From 45bcd7f3a120a3ae465e9dd149173352f239c556 Mon Sep 17 00:00:00 2001
From: Guoyi Zhang <kuoi@bioarchlinux.org>
Date: Sun, 15 Sep 2024 16:12:47 +1000
Subject: [PATCH] add: count fasta taxa from one folder

---
 countTaxa.d | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 countTaxa.d

diff --git a/countTaxa.d b/countTaxa.d
new file mode 100644
index 0000000..08825e2
--- /dev/null
+++ b/countTaxa.d
@@ -0,0 +1,72 @@
+import std.stdio;
+import std.file;
+import std.algorithm;
+import std.array;
+import std.conv;
+import std.getopt;
+import std.path;
+
+void main(string[] args)
+{
+    if (args.length < 4 || args.length > 5 )
+    {
+        writeln("Usage: "~ args[0] ~" <folder> <condition> <number> [output_file]");
+        return;
+    }
+
+    // getargs
+    string folder = args[1];
+    string condition = args[2];
+    long threshold = to!long(args[3]);
+    bool hasOutputFile = args.length > 4;
+    string outputFile = hasOutputFile ? args[4] : "";
+
+    // resotre results
+    string result;
+
+    // ie all the file
+    foreach (entry; dirEntries(folder, SpanMode.shallow))
+    {
+        if (entry.isFile)
+        {
+            // count  '>' 
+            size_t count = 0;
+            foreach (line; File(entry.name).byLine())
+            {
+                if (line.length > 0 && line[0] == '>')
+                {
+                    count++;
+                }
+            }
+
+            // judge
+            bool conditionMet = false;
+            if (condition == "=" && count == threshold) conditionMet = true;
+            else if (condition == "<" && count < threshold) conditionMet = true;
+            else if (condition == ">" && count > threshold) conditionMet = true;
+            else if (condition == "<=" && count <= threshold) conditionMet = true;
+            else if (condition == ">=" && count >= threshold) conditionMet = true;
+	    else if (condition == "><" && count != threshold) conditionMet = true;
+            else if (condition == "<>" && count != threshold) conditionMet = true;
+
+
+            if (conditionMet)
+            {
+                result ~= baseName(entry.name) ~ " : " ~ to!string(count) ~ "\n";
+            }
+        }
+    }
+
+    // write
+    if (hasOutputFile)
+    {
+	// write to file
+        std.file.write(outputFile, result);
+    }
+    else
+    {
+        // output to consol
+        writeln(result);
+    }
+}
+