[Bioperl-l] proposed change -- symbols SimpleAlign

Albert Vilella avilella at gmail.com
Thu Nov 22 16:55:10 EST 2007


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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