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snd297 / penn-ppod

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Multiple states in a DNA Matrix question #23

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Is it a problem that when there's cell with multiple elements in a DNA matrix 
in Mesquite (I've tried 
"A&C") that we can't upload the matrix as a sequence set? 

It looks like this happens because InterpretFasta does not handle multiple 
states.

Called from mesquite.pPod.lib.mesquite2ppod.MesqMolecData2PPodSequenceSet<S>.

In InterpretFasta here's the code that does't handle the multiple states. 

When I put in M instead of A&C (which is the single character representaion as 
defined here 
http://www.ncbi.nlm.nih.gov/blast/fasta.shtml, the sequences work but the 
matrices break.

Original issue reported on code.google.com by snd...@gmail.com on 26 May 2010 at 6:32

GoogleCodeExporter commented 9 years ago 
When we upload a matrix with M instead of A & C, it uploads fine. Then when we 
download it, the cell turns into A & C.

Original comment by snd...@gmail.com on 19 Jul 2010 at 3:58

GoogleCodeExporter commented 9 years ago 
Note: really, M=A/C, not A&C. 

When we uploaded a matrix with M, it was downloaded w/ A&C which was causing 
our problems. It's fixed now.

Original comment by snd...@gmail.com on 22 Jul 2010 at 5:50