[Biopython] Ace Contig parsing Bio.AlignIO
Eike Mayland-Quellhorst
eike.mayland.quellhorst at uni-oldenburg.de
Thu Nov 26 13:06:41 UTC 2015
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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: eike_mayland_quellhorst.vcf
Type: text/x-vcard
Size: 394 bytes
Desc: not available
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20151126/f6ee68fb/attachment.vcf>
More information about the Biopython
mailing list