From 78d7aad8692bfc6f74099d45cce682a14035439e Mon Sep 17 00:00:00 2001
From: Guoyi Zhang <kuoi@bioarchlinux.org>
Date: Mon, 9 Dec 2024 12:09:48 +1100
Subject: [PATCH] add: splitfasta d version

---
 splitfasta.d | 71 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 splitfasta.d

diff --git a/splitfasta.d b/splitfasta.d
new file mode 100644
index 0000000..cf9cb62
--- /dev/null
+++ b/splitfasta.d
@@ -0,0 +1,71 @@
+import std.file;
+import std.stdio;
+import std.string;
+import std.path;
+
+string removeExtension(const string filename) {
+    size_t lastdot = filename.lastIndexOf(".");
+    if (lastdot != -1) {
+        return filename[0 .. lastdot];
+    }
+    return filename;
+}
+
+void splitFasta(const string input_fasta) {
+    File infile;
+    try {
+        infile = File(input_fasta, "r");
+    } catch (FileException e) {
+        stderr.writeln("Error: Unable to open input file ", input_fasta);
+        return;
+    }
+
+    string line;
+    string dir_name;
+    File outfile;
+    bool in_sequence = false;
+
+    foreach (lineContent; infile.byLine()) {
+        if (lineContent.empty) continue;
+
+        if (lineContent[0] == '>') {
+            // New sequence header
+            if (in_sequence) {  // if found new sequence, close
+                outfile.close();  // previous output file
+            }
+            dir_name = cast(string)lineContent[1 .. $];  // Remove '>'
+            // directory
+            mkdirRecurse(dir_name);
+            auto output_file = buildPath(dir_name, input_fasta);  // suitable to many os
+            outfile = File(output_file, "w");
+            outfile.writeln(">", removeExtension(input_fasta));
+            // will enter sequence
+            in_sequence = true;
+        } else if (in_sequence) {
+            // Inside sequence content
+            outfile.writeln(lineContent);
+        }
+    }
+
+    if (in_sequence) {
+        outfile.close();
+    }
+
+    if (infile.eof) {
+        writeln("Sequences have been split into individual files.");
+    } else {
+        stderr.writeln("Error occurred while reading file.");
+    }
+
+    infile.close();
+}
+
+void main(string[] args) {
+    if (args.length != 2) {
+        stderr.writeln("splitFasta\nAuthor: Guoyi Zhang\nLicense:GPL-2.0-only\nUsage: ",
+                       args[0], " <input_fasta>");
+        return;
+    }
+
+    splitFasta(args[1]);
+}