[Bioperl-l] Bioperl-l Digest, Vol 87, Issue 20

Mon Jul 19 17:05:24 UTC 2010

Greetings,
R has a jaccard function also. See http://pbil.univ-lyon1.fr/library/prabclus/html/jaccard.html for a description.

cheers,

Thomas (Tom) Keller, PhD
kellert at ohsu.edu
503.494.2442
6339b R Jones Hall (BSc/CROET)
www.ohsu.edu/xd/research/research-cores/dna-analysis/

On Jul 19, 2010, at 9:00 AM, <bioperl-l-request at lists.open-bio.org> <bioperl-l-request at lists.open-bio.org> wrote:

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> Today's Topics:
> 
>   1. Re:  Jaccard Dendrogram (Dave Messina)
>   2.  New Bio::Root::IO->_insert() method (Florent Angly)
>   3. Re:  Recoding Bio::SimpleAlign (Jun Yin)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 18 Jul 2010 11:26:52 -0600
> From: Dave Messina <David.Messina at sbc.su.se>
> Subject: Re: [Bioperl-l] Jaccard Dendrogram
> To: Rondon Neto <rondonbio at yahoo.com.br>
> Cc: bioperl-l at lists.open-bio.org
> Message-ID:
> 	<AANLkTim3RP5rsN68eJgBRH_nHFrVWPXgCM76u-jxPmIT at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Hi Rondon,
> 
> No, I don't think BioPerl has the ability to do Jaccard distance
> calculations. Looks like SciPy-cluster can, though:
> 
>    http://code.google.com/p/scipy-cluster/
> 
> Also MATLAB probably.
> 
> However, if you or anyone ese should be so inclined, it should be
> straightforward to adapt one of the existing BioPerl distance methods. See
> e.g. Bio::Align::DNAStatistics:
> 
>    http://doc.bioperl.org/bioperl-live/Bio/Align/DNAStatistics.html
> 
> 
> 
> 
> Dave
> 
> 
> 
> 
> 
> On Sun, Jul 18, 2010 at 05:55, Rondon Neto <rondonbio at yahoo.com.br> wrote:
> 
>> Hi! Please, can I build a dendrogram from a jaccard distance matrix by
>> Phylogenetic Analysis Pipeline?
>> How to do that?
>> 
>> Thank you
>> 
>> Rondon
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 19 Jul 2010 18:47:39 +1000
> From: Florent Angly <florent.angly at gmail.com>
> Subject: [Bioperl-l] New Bio::Root::IO->_insert() method
> To: bioperl-l BioPerl <bioperl-l at bioperl.org>
> Message-ID: <4C44112B.1060701 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi list,
> I needed a feature to insert text at an arbitrary line in a file for a 
> Bioperl module I am working on. I coded it, called the new method 
> _insert( ) and added it to the Bio::Root::IO module because I realized 
> that it could be useful to other Bioperl modules. The method seems to be 
> working well and does not cause tests to fail but let me know if you 
> encounter issues with it.
> Regards,
> Florent
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Mon, 19 Jul 2010 11:43:50 +0100
> From: Jun Yin <jun.yin at ucd.ie>
> Subject: Re: [Bioperl-l] Recoding Bio::SimpleAlign
> To: "'Bernd Web'" <bernd.web at gmail.com>
> Cc: bioperl-l at lists.open-bio.org, 'Chris Fields'
> 	<cjfields at illinois.edu>,	bernd.web at gmail.com
> Message-ID: <004c01cb272f$4626b880$d2742980$%yin at ucd.ie>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi,
> 
> Thx for all your comments.
> 
> 1. About each_seq(each_Seq)
> As Chris Fields says, we tend to capitalize the method name which returns
> objects. each_Seq actually returns a list of Bio::LocatableSeq objects, so
> it is better to use a capitalized name as each_Seq.
> But as Hilmar Lapp mentioned, each_XXX is not a clear name either, because
> it may be confused with the each() function in Core. So it may need to be
> renamed to next_Seq eventually.
> 
> Usually, what I do for the old method is:
> 
> sub each_seq {
>    my $self = shift;
>    $self->deprecated("each_seq - deprecated method. Use each_Seq()
> instead.");
>    $self->each_Seq();
> }
> 
> Thus, if you call the old method, it will still continue to run, but give a
> deprecated warning. This is done on all deprecated methods.
> 
> 
> 2. To Bernd Web, " So the change here is that now the default values are
> actually set in new, instead of setting a the default by calling gap_char."
> 
> Yes, gap_char has a default value "-" now, so is missing_char "?" and
> match_char ".".
> 
> 3. To Bernd Web and Chris Fields,
> remove_redundant_Seqs() is just an alias for purge(). 
> However, splice_by_seq_pos() is reimplemented and merged with the old
> remove_gaps(), because these two methods are actually doing similar things.
> The new remove_gaps() is:
> 
> Title     : remove_gaps
> Usage     : $aln2 = $aln->remove_gaps(-reference=>5)
> Function  : Creates an aligment with gaps removed
> Returns   : a Bio::SimpleAlign object
> Args      : -GAPCHAR a gap character(optional) if none specified taken
>                from $self->gap_char,
>             -ALLGAPCOL $all_gaps_columns flag (1 or 0, default is 0)
>                 indicates that only all-gaps columns should be deleted
>             -REFERENCE splices all aligned sequences where the specified 
>                 sequence has gaps.
> 
> If you call the old splice_by_seq_pos(), it will be redirected to
> remove_gaps() by:
> sub splice_by_seq_pos{
>    my $self = shift;
>    $self->deprecated("splice_by_seq_pos - deprecated method. Use
> remove_gaps() instead.");
>    $self->remove_gaps(-reference=>$_[0]);
> }
> 
> When I finally finish the recoding for Bio::SimpleAlign, I will write an
> online HOWTO. 
> Plus, I think I will include an update log, to show which method is renamed
> and which is reimplemented, thus to make things clearer.
> 
> Cheers,
> Jun Yin
> Ph.D.?student in U.C.D.
> 
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
> 
> 
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> End of Bioperl-l Digest, Vol 87, Issue 20
> *****************************************