private static void Main(string[] args)
{
Console.WriteLine("Welcome to TransferModifications!");
var p = new FluentCommandLineParser <ApplicationArguments>();
p.Setup(arg => arg.UniProtXml)
.As('x', "uniprot_xml")
.Required()
.WithDescription("UniProt protein XML file.");
p.Setup(arg => arg.SpritzXml)
.As('y', "spritz_xml")
.WithDescription("Custom protein XML file, e.g. from Spritz.");
p.Setup(arg => arg.FusionCodingEffects)
.As('f', "fusion_coding_effect")
.WithDescription("Coding effects from STAR-Fusion, comma separated");
p.SetupHelp("h", "help")
.Callback(text => Console.WriteLine(text));
var result = p.Parse(args);
TransferModifications(p.Object.UniProtXml, p.Object.SpritzXml ?? ProteinAnnotation.ParseCodingEffectsToXml(p.Object.FusionCodingEffects));
DatabaseSummary(p.Object.UniProtXml, p.Object.SpritzXml);
}
private static void Main(string[] args)
{
Console.WriteLine("Welcome to TransferModifications!");
var p = new FluentCommandLineParser <ApplicationArguments>();
p.Setup(arg => arg.UniProtXml)
.As('x', "uniprot_xml")
.WithDescription("UniProt protein XML file.");
p.Setup(arg => arg.SpritzXml)
.As('y', "spritz_xml")
.WithDescription("Custom protein XML file, e.g. from Spritz.");
p.Setup(arg => arg.FusionCodingEffects)
.As('f', "fusion_coding_effect")
.WithDescription("Coding effects from STAR-Fusion, comma separated");
p.Setup(arg => arg.SpritzModXml)
.As('z', "spritz_mod_xml")
.WithDescription("Custom protein XML withmods file, e.g. from Spritz.");
p.Setup(arg => arg.Setup)
.As('s', "setup")
.WithDescription("Perform setup for machines without internet connection.");
p.SetupHelp("h", "help")
.Callback(text => Console.WriteLine(text));
var result = p.Parse(args);
if (p.Object.Setup)
{
Console.WriteLine("Downloading files for TransferUniProtModifications.");
var uniprotPtms = ProteinAnnotation.GetUniProtMods(Environment.CurrentDirectory);
return;
}
Console.WriteLine($"Analyzing UniProt database {p.Object.UniProtXml} and {p.Object.SpritzXml ?? p.Object.SpritzModXml ?? p.Object.FusionCodingEffects}");
if (p.Object.SpritzModXml == null)
{
TransferModifications(p.Object.UniProtXml, p.Object.SpritzXml ?? ProteinAnnotation.ParseCodingEffectsToXml(p.Object.FusionCodingEffects));
}
DatabaseSummary(p.Object.UniProtXml, Path.Combine(Path.GetDirectoryName(p.Object.SpritzXml), Path.GetFileNameWithoutExtension(p.Object.SpritzXml) + ".withmods.xml"),
Path.Combine(Path.GetDirectoryName(p.Object.SpritzXml), Path.GetFileNameWithoutExtension(p.Object.SpritzXml) + ".accname.tsv"),
Path.Combine(Path.GetDirectoryName(p.Object.SpritzXml), Path.GetFileNameWithoutExtension(p.Object.SpritzXml) + ".vardesc.tsv"), true);
DatabaseSummary(p.Object.UniProtXml, Path.Combine(Path.GetDirectoryName(p.Object.SpritzXml), Path.GetFileNameWithoutExtension(p.Object.SpritzXml) + ".withmods.xml"),
Path.Combine(Path.GetDirectoryName(p.Object.SpritzXml), Path.GetFileNameWithoutExtension(p.Object.SpritzXml) + ".accname.decoy.tsv"),
Path.Combine(Path.GetDirectoryName(p.Object.SpritzXml), Path.GetFileNameWithoutExtension(p.Object.SpritzXml) + ".vardesc.decoy.tsv"), false);
}