public override bool PrepareOptions()
{
if (File.Exists(ParamFile))
{
SmallRNADatabaseBuilderOptions op = new SmallRNADatabaseBuilderOptions();
op.LoadFromFile(ParamFile);
Console.WriteLine("param:mirna=" + op.MiRBaseFile);
Console.WriteLine("param:mirbase_key=" + op.MiRBaseKey);
Console.WriteLine("param:ensembl=" + op.EnsemblGtfFile);
Console.WriteLine("param:trna=" + op.UcscTrnaFile);
Console.WriteLine("param:rrna=" + op.RRNAFile);
Console.WriteLine("param:genome=" + op.FastaFile);
Console.WriteLine("param:output=" + op.OutputFile);
if (string.IsNullOrEmpty(this.MiRBaseFile))
{
this.MiRBaseFile = op.MiRBaseFile;
}
if (string.IsNullOrEmpty(this.MiRBaseKey))
{
this.MiRBaseKey = op.MiRBaseKey;
}
if (string.IsNullOrEmpty(this.UcscTrnaFile))
{
this.UcscTrnaFile = op.UcscTrnaFile;
}
if (string.IsNullOrEmpty(this.RRNAFile))
{
this.RRNAFile = op.RRNAFile;
}
if (string.IsNullOrEmpty(this.EnsemblGtfFile))
{
this.EnsemblGtfFile = op.EnsemblGtfFile;
}
if (string.IsNullOrEmpty(this.FastaFile))
{
this.FastaFile = op.FastaFile;
}
if (string.IsNullOrEmpty(this.OutputFile))
{
this.OutputFile = op.OutputFile;
}
}
if (!string.IsNullOrEmpty(this.MiRBaseFile) && !File.Exists(this.MiRBaseFile))
{
ParsingErrors.Add(string.Format("Input miRBase file not exists {0}.", this.MiRBaseFile));
}
if (!string.IsNullOrEmpty(this.UcscTrnaFile) && !File.Exists(this.UcscTrnaFile))
{
ParsingErrors.Add(string.Format("Input tRNA file not exists {0}.", this.UcscTrnaFile));
}
if (!string.IsNullOrEmpty(this.RRNAFile) && !File.Exists(this.RRNAFile))
{
ParsingErrors.Add(string.Format("Input rRNA file not exists {0}.", this.RRNAFile));
}
if (!string.IsNullOrEmpty(this.EnsemblGtfFile) && !File.Exists(this.EnsemblGtfFile))
{
ParsingErrors.Add(string.Format("Input ensembl GTF file not exists {0}.", this.EnsemblGtfFile));
}
if (!File.Exists(this.FastaFile))
{
ParsingErrors.Add(string.Format("Input genome sequence file not exists {0}.", this.FastaFile));
}
return ParsingErrors.Count == 0;
}
public SmallRNADatabaseBuilder(SmallRNADatabaseBuilderOptions options)
{
this.options = options;
}
public SmallRNADatabaseBuilder(SmallRNADatabaseBuilderOptions options)
{
this.options = options;
}
public override bool PrepareOptions()
{
if (File.Exists(ParamFile))
{
SmallRNADatabaseBuilderOptions op = new SmallRNADatabaseBuilderOptions();
op.LoadFromFile(ParamFile);
if (string.IsNullOrEmpty(this.MiRBaseFile))
{
this.MiRBaseFile = op.MiRBaseFile;
}
if (string.IsNullOrEmpty(this.MiRBaseKey))
{
this.MiRBaseKey = op.MiRBaseKey;
}
if (string.IsNullOrEmpty(this.UcscTrnaFile))
{
this.UcscTrnaFile = op.UcscTrnaFile;
}
if (string.IsNullOrEmpty(this.UcscMatureTrnaFastaFile))
{
this.UcscMatureTrnaFastaFile = op.UcscMatureTrnaFastaFile;
}
if (string.IsNullOrEmpty(this.RRNAFile))
{
this.RRNAFile = op.RRNAFile;
}
if (string.IsNullOrEmpty(this.EnsemblGtfFile))
{
this.EnsemblGtfFile = op.EnsemblGtfFile;
}
if (string.IsNullOrEmpty(this.FastaFile))
{
this.FastaFile = op.FastaFile;
}
if (string.IsNullOrEmpty(this.OutputFile))
{
this.OutputFile = op.OutputFile;
}
}
if (!string.IsNullOrEmpty(this.MiRBaseFile) && !File.Exists(this.MiRBaseFile))
{
ParsingErrors.Add(string.Format("Input miRBase file not exists {0}.", this.MiRBaseFile));
}
if (!string.IsNullOrEmpty(this.UcscTrnaFile) && !File.Exists(this.UcscTrnaFile))
{
ParsingErrors.Add(string.Format("Input tRNA file not exists {0}.", this.UcscTrnaFile));
}
if (!string.IsNullOrEmpty(this.UcscMatureTrnaFastaFile) && !File.Exists(this.UcscMatureTrnaFastaFile))
{
ParsingErrors.Add(string.Format("Input mature tRNA FASTA file not exists {0}.", this.UcscMatureTrnaFastaFile));
}
if (!string.IsNullOrEmpty(this.RRNAFile) && !File.Exists(this.RRNAFile))
{
ParsingErrors.Add(string.Format("Input rRNA file not exists {0}.", this.RRNAFile));
}
if (!string.IsNullOrEmpty(this.EnsemblGtfFile) && !File.Exists(this.EnsemblGtfFile))
{
ParsingErrors.Add(string.Format("Input ensembl GTF file not exists {0}.", this.EnsemblGtfFile));
}
if (!File.Exists(this.FastaFile))
{
ParsingErrors.Add(string.Format("Input genome sequence file not exists {0}.", this.FastaFile));
}
Console.WriteLine("param:mirna=" + this.MiRBaseFile);
Console.WriteLine("param:mirbase_key=" + this.MiRBaseKey);
Console.WriteLine("param:ensembl=" + this.EnsemblGtfFile);
Console.WriteLine("param:trna=" + this.UcscTrnaFile);
Console.WriteLine("param:mature_trna=" + this.UcscMatureTrnaFastaFile);
Console.WriteLine("param:rrna=" + this.RRNAFile);
Console.WriteLine("param:genome=" + this.FastaFile);
Console.WriteLine("param:output=" + this.OutputFile);
return(ParsingErrors.Count == 0);
}