Re: [Seqan-dev] how to read fasta files to uses in Hoorspol program
Hi Julio,
you can use the FileReader data structure to load sequences from Fasta files. So for example, if you pass the Fasta filenames via the command line:
String<char> haystack = String<char, FileReader<Fasta> >(argv[1]);
String<char> needle = String<char, FileReader<Fasta> >(argv[2]);
Take a look at file_format.cpp for more options on reading Fasta sequences.
Cheers,
Anne-Katrin
-----------------------------------------------
Anne-Katrin Emde
+49 30 83875240
emde@inf.fu-berlin.de
Algorithmic Bioinformatics
Department of Computer Science
Freie Universität Berlin
----------------------------------------------
________________________________________
Von: Julio Cesar Carbajal [carbaj1@hotmail.com]
Gesendet: Mittwoch, 9. Februar 2011 14:01
An: seqan-dev@lists.fu-berlin.de
Betreff: [Seqan-dev] how to read fasta files to uses in Hoorspol program
Hey,
Could you help me.
How to read fasta files to uses in Hoorspol program or modify de find_exact program.
Julio
> From: Tobias.Rausch@fu-berlin.de
> To: seqan-dev@lists.fu-berlin.de
> Date: Tue, 8 Feb 2011 10:02:35 +0100
> Subject: Re: [Seqan-dev] Using EdgeProperties and VertexProperties
>
> Hey Mat,
>
> In the write function in graph_types/graph_drawing.h, for each vertex and edge property the following call is used:
>
> _streamWrite(file, getProperty(nodeMap, *itVertex));
>
> _streamWrite(file, getProperty(edgeMap, *itEdge));
>
>
> Best, Tobias
>
>
>
> ________________________________________
> From: Mat [matthias.dodt@mdc-berlin.de]
> Sent: Monday, February 07, 2011 4:34 PM
> To: SeqAn Development
> Subject: [Seqan-dev] Using EdgeProperties and VertexProperties
>
> Hey guys!
>
> I would like to create a .dot file of my graph using the
>
> write(strmWrite, *graph, *vertexPropertyMap,*edgePropertyMap,DotDrawing());
>
> method.
>
> The two maps are defined as follows:
>
> seqan::String<VertexProperty> *vertexPropertyMap = new seqan::String<VertexProperty>();
> seqan::String<EdgeProperty> *edgePropertyMap = new seqan::String<EdgeProperty>();
>
> VertexProperty and EdgeProperty are two custom classes...
>
> Now if i use the DotDrawing() method i get the message "cannot convert form VertexProperty to char"...
>
> So i guess i would have to implement my own "_streamPut" method for these classes in seqans "cstream.h", so something like:
>
> inline void _streamPut(::std::FILE * target,
> const EdgeProperty e)
> {
> SEQAN_CHECKPOINT
> //putc(e.toChar(), target);
> }
>
> or is there an easier way to do that?
>
> Thanks!
>
> best,
>
> mat
>
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