[Biopython] Ace Contig parsing Bio.AlignIO

[Peter Cock]

That's good news Eike,

For anyone interested, I think Eike was referring to these old threads:

http://lists.open-bio.org/pipermail/biopython/2008-June/010448.html
http://lists.open-bio.org/pipermail/biopython-dev/2008-June/012957.html
http://lists.open-bio.org/pipermail/biopython/2009-April/011305.html

The result was SeqIO has support for ACE files where you get a
SeqRecord using the consensus sequence (and ignoring all the
supporting reads), using the ACE parser under Bio.Sequencing.

It would still be possible to add AlignIO support returning each
contig as a multiple sequence alignment containing all the supporting
reads, based on the recipe from David Winters:

http://biopython.org/wiki/ACE_contig_to_alignment

I've not used ACE files for a long time now, and you are the first
person to ask about this in a while now. However, since we already
have the ACE parser, the new code for Bio.AlignIO would not be
that much work - and it sounds like you're willing to test this on
real world data which is always useful :)

David - are you still interested in this?

(Separately I have wondered about adding support for MIRA's
alignment format which is a bit like the ACE format - although
now MIRA can output SAM, I have tended to use that instead.)

Peter

On Thu, Nov 26, 2015 at 2:01 PM, Eike Mayland-Quellhorst
<eike.mayland.quellhorst at uni-oldenburg.de> wrote:
> 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
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