public static int Main(string[] args)
{
if (args.Length % 2 != 0)
{
DisplayUsage("odd number of arguments");
return(1);
}
string RegexFile = "";
string PssmFile = "";
string DatabaseFile = "";
string VariantsFile = "";
string OutputDir = ".";
bool grouping = false;
for (int i = 0; i < args.Length; i += 2)
{
if (args[i][0] != '-' || args[i].Length != 2)
{
DisplayUsage("incorrect argument specifier");
return(1);
}
switch (args[i][1])
{
case 'o': OutputDir = args[i + 1]; break;
case 'd': DatabaseFile = args[i + 1]; break;
case 'r': RegexFile = args[i + 1]; break;
case 'p': PssmFile = args[i + 1]; break;
case 'v': VariantsFile = args[i + 1]; break;
case 'g': grouping = args[i + 1][0] != '0'; break;
default: DisplayUsage("specifier '" + args[i] + "'not known"); return(1);
}
}
if (DatabaseFile.Length == 0 || RegexFile.Length == 0)
{
DisplayUsage("missing mandatory parameters");
return(1);
}
if (!DatabaseFile.Contains(".fasta") && !DatabaseFile.Contains(".xml.gz"))
{
DisplayUsage("database file format not recognized");
return(1);
}
if (!DatabaseFile.Contains(".xml.gz") && VariantsFile.Length != 0)
{
DisplayUsage("variants are only supported with UniProt XML input file");
return(1);
}
// Use '.' as decimal separator
Thread.CurrentThread.CurrentCulture = new System.Globalization.CultureInfo("en-US", false);
WregexConsole app = new WregexConsole();
app.Create(RegexFile, PssmFile, DatabaseFile, VariantsFile, OutputDir, grouping);
//app.Dump();
app.Run();
return(0);
}
public static int Main( string[] args )
{
if( args.Length % 2 != 0 ) {
DisplayUsage( "odd number of arguments" );
return 1;
}
string RegexFile="";
string PssmFile="";
string DatabaseFile="";
string VariantsFile="";
string OutputDir=".";
bool grouping = false;
for( int i = 0; i < args.Length; i += 2 ) {
if( args[i][0] != '-' || args[i].Length != 2 ) {
DisplayUsage( "incorrect argument specifier" );
return 1;
}
switch( args[i][1] ) {
case 'o': OutputDir = args[i+1]; break;
case 'd': DatabaseFile = args[i+1]; break;
case 'r': RegexFile = args[i+1]; break;
case 'p': PssmFile = args[i+1]; break;
case 'v': VariantsFile = args[i+1]; break;
case 'g': grouping = args[i+1][0] != '0'; break;
default: DisplayUsage( "specifier '" + args[i] + "'not known" ); return 1;
}
}
if( DatabaseFile.Length == 0 || RegexFile.Length == 0 ) {
DisplayUsage( "missing mandatory parameters" );
return 1;
}
if( !DatabaseFile.Contains(".fasta") && !DatabaseFile.Contains(".xml.gz") ) {
DisplayUsage( "database file format not recognized" );
return 1;
}
if( !DatabaseFile.Contains(".xml.gz") && VariantsFile.Length != 0 ) {
DisplayUsage( "variants are only supported with UniProt XML input file" );
return 1;
}
// Use '.' as decimal separator
Thread.CurrentThread.CurrentCulture = new System.Globalization.CultureInfo( "en-US", false );
WregexConsole app = new WregexConsole();
app.Create( RegexFile, PssmFile, DatabaseFile, VariantsFile, OutputDir, grouping );
//app.Dump();
app.Run();
return 0;
}