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