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/*
This file is part of BioD.
Copyright (C) 2016 George Githinji <biorelated@gmail.com>
Copyright (C) 2018 Emilio Palumbo <emiliopalumbo@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.std.file.fai;
import std.stdio;
import std.range;
import std.algorithm;
import std.string;
import std.conv;
import std.file;
import std.path;
struct FaiRecord {
string header, lineTerm;
ulong seqLen, lineLen, offset;
@property ulong lineOffset() {
return lineLen + lineTerm.length;
}
string toString() {
return format("%s\t%s\t%s\t%s\t%s", header, seqLen, offset, lineLen, lineOffset);
}
this(string str) {
auto res = str.split("\t");
header ~= res[0];
seqLen = to!ulong(res[1]);
offset = to!ulong(res[2]);
lineLen = to!ulong(res[3]);
lineTerm = (to!ulong(res[4])-lineLen) == 1 ? "\n" : "\r\n";
}
this(string header, string lineTerm, ulong seqLen, ulong lineLen, ulong offset) {
this.header = header;
this.seqLen = seqLen;
this.offset = offset;
this.lineLen = lineLen;
this.lineTerm = lineTerm;
}
}
auto readFai(string fai_filename) {
auto f = new File(fai_filename, "r");
return f.byLineCopy()
.map!(x => FaiRecord(x));
}
auto makeIndex(T)(T records) {
FaiRecord[string] index;
foreach (record; records) {
index[record.header] = record;
}
index.rehash;
return index;
}
auto buildFai(string fasta_filename) {
auto f = new File(fasta_filename, "r");
FaiRecord[] records;
string lineTerm = f.byLine(KeepTerminator.yes).take(1).front.endsWith("\r\n") ? "\r\n" : "\n";
f.seek(0);
ulong offset;
foreach(line; f.byLine(KeepTerminator.no, lineTerm)) {
offset+= line.length + lineTerm.length;
if ( line.startsWith(">") ) {
records~=FaiRecord();
records[$-1].lineTerm = lineTerm;
records[$-1].header ~= line.split(" ").front[1..$];
records[$-1].offset = offset;
} else {
if ( records[$-1].lineLen == 0 ) {
records[$-1].lineLen = line.length;
}
records[$-1].seqLen += line.length;
}
}
f.close();
return records;
}
version(Broken) unittest {
auto testFa = tempDir.buildPath("test1.fa");
// scope(exit) remove(testFa);
auto fa = new File(testFa, "w");
fa.writeln(q"(
>chr1
acgtgagtgc
>chr2
acgtgagtgcacgtgagtgcacgtgagtgc
acgtgagtgcacgtgagtgc
)".outdent().strip());
fa.flush();
fa.close();
auto recs = buildFai(testFa).array;
assert(recs.length == 2, recs[0].toString());
assert(recs.all!(x => is(typeof(x)==FaiRecord)));
assert(recs[0].toString() == "chr1\t10\t6\t10\t11");
assert(recs[1].toString() == "chr2\t50\t23\t30\t31");
}
unittest {
auto records = to!(FaiRecord[])(["chr2\t10\t4\t50\t51"]);
auto i = makeIndex(records);
assert( i.length == 1);
assert( "chr2" in i);
assert( i["chr2"] == FaiRecord("chr2\t10\t4\t50\t51"));
}
version(Broken) unittest {
auto faiString = "chr2\t10\t4\t50\t51";
auto testIndex = tempDir.buildPath("test1.fa.fai");
auto f = new File(testIndex,"w");
f.writeln(faiString);
f.flush();
f.close();
auto recs = readFai(testIndex).array;
assert(recs.length == 1);
assert(is(typeof(recs[0])==FaiRecord));
assert(recs[0].toString() == faiString);
}
unittest {
auto rec = FaiRecord("chr2", "\n", 10, 50, 4);
assert(rec.toString() == "chr2\t10\t4\t50\t51");
rec.lineTerm = "\r\n";
assert(rec.toString() == "chr2\t10\t4\t50\t52");
}
unittest {
auto s = "chr2\t10\t4\t50\t51";
assert(FaiRecord(s).toString() == s);
}
unittest {
assert(FaiRecord("chr2", "\n", 10, 50, 4).toString() == "chr2\t10\t4\t50\t51");
}
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