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added a fastq parser

bio2
George Githinji 6 years ago
parent
commit
a06f4c21d9
  1. 145
      bio/core/fastq.d

145
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);
}
}
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