[Bioperl-l] t/SeqIO.t -- improvements?

Hilmar Lapp hlapp at gmx.net
Thu Sep 7 14:56:21 EDT 2006


On Sep 7, 2006, at 1:37 PM, Jay Hannah wrote:

> Wouldn't it be better if:
> (1) fasta.out was generated to contain *all* sequences, not just  
> the first.

Possibly.

> (2) a test was added to verify that fasta.out exactly matches  
> test.fasta (diff is blank).

No. The goal is not exact reproduction (you'd use cp for that) but  
writing out a file that is valid FASTA format and contains the same  
information as the input file.

You could (and should) still do a semantic diff; just that's a lot  
harder to implement. There have been threads previously about  
comparing objects for equality (in the notion that two files which  
are semantically equal should result in 'equal' objects once read  
into the object model).

	-hilmar
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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