[Bioperl-l] proposed change -- symbols SimpleAlign

Bernd Web bernd.web at gmail.com
Sun Nov 25 11:13:44 EST 2007


Hi,

I am not sure if this is related, but I remember SimpleAlign was
adapted to cope with more gap symbols that can occur in
alignments/FastA sequences, as: . _ - =
Previous versions would throw an error on 'illegal' gap characters,

Regards,
Bernd

On Nov 25, 2007 4:38 PM, Chris Fields <cjfields at uiuc.edu> wrote:
> 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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