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 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;
}