Bioperl: WRITTEN standards for sequence file formats

[cdagdigian@genetics.com]

Lincoln wrote:
>I guess this is just another illustration of why it's useful to have
>solid WRITTEN standards for file formats, not just informal standards
>based on how some program written years ago parsed its input.

This is a major problem. Much of the sequence formatting/output code
in Parse.pm was reverse-engineered from looking at various sequence
files. When looking around for help on sequence formats I think the
only "standards" I ever found were for GCG and GenBank format files.

I've also hit my head against the "what is the identifier and what is
the descriptive info" problem when trying to parse fasta formatted files.

-chris dagdigian
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