[Biojava-dev] SeqIOTools problems

[Keith James]

>>>>> "Kalle" == Kalle Näslund <kalle.naslund at genpat.uu.se> writes:

    Kalle> Hi/Hello/Hej/Hola!  Seems i have some problems with
    Kalle> SeqIOTools. After my last CVS uppdate ( havent done one in
    Kalle> quite a while i must admit ) i am having problems using
    Kalle> SeqIOTools, i get exceptions thrown when using what have
    Kalle> previously been working code. The problems seems to be
    Kalle> related to some larger changes in the class. and
    Kalle> deprecation of some parts of the api.( but as i understand
    Kalle> the general convetion, deprecated methods should still work
    Kalle> )

Yep. If it's deprecated and not working, that's a bug.

    Kalle> So, the problems i get are when i use the following two
    Kalle> methods togheter.

    Kalle> int guessFileType(java.io.File seqFile ) java.lang.Object
    Kalle> fileToBiojava(int fileType, java.io.BufferedReader br)

    Kalle> What happens is that the first method, tries to guess the
    Kalle> fileformat of the file, it then returns an integer
    Kalle> representing the fileformat it think it is ( currently only
    Kalle> based on filename ending ). But, this method isnt aware of
    Kalle> the changes to the fileformat numbering scheme, so the
    Kalle> number returned cant be used in the fileToBiojava( int
    Kalle> fileType, java.io.BufferedReader br ) method call.

I assume the files which were failing were EMBL and/or Genbank? There
were a couple of cases where it was returning just the sequence format
bytes as you say. This was an oversight on my part. I have just fixed
them to return SeqIOConstants.EMBL_DNA or SeqIOConstants.GENBANK_DNA
(which are equal to SeqIOConstants.EMBL | SeqIOConstants.DNA and
SeqIOConstants.GENBANK | SeqIOConstants.DNA). There shouldn't be any
cases where the guessing code returns a value without the alphabet
bytes set.

Please let me know if there are further problems.

Keith

-- 

- Keith James <kdj at sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -