[Bioperl-l] proposed change -- symbols SimpleAlign

Albert Vilella avilella at gmail.com
Sun Nov 25 06:50:42 EST 2007


cvs commited now. it is calculated anyway when calling symbol_chars so...

On Nov 23, 2007 12:49 AM, Chris Fields <cjfields at uiuc.edu> wrote:
> Albert,
>
> Found it:
>
> http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/
> SimpleAlign.pm.diff?r1=1.36&r2=1.37
>
> If it slows performance that dramatically, maybe we can move this to
> a separate AlignUtils method instead.  Maybe something to ask Jason
> about?
>
> chris
>
> On Nov 22, 2007, at 3:55 PM, Albert Vilella wrote:
>
>
> > Hi,
> >
> > Am I right in thinking that the '_symbols' hash in SimpleAlign is only
> > used if one calls the symbol_chars method?
> >
> > When I comment out this line:
> >
> > map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq) if
> > $seq->seq; # line 257
> >
> > I get a nice speed boost on loading alignments.
> >
> > Can I comment this line out in the CVS HEAD?
> >
> > Cheers,
> >
> >     Albert.
> >
> > [init] 5.96046447753906e-06 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000162399.chr1.fasta]
> > 0.0022270679473877 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000158022.chr1.fasta]
> > 2.14348912239075 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000162585.chr1.fasta]
> > 6.91910791397095 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000121957.chr1.fasta]
> > 15.8402290344238 secs...
> >
> > avilella at magneto:~$ perl
> > /home/avilella/src/ensembl_main/ensembl-personal/avilella/exoseq/
> > ancestral_alleles.pl
> > -dir /home/avilella/ensembl/exoseq/test -verbose
> > [init] 1.21593475341797e-05 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000162399.chr1.fasta]
> > 0.00294303894042969 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000158022.chr1.fasta]
> > 0.510555982589722 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000162585.chr1.fasta]
> > 1.6192569732666 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000121957.chr1.fasta]
> > 3.86473417282104 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000203717.chr1.fasta]
> > 6.99602198600769 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000196188.chr1.fasta]
> > 7.26704716682434 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000025800.chr1.fasta]
> > 8.44332504272461 secs...
> > [loading aln /home/avilella/ensembl/exoseq/test/
> > ENSG00000117475.chr1.fasta]
> > 12.103296995163 secs...
>
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


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