[Biopython] Ace Contig parsing Bio.AlignIO

[Eike Mayland-Quellhorst]

Sorry, I found my mistake (missplaced align object, so it was not updated after each iteration), so my script is working now. But in gerenal I would like to see an option in AlignIO for .ace files, as we like the old Cap3 assembler for assembling MiSeq Amplicon data (in a pipe starting with BBmap tools, cap3, filtering, MAFFT alignment with reference sequence of locus, visual inspection of alignments).

all the best
Eike Mayland-Quellhorst


Am 26.11.2015 um 14:06 schrieb 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
>

-- 
__________________________________
Eike Mayland-Quellhorst
AG Biodiversität und Evolution der Pflanzen
Fakultät V - IBU
Carl von Ossietzky Universität Oldenburg

Carl-von-Ossietzky Str. 9-11
26111 Oldenburg
Germany

Tel. 0049-441-798-3386

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