[Bioperl-l] Announcement: infernal/erpin/rnamotif parsers

Chris Fields cjfields at uiuc.edu
Thu Aug 16 10:37:31 EDT 2007


To anyone using the aforementioned parsers:

I don't plan on continuing development of the Bio::Tools-related  
Infernal, RNAMotif, and ERPIN parsers at this time unless there is  
substantial interest in doing so.  Instead, I plan on focusing my  
efforts on the Bio::SearchIO-based parsers as I feel they are much  
better at representing the data present in the output.  In my opinion  
having two sets of parsers that accomplish essentially the same task  
is redundant and non-productive.  Again, if there is considerable  
interest in keeping them I suggest responding to this message,  
otherwise I would consider them deprecated and removed completely by  
rel 1.7 (maybe sooner).

Infernal: It's very likely that a new stable version (v. 1.0) of  
Infernal will be released in the near future.  I may upgrade the  
Bio::SearchIO-based parser in the meantime to parse the latest  
Infernal output (v 0.81), but I don't plan on supporting pre-1.0  
releases once the final version is out.  Infernal has been in  
developer release for some time now and the program output has  
changed dramatically over time; however, the format is expected to  
solidify once a stable release is made, which makes supporting the  
parser much easier over time.

Questions?  Gripes?

chris



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