public YSTRLib(string input_vcf_gz)
{
_input_vcf_gz = input_vcf_gz;
string exe_path = @"bin\ubin\";//Path.GetTempPath();
bcftools_exe = exe_path + "bcftools.exe";
//if (!File.Exists(bcftools_exe))
// File.WriteAllBytes(bcftools_exe, Y_STR_Finder.Properties.Resources.bcftools_exe);
//if (!File.Exists(exe_path + "cygwin1.dll"))
// File.WriteAllBytes(exe_path + "cygwin1.dll", Y_STR_Finder.Properties.Resources.cygwin1_dll);
//if (!File.Exists(exe_path + "cygz.dll"))
// File.WriteAllBytes(exe_path + "cygz.dll", Y_STR_Finder.Properties.Resources.cygz_dll);
_lib = this;
}
// bin\bgzip.exe bam_chrY.vcf
// bin\tabix.exe bam_chrY.vcf.gz
// bin\bcftools.exe query -f '%POS\t[%TGT]\n' -r chrY:3131128-3131246 bam_chrY.vcf.gz > DYS393.txt
static void Main(string[] args)
{
StringBuilder report = new StringBuilder();
if (args.Length != 3)
{
Console.WriteLine("*** This program is not designed to work independently. Use it at your own risk ***");
Console.WriteLine("ystrfinder.exe <ref> <in_vcf_bgz> <out_report_html>");
return;
}
string yref_file = args[0]; //"ystr_info.txt";
string intput_file = args[1]; // @"C:\Genetics\Y-STR Kit\bam_chrY.vcf.gz";
string out_file = args[2];
if (!File.Exists(yref_file) || !File.Exists(intput_file))
{
Console.WriteLine("input/ref does not exist!");
return;
}
YSTRLib ylib = new YSTRLib(intput_file);
string[] lines = File.ReadAllLines(yref_file);
string[] data = null;
string ystr = null;
long begin_pos = 0;
long end_pos = 0;
string regex_motif = null;
string filter_motif = null;
string replace_regex = null;
String rpt_table_overview = Y_STR_Finder.Properties.Resources.ystr_overview;
report.Append("<html><head><title>Y-STR Kit Report</title></head><body style='font-family:Calibri; Color:black; font-style:normal'><h1>Y-STR Kit Report</h1>");
report.Append("@TABLE@");
foreach (string line in lines)
{
if (line.StartsWith("#") || line.Trim() == "")
{
continue;
}
data = line.Split(new char[] { '\t' });
if (data[0].StartsWith("TITLE"))
{
report.Append("<h2>" + data[1] + "</h2>");
continue;
}
ystr = data[0];
begin_pos = long.Parse(data[1]);
end_pos = long.Parse(data[2]);
regex_motif = data[3];
filter_motif = data[4];
replace_regex = data[5];
YStrResult result = ylib.getYSTR(begin_pos, end_pos, regex_motif, filter_motif, replace_regex);
//Console.WriteLine(ystr + " = " + result.value+"\t["+result.reliability+"]");
report.Append("<a name='" + ystr + "'></a>");
report.Append("<h3>" + ystr + " = " + result.value + "</h3>");
report.Append("<i>Location: ChrY:" + begin_pos + "-" + end_pos + "</i><br>");
report.Append("<div style='width:600px; padding:10px;word-wrap: break-word;color:#909090;font-family: monospace;'>" + result.html_seq + "</div>");
report.Append("<i>Reliability is " + result.reliability + "%</i><br><br>");
rpt_table_overview = rpt_table_overview.Replace("@" + ystr + "@", result.value.ToString());
if (result.reliability == 100)
{
rpt_table_overview = rpt_table_overview.Replace("@" + ystr + "_COLOR@", "green");
}
else
{
rpt_table_overview = rpt_table_overview.Replace("@" + ystr + "_COLOR@", "red");
}
//Console.WriteLine(result.raw_seq);
//Console.WriteLine();
}
report.Append("<i>Report generated by <a href='http://www.y-str.org/'>Y-STR Kit</a>.</i>");
report.Append("</body></html>");
string final_report = report.ToString();
final_report = final_report.Replace("@TABLE@", rpt_table_overview);
File.WriteAllText(out_file, final_report);
}
