public AmericanGut(FileInfo file)
{
SampleId = file.Name;
char[] sep1 = { '\t' };
char[] sep2 = { ';' };
_dataTable = DataInterfaces.GetTaxNameRankDataTable();
var lines = File.ReadAllLines(file.FullName);
//First line is the header
for (var i = 1; i < lines.Length; i++)
{
if (!string.IsNullOrWhiteSpace(lines[i]))
{
var parts1 = lines[i].Split(sep1, StringSplitOptions.RemoveEmptyEntries);
if (parts1.Length == 2)
{
var rank = "no rank";
var name = "";
double count = 0.0;
double.TryParse(parts1[1], out count);
count = count * 1000000;
var parts2 = parts1[0].Split(sep2, StringSplitOptions.RemoveEmptyEntries);
// We start with the last one and walk back.
for (var j = parts2.Length - 1; j > 0; j--)
{
var part = parts2[j];
if (part.Length > 5) //elimate empty ones, i.e. ;g__ with nothing
{
switch (part.Substring(0, 1))
{
case "k": rank = "kingdom"; break;
case "p": rank = "phylum"; break;
case "c": rank = "class"; break;
case "o": rank = "order"; break;
case "f": rank = "family"; break;
case "g": rank = "genus"; break;
case "s": rank = "species"; break;
}
name = part.Substring(3);
break;
}
}
if (name.Length > 3)
{
var row = _dataTable.NewRow();
row["tax_rank"] = rank;
row["tax_name"] = name;
row["BaseOneMillion"] = count;
_dataTable.Rows.Add(row);
}
}
}
}
}
public Thryve(FileInfo ubiomeFile)
{
char[] sep = { ',' };
var lines = File.ReadAllLines(ubiomeFile.FullName);
_dataTable = DataInterfaces.GetTaxonDataTable();
for (var i = 1; i < lines.Length; i++)
{
if (string.IsNullOrWhiteSpace(lines[i]))
{
var parts = lines[i].Split(sep, StringSplitOptions.None);
int count = 0;
int.TryParse(parts[parts.Length - 1], out count);
var row = _dataTable.NewRow();
row["taxon"] = parts[0];
row["taxonBaseOneMillion"] = (double)count;
row["count"] = count;
_dataTable.Rows.Add(row);
}
}
SampleId = Guid.NewGuid().ToString();;
DateTime sampleDate = DateTime.UtcNow;
SampleDateTime = sampleDate;
}
public static void ComputeAllLabs(int quantiles)
{
var labTests = DataInterfaces.GetLabTests();
foreach (DataRow row in labTests.Rows)
{
ComputeOneLab((int)row["LabTestId"], quantiles);
}
}
static void Main(string[] args)
{
DataInterfaces.ConnectionString = "Server=LAPTOP-BQ764BQT;Database=MicrobiomeV2;Trusted_Connection=True; Connection Timeout=1000";
var export = DataInterfaces.GetFlatTaxonomy("species").ToCsvString();
File.WriteAllLines("DataScience_Taxon.csv", DataInterfaces.GetFlatTaxonomy("species").ToCsvString());
File.WriteAllLines("DataScience_Continuous.csv", DataInterfaces.GetFlatContinuous( ).ToCsvString());
File.WriteAllLines("DataScience_Category.csv", DataInterfaces.GetFlatCategory().ToCsvString());
File.WriteAllLines("DataScience_LabReport.csv", DataInterfaces.GetLabReport().ToCsvString());
}
static void Main(string[] args)
{
DataInterfaces.ConnectionString = "Server=LAPTOP-BQ764BQT;Database=MicrobiomeV2;Trusted_Connection=True; Connection Timeout=1000";
var data = DataInterfaces.GetNonParametricCategoryDataSet(1, 1, "Q4_", 20);
var matrix = MicrobiomeLibrary.Statistics.NonParametric.CategoricSignficance(data);
if (matrix.Rows.Count > 0) //Only write when we have data
{
matrix.WriteXml("Matrix.xml");
}
}
public static void ComputeFull()
{
var labTests = DataInterfaces.GetLabTests();
foreach (DataRow row in labTests.Rows)
{
for (var q = 3; q < 20; q++)
{
if (!ComputeOneLab((int)row["LabTestId"], q))
{
break;
}
}
}
}
static void Main(string[] args)
{
DataInterfaces.ConnectionString = "Server=LAPTOP-BQ764BQT;Database=OnlineClone;Trusted_Connection=True; Connection Timeout=1000";
var exportFile = new FileInfo("data\\Biome2Data.xml");
var schemaFile = new FileInfo("data\\Biome2Schema.xml");
if (!(exportFile.Exists && schemaFile.Exists))
{
throw new Exception($"Data file does not exits {exportFile.FullName} or schema {schemaFile.FullName}");
}
var import = new DataSet();
import.ReadXmlSchema(schemaFile.FullName);
import.ReadXml(exportFile.FullName);
DataInterfaces.Import(import);
LabTests.ComputeFull();
}
static void Main(string[] args)
{
var exportName = "some site";
var filename = "MyExport";
if (args.Length > 0)
{
exportName = args[0];
}
if (args.Length > 1)
{
filename = args[1];
}
DataInterfaces.ConnectionString = "Server=LAPTOP-BQ764BQT;Database=MicrobiomeV2;Trusted_Connection=True; Connection Timeout=1000";
var schemaFile = new FileInfo($"{filename}Schema.xml");
var exportFile = new FileInfo($"{filename}.xml");
var export = DataInterfaces.Export(exportName);
export.WriteXmlSchema(schemaFile.FullName);
export.WriteXml(exportFile.FullName);
}
public static bool ComputeOneLab(int labTestId, int quantiles)
{
var dataTable = DataInterfaces.GetTaxonReports(labTestId);
var statistics = new CoreStatistics(quantiles);
int activeTaxon = -1;
var values = new List <double>();
foreach (DataRow row in dataTable.Rows)
{
var id = (int)row["taxon"];
if (activeTaxon < 0)
{
activeTaxon = id;
}
if (activeTaxon != id)
{
if (values.Count > 0 && activeTaxon > 0)
{
if (values.Count >= quantiles * MinCountInQuantile)
{
statistics.ProcessATaxon(activeTaxon, values.ToArray());
}
values.Clear();
activeTaxon = (int)row["taxon"];
}
}
values.Add((double)row["value"]);
}
// get the last taxon processed
if (values.Count >= quantiles * MinCountInQuantile)
{
statistics.ProcessATaxon(activeTaxon, values.ToArray());
}
DataInterfaces.UpdateStatistics(statistics.StatsDatatable, labTestId);
return(statistics.StatsDatatable.Rows.Count > 5);
}
public Ubiome(FileInfo ubiomeFile)
{
var filestream = new System.IO.FileStream(ubiomeFile.FullName,
System.IO.FileMode.Open,
System.IO.FileAccess.Read);
var file = new System.IO.StreamReader(filestream, System.Text.Encoding.UTF8, true, 128);
var json = JsonConvert.DeserializeObject <UbiomeHeaders>(file.ReadToEnd());
_dataTable = DataInterfaces.GetTaxonDataTable();
foreach (var count in json.UbiomeBacteriacounts)
{
var row = _dataTable.NewRow();
row["taxon"] = count.Taxon;
row["taxonBaseOneMillion"] = (double)count.CountNorm;
row["count"] = count.Count;
row["count_norm"] = count.CountNorm;
_dataTable.Rows.Add(row);
}
SampleId = json.SequencingRevision.ToString();
DateTime sampleDate = DateTime.UtcNow;
DateTime.TryParse(json.SamplingTime, out sampleDate);
SampleDateTime = sampleDate;
}
public int SaveToDatabase(string ownerEmail)
{
return(DataInterfaces.Savedata(ownerEmail, LabName, LabTestName, SampleId, SampleDateTime, _dataTable));
}
public XenoGene(FileInfo file)
{
_dataTable = DataInterfaces.GetTaxNameRankDataTable();
SampleDateTime = DateTime.UtcNow;
char[] lineSep = { '\r', '\n' };
char[] sep = { ' ' };
var txt = ReadPdfFile(file.FullName);
var lines = txt.Split(lineSep, StringSplitOptions.RemoveEmptyEntries);
string appliesToNextLine = "";
int lineNo = 0;
double amount = 0.0;
foreach (var line in lines)
{
var skip = false;
string rank = "";
string name = "";
if (line.IndexOf("ORDEN", StringComparison.OrdinalIgnoreCase) == 0)
{
skip = true;
}
if (line.IndexOf("INFO", StringComparison.OrdinalIgnoreCase) == 0)
{
skip = true;
}
if (line.IndexOf("REPORT", StringComparison.OrdinalIgnoreCase) == 0)
{
skip = true;
}
if (line.IndexOf("Xeno", StringComparison.OrdinalIgnoreCase) == 0)
{
skip = true;
}
if (line.IndexOf("Inscrita", StringComparison.OrdinalIgnoreCase) == 0)
{
skip = true;
}
if (line.IndexOf("Pág", StringComparison.OrdinalIgnoreCase) == 0)
{
skip = true;
}
if (!skip)
{
var firstSpace = line.IndexOf(" ");
var firstComma = line.IndexOf(",");
var lineNoTest = firstSpace < 0 ? "na" : line.Substring(0, firstSpace);
if (int.TryParse(lineNoTest, out lineNo))
{
//If missing no number
if (firstComma < 0)
{
name = line;
}
else
{
var parts = line.Split(sep, StringSplitOptions.RemoveEmptyEntries);
var lastItem = parts[parts.Length - 1];
if (lastItem.Contains(",")) //european number
{
lastItem = lastItem.Replace(",", ".");
if (double.TryParse(lastItem, out amount))
{
amount = amount * 10000.0; //permission
switch (parts[2])
{
case "G": rank = "genus"; break;
case "G1": rank = "genus"; break;
case "G2": rank = "genus"; break;
case "C": rank = "class"; break;
case "C1": rank = "class"; break;
case "C2": rank = "class"; break;
case "F": rank = "family"; break;
case "S": rank = "species"; break;
case "S1": rank = "strain"; break;
case "S2": rank = "strain"; break;
case "S3": rank = "strain"; break;
case "O": rank = "Order"; break;
case "F1": rank = "no rank"; break;
case "F2": rank = "no rank"; break;
case "F3": rank = "no rank"; break;
case "O1": rank = "no rank"; break;
case "O2": rank = "no rank"; break;
case "O3": rank = "no rank"; break;
case "P1": rank = "no rank"; break;
case "D1": rank = "skip"; break;
case "D2": rank = "skip"; break;
case "D3": rank = "skip"; break;
case "U": rank = "skip"; break;
case "R": rank = "skip"; break;
case "R1": rank = "skip"; break;
case "P": rank = "phylum"; break;
default:
rank = "skip";
Console.WriteLine($"Unknown {parts[2]}");
break;
}
if (parts.Length > 4)
{
var sb = new StringBuilder(parts[3]);
for (var p = 4; p < parts.Length - 1; p++)
{
sb.Append($" {parts[p]}");
}
name = sb.ToString();
}
if (!rank.Equals("skip", StringComparison.OrdinalIgnoreCase) && amount > 0.0 && !string.IsNullOrWhiteSpace(name))
{
Console.WriteLine(name);
var row = _dataTable.NewRow();
row["tax_rank"] = rank;
row["tax_name"] = name;
row["BaseOneMillion"] = amount;
_dataTable.Rows.Add(row);
}
}
}
}
}
else
{
appliesToNextLine = line;
}
}
}
SampleId = file.Name;
}
