Re: [Seqan-dev] how to read fasta files to uses in Hoorspol program

["Emde, Anne-Katrin" <Anne-Katrin.Emde@fu-berlin.de>]

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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