23 May 2013 15:56
Re: Speed issues with making IUPAC consensus from alignment
Fields, Christopher J <cjfields <at> illinois.edu>
2013-05-23 13:56:32 GMT
2013-05-23 13:56:32 GMT
(keep the list cc'd) On May 22, 2013, at 6:31 PM, Senanu <senanu.junk <at> gmail.com> wrote: > On May 22, 2013, at 4:17 PM, Fields, Christopher J wrote: > >> Hi all, >>> >>> I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. >> >> Probably the former, but... >> >>> I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. >> >> It shouldn't take that long, 7 Mb isn't that large. Or is that 7 Mb for one genome? > > It is 7Mb per genome, but there are only 2 genomes in the alignment, and the sequences are very similar to one another. > >> >>> Is this a known problem? Is there another way to generate such a consensus? >> >> The code isn't really optimized for this, but again this isn't terribly large. Is the bottleneck reading the alignment in, or is it the consensus_iupac() step? Hard to say w/o seeing the alignment data itself. > > The bottleneck is definitely with the consensus_iupac step. Reading the alignment in takes a few(Continue reading)
-hilmar
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