[Biopython] Ace Contig parsing Bio.AlignIO

[Eike Mayland-Quellhorst]

Dear list, dear Peter (as you have asked years ago in 2008 whether 
implementing into SeqIO or AlignIO),

for a Amplicon sequencing project I am doing Cap3 assemblies with 
pre-treated sequences. The consensus of these assemblies should go into 
MAFFT alignments. But as input I would like to have consensus sequences 
with ambiguities as produced with AlignInfo:dumb_consensus. For now I am 
struggling with iterating through the contigs and produce this 
information. I tried the cookbook example (and modifications of it), but 
I am not able to produce an object and consensus for each contig. The 
cookbook script seems to expect only one individual contig in the file. 
Is there a way to get the .ace contigs as an alignment, with which I 
could make the dumb_consensus, which I can export as fasta to pipe it to 
MAFFT?

with best regards
Eike Mayland-Quellhorst

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