src/mfaToMultiFiles.cpp

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00001 #include "libGenome/gnSequence.h"
00002 #include "libGenome/gnFASSource.h"
00003 #include <algorithm>
00004 
00005 using namespace std;
00006 using namespace genome;
00007 
00008 int main( int argc, char* argv[] )
00009 {
00010         if( argc != 2 )
00011         {
00012                 cerr << "Usage: " << argv[0] << " <mfa name>\n";
00013                 cerr << "One file will be written for each sequence entry in the MFA file\n";
00014                 return -1;
00015         }
00016         gnSequence mfa_seq;
00017         mfa_seq.LoadSource( argv[1] );
00018         for( uint i = 0; i < mfa_seq.contigListSize(); ++i )
00019         {
00020                 string ofname = mfa_seq.contigName(i);
00021                 remove( ofname.begin(), ofname.end(), ';' );
00022                 remove( ofname.begin(), ofname.end(), ' ' );
00023                 ofstream ofile( ofname.c_str() );
00024                 if( !ofile.is_open() )
00025                 {
00026                         cerr << "Error opening \"" << ofname << "\"\n";
00027                         return -1;
00028                 }
00029                 gnSequence contig_seq = mfa_seq.contig(i);
00030                 gnFASSource::Write( contig_seq, ofile, false, false );
00031         }
00032         return 0;
00033 }
00034 

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