[Bioperl-l] proposed change -- symbols SimpleAlign

Chris Fields cjfields at uiuc.edu
Sun Nov 25 10:38:40 EST 2007


Albert,

I was getting a single AlignIO.t fail which appeared to be related to  
this:

...
ok 122 - The object isa Bio::Align::AlignI
ok 123 - consensus_string on metafasta

not ok 124 - symbol_chars() using metafasta
#   Failed test 'symbol_chars() using metafasta'
#   in t/AlignIO.t at line 346.
#          got: '0'
#     expected: '23'

It was b/c the symbol hash was initialized in the constructor (so it  
was present, just empty).  I have changed that in CVS; all tests pass  
now.

chris

On Nov 25, 2007, at 5:50 AM, Albert Vilella wrote:

> 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...
>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> 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
>>
>>
>>
>>

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





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