public Pragma Parse(string line)
{
string[] pragmaParts = line.Trim().Replace(Prefix, "").Split(new char[] { ' ' }, 2);
Pragma pragma = new Pragma() {
Name = pragmaParts[0]
};
// The sequence region pragma has values without keys, so we are going to
// add them here to enrich the data (instead of storing it as a flat string).
if (pragma.Name == "sequence-region")
{
var sequenceParts = pragmaParts[1].Split(new char[] { ' ', '\t' }, StringSplitOptions.RemoveEmptyEntries);
pragmaParts = new string[2]
{
pragma.Name,
string.Format("Chromosome={0};Start position={1};End position={2}", sequenceParts[0], sequenceParts[1], sequenceParts[2])
};
}
// Some pragmas are just a string value. We can identify those by their lack of a delimiter
// for a tag key-value pair.
if (!pragmaParts[1].Contains(KeyValueParser.TagKeyValueDelimiter))
{
pragma.Value = pragmaParts[1];
return pragma;
}
KeyValueParser kvParser = new KeyValueParser();
pragma.Tags.AddRange(kvParser.Parse(pragmaParts[1]));
return pragma;
}
private phenotype CreatePhenotype(Pragma pragma)
{
phenotype phenotype = new phenotype();
var tag = pragma.Tags.FirstOrDefault(x => x.Name == "Ontology");
if (tag != null)
{
phenotype.external_source = tag.Value;
}
tag = pragma.Tags.FirstOrDefault(x => x.Name == "Term");
if (tag != null)
{
phenotype.external_id = tag.Value;
}
tag = pragma.Tags.FirstOrDefault(x => x.Name == "Comment");
if (tag != null)
{
phenotype.name = tag.Value;
}
return phenotype;
}
