added a fastq parser

bio/core/fastq.d

@@ -0,0 +1,145 @@
+/*
+    This file is part of BioD.
+    Copyright (C) 2016   George Githinji <biorelated@gmail.com>
+    Permission is hereby granted, free of charge, to any person obtaining a
+    copy of this software and associated documentation files (the "Software"),
+    to deal in the Software without restriction, including without limitation
+    the rights to use, copy, modify, merge, publish, distribute, sublicense,
+    and/or sell copies of the Software, and to permit persons to whom the
+    Software is furnished to do so, subject to the following conditions:
+
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+    DEALINGS IN THE SOFTWARE.
+*/
+
+module bio.core.fastq;
+
+struct FastQRecord {
+    const(char)[] id;
+    const(char)[] seq;
+    const(char)[] qual;
+
+    static auto read(const(char)[] from) {
+        struct Result {
+            private {
+                const(char)[] source;
+                FastQRecord value;
+                bool isEmpty;
+            }
+
+            this(const(char)[] source) {
+                this.source = source;
+                popFront;
+            }
+
+            @property {
+                FastQRecord front() {
+                    return value;
+                }
+
+                bool empty() {
+                    return isEmpty;
+                }
+            }
+
+            void popFront() {
+                import std.string : indexOf;
+
+                if (source is null) {
+                    isEmpty = true;
+                    return;
+                }
+
+                void tidyInput() {
+                    foreach(i, c; source) {
+                        switch(c) {
+                            case 0: .. case ' ':
+                                    break;
+                            default:
+                                    source = source[i .. $];
+                                    return;
+                        }
+                    }
+                    source = null;
+                }
+
+                tidyInput();
+
+                if (source is null)
+                    return;
+
+                // id
+                assert(source[0] == '@');
+
+                ptrdiff_t len = source.indexOf("\n");
+                assert(len > 0);
+
+                value.id = source[1 .. len];
+                if (value.id[$-1] == "\r"[0])
+                    value.id = value.id[0 .. $-1];
+
+                source = source[len + 1 .. $];
+
+                // seq
+                len = source.indexOf("\n");
+                assert(len > 0);
+
+                value.seq = source[0 .. len];
+                if (value.seq[$-1] == "\r"[0])
+                    value.seq = value.seq[0 .. $-1];
+
+                source = source[len + 1 .. $];
+
+                // +id
+                len = source.indexOf("\n");
+                assert(len > 0);
+                source = source[len + 1 .. $];
+
+                // qual
+                len = source.indexOf("\n");
+                assert(len > 0);
+
+                value.qual = source[0 .. len];
+                if (value.qual[$-1] == "\r"[0])
+                    value.qual = value.qual[0 .. $-1];
+
+                if (source.length > len + 1) {
+                    source = source[len + 1 .. $];
+                    tidyInput();
+                } else
+                    source = null;
+            }
+        }
+        return Result(from);
+    }
+}
+
+unittest {
+    string input = """
+        @seq1
+        TTATTTTAAT
+        +
+        ?+BBB/DHH@
+        @seq2
+        GACCCTTTGCA
+        +
+        ?+BHB/DIH@
+        @SEQ_ID
+        GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+        +
+        !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
+        """[1 .. $];
+
+    foreach(record; FastQRecord.read(input)) {
+        import std.stdio;
+        writeln(record);
+    }
+}