Re: [Seqan-dev] multiLocalAlignment function

["Rausch, Tobias" <Tobias.Rausch@fu-berlin.de>]

Hi Andres,

So here is an example:

#include <iostream>
#include <seqan/align.h>
#include <seqan/graph_align.h>
#include <seqan/graph_msa.h>

using namespace seqan;

int main()
{
	typedef String<Dna> TSequence;
	TSequence seq1 = "atcgaatgcgga";
	TSequence seq2 = "actcgttgca";
	Score<int> score(2, -1, -1, -2);

	typedef StringSet<TSequence, Dependent<> > TStringSet;
	TStringSet string_set;
	appendValue(string_set, seq1);
	appendValue(string_set, seq2);

	typedef String<Fragment<> > TFragmentString;
	TFragmentString matches;
	typedef String<int> TScoreValues;
	TScoreValues scores;

	multiLocalAlignment(string_set, matches, scores, score, 2, SmithWatermanClump());
	_debugMatches(string_set, matches);
	return 0;
}


It returns the two best local alignments as a string of fragments. The fragments are the gapless
aligned segments of an alignment:
0,5,ATGC,1,5,TTGC
0,1,TCG,1,2,TCG
The first number is the sequence id, then comes the begin position. So the alignment is:
TCGAAATGC
TCG--TTGC

The second local alignment is:
0,8,CG,1,3,CG
0,4,AAT,1,0,ACT

The score string has the same length as the string of segment matches. Each fragment gets
the score of the local alignment it comes from.
 
I am not sure if this was already working in the last release, so please use the SVN.
http://trac.mi.fu-berlin.de/seqan/wiki/Development


Best regards, Tobias



> -----Ursprüngliche Nachricht-----
> Von: seqan-dev-bounces@lists.fu-berlin.de 
> [mailto:seqan-dev-bounces@lists.fu-berlin.de] Im Auftrag von 
> andres.burgos@irisa.fr
> Gesendet: Sunday, August 23, 2009 7:55 PM
> An: Rausch, Tobias
> Cc: seqan-dev@lists.fu-berlin.de
> Betreff: Re: [Seqan-dev] multiLocalAlignment function
> 
> 
> Hi Tobias, thanks for your reply, I'll take a closer look at 
> the code so maybe I'll figure it out, but the example will 
> still be helpful.
> 
> Danke schoen!
> Andres
> 
> > Hello Andres,
> >
> > The multi-local alignment algorithm we have implemented is the one 
> > from Waterman and Eggert.
> > It returns possibly overlapping local alignments, so it is not a 
> > repeated match finder.
> >
> > It is implemented in
> > ./seqan/graph_align/graph_align_smith_waterman_clump.h and 
> as you can 
> > see at the bottom of the file it repeatedly calls the standard 
> > smith-waterman alignment algorithm. Each found local 
> alignment is then 
> > forbidden in the next run.
> >
> > I send you an example on how to use it on Monday.
> >
> > Best regards,
> > Tobias
> >
> >
> > ________________________________________
> > From: seqan-dev-bounces@lists.fu-berlin.de
> > [seqan-dev-bounces@lists.fu-berlin.de] On Behalf Of 
> > andres.burgos@irisa.fr [andres.burgos@irisa.fr]
> > Sent: Friday, August 21, 2009 6:01 PM
> > To: seqan-dev@lists.fu-berlin.de
> > Subject: [Seqan-dev] multiLocalAlignment function
> >
> > Hi!
> >
> > I'm currently trying to make work the function
> >
> > multiLocalAlignment(graph, edgeMap, score, numAlign, tag)
> >
> > but I can't success, so I was hoping to get some help, 
> since it's not 
> > documented on the web site. I was also wondering weather 
> this function 
> > would return overlapping or non-overlapping alignments.
> >
> > Ok, so here is the code I'm working on:
> >
> >     typedef seqan::String<seqan::AminoAcid> TString;
> >     typedef seqan::StringSet<TString, seqan::Dependent<> > 
> TStringSet;
> >     typedef seqan::Graph<seqan::Alignment<TStringSet, 
> > seqan::AminoAcid> > TGraph;
> >
> >     TStringSet str;
> >     TString s1 ("some string");
> >     TString s2 ("some other string");
> >
> >     seqan::appendValue(str, s1);
> >     seqan::appendValue(str, s2);
> >
> >     seqan::Score<int, seqan::Pam<> > pam (250, -1, 0);
> >     TGraph g(str);
> >
> >     
> seqan::String<seqan::IntervalTreeNode<seqan::IntervalAndCargo<int,
> > int> > > propMap;
> >     seqan::resizeEdgeMap(g, propMap);
> >
> >     seqan::multiLocalAlignment(g, propMap, pam, 10, 
> > seqan::SmithWaterman());
> >
> > This won't compile, throwing this error:
> >
> > ../seqan-1.1/seqan/graph_align/graph_align_interface.h: In function 
> > 'void 
> > seqan::multiLocalAlignment(seqan::Graph<seqan::Alignment<TStringSet,
> > TCargo, TSpec> >&, TPropertyMap&, const seqan::Score<TScoreValue,
> > TSpec2>&, TSize, TTag) [with TStringSet =
> > seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, 
> > seqan::_AminoAcid>, seqan::Alloc<void> >, seqan::Dependent<const 
> > seqan::Tag<seqan::TagGenerous_> > >, TCargo = 
> > seqan::SimpleType<unsigned char, seqan::_AminoAcid>, TSpec = const 
> > seqan::Tag<seqan::Default_>, TPropertyMap = 
> > seqan::String<seqan::IntervalTreeNode<seqan::IntervalAndCargo<int, 
> > char>, seqan::StorePointsOnly>, seqan::Alloc<void> >, TScoreValue = 
> > int, TSpec2 = seqan::Pam<seqan::SimpleType<unsigned char, 
> > seqan::_AminoAcid>, seqan::Pam_Data_Dayhoff_MDM78>, TSize = 
> int, TTag 
> > =
> > seqan::Tag<seqan::SmithWaterman_>]':
> > readers/SWReader.cc:26:   instantiated from here
> > ../seqan-1.1/seqan/graph_align/graph_align_interface.h:234: 
> error: no 
> > matching function for call to 
> > '_localAlignment(seqan::String<seqan::Fragment<unsigned int, 
> > seqan::ExactFragment<const seqan::Tag<seqan::Default_> > >, 
> > seqan::Alloc<void> >&, 
> > seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, 
> > seqan::_AminoAcid>, seqan::Alloc<void> >, seqan::Dependent<const 
> > seqan::Tag<seqan::TagGenerous_> > >&, 
> > seqan::String<seqan::IntervalTreeNode<seqan::IntervalAndCargo<int, 
> > char>, seqan::StorePointsOnly>, seqan::Alloc<void> >&, const 
> > seqan::Score<int, seqan::Pam<seqan::SimpleType<unsigned char, 
> > seqan::_AminoAcid>, seqan::Pam_Data_Dayhoff_MDM78> >&, int&, 
> > seqan::Tag<seqan::SmithWaterman_>)'
> > make: *** [readers/SWReader.o] Error 1
> >
> > So, maybe an example would make things clearer...
> >
> > Thanks in advance,
> > Andres
> >
> >
> > _______________________________________________
> > seqan-dev mailing list
> > seqan-dev@lists.fu-berlin.de
> > https://lists.fu-berlin.de/listinfo/seqan-dev
> >
> 
> 
> 
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