[Bioperl-l] Why does Bio::DB::GFF::Feature::gff3_string swap start and stop coordinates??
johnsonm at gmail.com
Tue May 22 18:04:31 UTC 2007
Yes, Glimmer3 outputs the length of the input sequence. I don't
believe Glimmer2 does.
> The most complete file format to parse seems to be the details file;
> it contains the sequence length:
> Sequence length = 29940
> Since the parser currently only parses predict files, you could
> optionally supply the parser with the seq length and emit a warning
> if seqfeatures requiring it are produced, such as the sporadic ones
> which wrap around. If one were using the bioperl-run module this
> could be automated a bit by passing the seq length in to the parser
> object by adding the seq length to the constructor argument list.
I think we can spot wrap-around genes easily enough without knowing
the length of the input sequence. Having it just means we can perform
a sanity check or two, such as making sure 'wraparound' genes are
within N bases of the end of the input sequence. Any suggestions on a
good default value for N?
Parsing both output files for glimmer3 will be a little tricky. The
constructor for Bio::Tools::Glimmer calls $class->SUPER::new(@args);,
which hits the constructor for Bio::Tools::AnalysisResult, which does
the same thing. It all ends up in Bio::Root::IO::_initialize_io,
which grabs the -file arg and opens it. So, either let, Bio::Root::IO
handle -file and have Bio::Tools::Glimmer handle, say -detail file, or
have Bio::Tools::Glimmer just implement intialize_io() and hopefully
that will fly..
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