public async Task Index()
{
var reader = await FastaReader.CreateAsync(FastaPath);
foreach (var identifier in reader.Identifiers)
{
var comment = reader.CommentOf(identifier);
var attributes = AttributesParser.Parse(comment);
var id = attributes.GetValueOrDefault("protein_id");
if (id == null)
{
throw new Exception("Id missing");
}
var range = ParseRange(attributes.GetValueOrDefault("location", ""));
var data = new GeneData(id, SequenceId)
{
Symbol = attributes.GetValueOrDefault("gene"),
Product = attributes.GetValueOrDefault("protein"),
LocusTag = attributes.GetValueOrDefault("locus_tag") ?? throw new Exception("Locus tag missing"),
// We can infer this from the fasta reader if we prevent '\n' from being in the sequence
Position = range?.Item1,
Length = range != null ? range?.Item2 - range?.Item1 + 1 : null
};
await Database.Index(data);
}
}
}
public void TestAttributeParser()
{
// arrange
const string mapboxfile = "mapbox.vector.tile.tests.testdata.14-8801-5371.vector.pbf";
var pbfStream = Assembly.GetExecutingAssembly().GetManifestResourceStream(mapboxfile);
var tile = Serializer.Deserialize <Tile>(pbfStream);
var keys = tile.Layers[0].Keys;
var values = tile.Layers[0].Values;
var tagsf1 = tile.Layers[0].Features[0].Tags;
// act
var attributes = AttributesParser.Parse(keys, values, tagsf1);
// assert
Assert.IsTrue(attributes.Count == 2);
Assert.IsTrue(attributes[0].Key == "class");
Assert.IsTrue((string)attributes[0].Value == "park");
Assert.IsTrue(attributes[1].Key == "osm_id");
Assert.IsTrue(attributes[1].Value.ToString() == "3000000224480");
}
public PsaMovesetHandler(PsaFile psaFile)
{
PsaFile = psaFile;
AttributesHandler = new AttributesParser(PsaFile);
DataTableHandler = new DataTableHandler(PsaFile);
ExternalDataHandler = new ExternalDataHandler(PsaFile);
int dataSectionLocation = DataTableHandler.GetDataTableEntryByName("data").Location;
string movesetBaseName = GetMovesetBaseName();
int numberOfSpecialActions = (PsaFile.DataSection[dataSectionLocation + 10] - PsaFile.DataSection[dataSectionLocation + 9]) / 4;
int codeBlockDataStartLocation = 2014 + numberOfSpecialActions * 2;
PsaCommandHandler psaCommandHandler = new PsaCommandHandler(psaFile, dataSectionLocation, codeBlockDataStartLocation);
CodeBlocksHandler codeBlocksHandler = new CodeBlocksHandler(psaFile, dataSectionLocation, psaCommandHandler);
ActionsHandler = new ActionsHandler(PsaFile, dataSectionLocation, codeBlocksHandler, psaCommandHandler);
SubActionsHandler = new SubActionsHandler(PsaFile, dataSectionLocation, codeBlocksHandler, psaCommandHandler);
SubRoutinesHandler = new SubRoutinesHandler(PsaFile, dataSectionLocation, ActionsHandler, SubActionsHandler, psaCommandHandler);
ActionOverridesHandler = new ActionOverridesHandler(PsaFile, dataSectionLocation, ActionsHandler, psaCommandHandler);
ArticlesHandler = new ArticlesHandler(PsaFile, dataSectionLocation, movesetBaseName, psaCommandHandler);
CharacterParamsHandler = new CharacterParamsHandler(PsaFile, dataSectionLocation, movesetBaseName, psaCommandHandler);
MiscHandler = new MiscHandler(PsaFile, dataSectionLocation, movesetBaseName, numberOfSpecialActions);
}
