private void Create( string RegexFile, string PssmFile, string DatabaseFile, string VariantsFile, string OutputDir, bool grouping )
{
string line;
// regex
UnixCfg rd = new UnixCfg( RegexFile );
line = rd.ReadUnixLine();
if( line == null )
throw new ApplicationException( "Empty regex" );
rd.Close();
if( PssmFile.Length > 0 )
mRegex = new WregexManager( line, new PSSM(PssmFile), grouping );
else
mRegex = new WregexManager( line, grouping );
// Fasta
mSeqs = new List<Fasta>();
if( DatabaseFile.Contains(".fasta") )
LoadFasta( DatabaseFile );
else {
SortedList<string,List<Variant>> list = null;
if( VariantsFile.Length != 0 )
list = LoadVariants( VariantsFile );
LoadXml( DatabaseFile, list );
}
// Sort Variants
foreach( Fasta seq in mSeqs )
seq.mVariants.Sort();
mDataId = Path.GetFileNameWithoutExtension( DatabaseFile );
mOutputDir = OutputDir;
Directory.CreateDirectory( OutputDir );
}
private void LoadFasta( string path )
{
string line;
//char[] sep = new char[]{'|',' ','\t'};
char[] sep = new char[]{'|'};
Variant v;
UnixCfg rd = new UnixCfg( path );
line = rd.ReadUnixLine();
if( line == null || line[0] != '>' )
throw new ApplicationException( "FASTA header not found" );
Fasta f = new Fasta(Fasta.Type.Protein, line.Split(sep)[0].Substring(1), "");
do {
line = rd.ReadUnixLine();
if( line == null || line[0] == '>' ) { // EOF or next element
if( f.mSequence.Length == 0 )
throw new ApplicationException( "FASTA sequence not found" );
mSeqs.Add(f);
if( line != null )
f = new Fasta(Fasta.Type.Protein, line.Split(sep)[0].Substring(1), "");
} else if( line.StartsWith("NP_") ) { // Variant
v = new Variant(line);
if( !f.mVariants.Contains(v) )
f.mVariants.Add(v);
}
else // Sequence
f.mSequence += line;
} while( line != null );
rd.Close();
}
/*public void Load( string filename ) {
UnixCfg rd = new UnixCfg( filename );
string line = rd.ReadUnixLine();
char[] sep = new char[]{ ':' };
string[] fields;
while( line != null ) {
PSSMposition pos;
pos.order = uint.Parse( line.Replace("{","") );
pos.entries = new List<PSSMentry>();
line = rd.ReadUnixLine();
while( line != null && !line.Contains("}") ) {
PSSMentry entry;
fields = line.Split( sep );
entry.condition = fields[0].Trim();
entry.score = double.Parse( fields[1] );
pos.entries.Add( entry );
line = rd.ReadUnixLine();
}
if( line != null )
line = rd.ReadUnixLine();
m_pssm.Add( pos );
}
rd.Close();
}*/
public void Load( string filename )
{
UnixCfg rd = new UnixCfg( filename );
char[] sep = new char[]{ ' ', '\t' };
string[] fields;
PSSMentry entry;
string line = rd.ReadUnixLine();
if( line == null ) {
rd.Close();
return;
}
fields = line.Split( sep );
PSSMposition[] pos = new PSSMposition[fields.Length-1];
for( uint i = 0; i < pos.Length; i++ ) {
pos[i].order = i;
pos[i].entries = new List<PSSMentry>();
}
do {
fields = line.Split( sep );
entry.condition = fields[0].Trim();
for( uint i = 0; i < pos.Length; i++ ) {
entry.score = double.Parse( fields[i+1] );
pos[i].entries.Add( entry );
}
line = rd.ReadUnixLine();
} while( line != null );
rd.Close();
m_pssm.AddRange( pos );
}