[Bioperl-l] PAML parser

Michael Han mh6 at sanger.ac.uk
Fri Jul 21 09:04:57 UTC 2006


I have some questions about the PAML parser (Bio::Tools::Phylo::PAML in CVS HEAD). Maybe some of you could help.

If you call next_result, $self->_parse_summary might be called, which loops over $self->_readline .

Later in next_result when "while (defined ($_=$self->_readline))" is used isn't the filepointer/filehandle
already at the end of the output file and should return undef breaking the parsing?

I added a crude seek($self->{_filehandle},0,0) after the _parse_summary and it seemed to work, but I wonder if I missed something obvious.



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