[Bioperl-l] latest bioperl commit

[Nathan Liles]

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