Read SNP annotation file

bio/std/genotype/snp.d

@@ -0,0 +1,62 @@
+/*
+    This file is part of BioD.
+
+    Copyright (C) 2018 Pjotr Prins <pjotr.prins@thebird.nl>
+*/
+
+module bio.std.genotype.snp;
+
+import std.algorithm;
+import std.array;
+import std.conv;
+import std.exception;
+import std.experimental.logger;
+import std.stdio;
+
+/*
+
+  Functions around SNPs
+
+*/
+
+struct SNP {
+  string name;
+  string chr;
+  long pos;   // -1 if NA
+  double cm;  // centimorgan, -1 if NA
+}
+
+/*
+  Fetch SNP annotations from tab delimited file that looks like name,
+  pos, chr, cM
+
+  rs3668922       111771071       13      65.0648
+  rs13480515      17261714        10      4.72355
+  rs13483034      53249416        17      30.175
+
+  NA values can be used and the last cM column is optional.
+*/
+
+SNP[] fetch_snp_annotations(string filen) {
+  SNP[] list;
+
+  bool[string] names;
+
+  info("Parsing ",filen);
+  File f = File(filen);
+
+  foreach(line; f.byLine) {
+    auto fields = line.split("\t");
+    auto name = to!string(fields[0]);
+    if (name in names)
+      throw new Exception("SNP name "~name~" appears multiple times in "~filen);
+    auto pos = (fields[1] == "NA" ? -1 : to!ulong(fields[1]));
+    auto chr = to!string(fields[2]);
+    double cm = -1.0;
+    if (fields.length > 3)
+      cm = (fields[3] == "NA" ? -1.0 : to!double(fields[3]));
+    auto snp = SNP(name,chr,pos,cm);
+    list ~= snp;
+  }
+  return list;
+}