public IEnumerable <DigestedPeptide> DigestSequence(string proteinSequence, int maxMissedCleavages, int?maxPeptideSequenceLength)
{
if (string.IsNullOrEmpty(proteinSequence))
{
yield break;
}
FastaSequence fastaSequence;
try
{
fastaSequence = new FastaSequence(@"name", @"description", new List <ProteinMetadata>(), proteinSequence);
}
catch (InvalidDataException)
{
// It's possible that the peptide sequence in the fasta file was bogus, in which case we just don't digest it.
yield break;
}
var digestSettings = new DigestSettings(maxMissedCleavages, false);
foreach (var digest in _enzyme.Digest(fastaSequence, digestSettings, maxPeptideSequenceLength))
{
var digestedPeptide = new DigestedPeptide
{
Index = digest.Begin ?? 0,
Sequence = digest.Target.Sequence
};
yield return(digestedPeptide);
}
}
public IEnumerable <DigestedPeptide> Digest(Protein protein)
{
if (string.IsNullOrEmpty(protein.Sequence))
{
yield break;
}
FastaSequence fastaSequence;
try
{
fastaSequence = new FastaSequence("name", "description", new List <ProteinMetadata>(), protein.Sequence); // Not L10N
}
catch (InvalidDataException)
{
// It's possible that the peptide sequence in the fasta file was bogus, in which case we just don't digest it.
yield break;
}
DigestSettings digestSettings = new DigestSettings(6, false);
foreach (var digest in _enzyme.Digest(fastaSequence, digestSettings))
{
var digestedPeptide = new DigestedPeptide
{
Index = digest.Begin ?? 0,
Sequence = digest.Sequence
};
yield return(digestedPeptide);
}
}
public static DigestedFastaFile parseDigestedFasta(String fileName)
{
// List to store the objects of each in-silico digested peptide
List <DigestedPeptide> ArrDigest = new List <DigestedPeptide>();
log.Debug("Parsing the digested FASTA file.");
try
{
log.Debug("File path: " + fileName);
StreamReader reader = new StreamReader(fileName);
String line = reader.ReadLine();
// read lines
while (line != null)
{
/*-
* Reads the lines of the file into an array of Strings, after each "tab", text
* is stored in new cell. Header shown below:
* sequence/protein/mass/missedCleavages/specificity/nTerminusIsSpecific/cTerminusIsSpecific
*/
String[] values = line.Split("\t".ToCharArray());
// Skip the header
if (values[0].Equals("sequence"))
{
// Move to the next line
line = reader.ReadLine();
values = line.Split("\t".ToCharArray());
}
String sequence = values[0]; // peptide sequence
String accession = values[1]; // accession of the parent protein
double mass = Double.Parse(values[2]);
DigestedPeptide digPeps = new DigestedPeptide(sequence, accession, mass);
ArrDigest.Add(digPeps);
line = reader.ReadLine();
}
reader.Close();
log.Debug("Done parsing the digested FASTA file.");
}
catch (Exception e)
{
Console.WriteLine(e.ToString());
log.Error("Digested FASTA file not correctly parsed.");
Environment.Exit(0);
}
return(new DigestedFastaFile(fileName, ArrDigest));
}
