[Bioperl-l] proposed change -- symbols SimpleAlign

Chris Fields cjfields at uiuc.edu
Thu Nov 22 19:49:15 EST 2007


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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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