brief  
> synopsis of the changes:
> New command line options added:
> /--noinfer /: don't infer exon/mRNA subfeatures
>        For prokaryotes, sometimes having the converter infer these  
> subfeatures from genes is less than desirable. This will turn that  
> off.
> /
>    --sofile=so.obo /: obo file used to create up-to-date type mappings
>        If you pass a so.obo file to the converter, it will try to  
> match every primary tag with a valid SO ID. So, for nebulous tags  
> like misc_feature, it will try give it a more descriptive name based  
> on the note field. It will also validate parent/child SO  
> relationships and ID uniqueness. If you don't have a local file, you  
> can use --sofile=live to grab the latest file from  
> sequenceontology.org.
> /--manual /: manual curation
>        Since the converter will likely do a terrible job guessing  
> tags, passing this flag will allow you manually choose the proper  
> term for a GenBank entry. It will give you a list of best matches,  
> search SO from the command line, and allow user input when all else  
> fails. This flag only works in conjunction with --sofile
> /--conf/ : path to config file
>        Because no one wants to manually annotate a GenBank file  
> every time they convert it, and because even the best matches can't  
> beat a human curator, the converter also has the option to save  
> manual curation preferences to a conf file. Any preferences saved to  
> a conf file will be automatically applied to the GFF3 everytime you  
> convert it. The conf file consists of "rules" for when to match a  
> primary tag to a GenBank entry. The generated conf file will be in  
> YAML format. So, if you are comfortable with the format, it should  
> be easy to manually create/edit the file. If you use the --manual  
> flag and input a term, it will ask you if you want to save your  
> preference to the conf file. At the moment, there is no conf file  
> documentation.
> I'm always open to hearing any feedback/suggestions/bug reports.
>   -Nathan Liles
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :

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