dhtslib.bed source code

1 module dhtslib.bed;
2 /**
3 
4 BED file reading and writing
5 
6 This module provides a readable, writeable abstraction of BED records and files.
7 
8 Authors: Thomas Gregory <charles.gregory@osumc.edu>
9 
10 Standards: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
11 */
12 
13 public import dhtslib.bed.record;
14 public import dhtslib.bed.reader;
15 public import dhtslib.bed.writer;
16 
17 debug(dhtslib_unittest) unittest
18 {
19     import dhtslib.coordinates;
20     import std.stdio;
21     import htslib.hts_log;
22     import std.algorithm : map;
23     import std.array : array;
24     import std.path : buildPath, dirName;
25     hts_set_log_level(htsLogLevel.HTS_LOG_INFO);
26     hts_log_info(__FUNCTION__, "Testing BedReader");
27     hts_log_info(__FUNCTION__, "Loading test file");
28 
29     auto bed = BedReader(buildPath(dirName(dirName(dirName(dirName(__FILE__)))),"htslib","test","tabix","bed_file.bed"));
30     auto rec = bed.front;
31     assert(rec.contig == "X");
32     assert(rec.coordinates == ZBHO(1000, 1100));
33     assert(rec.name == "X1");
34     assert(rec.score == 500);
35     assert(rec.strand == '+');
36     assert(rec.thickStart == 1000);
37     assert(rec.thickEnd == 1100);
38     assert(rec.itemRGB == RGB(255,0,0));
39     bed.popFront;
40 
41     rec = bed.front;
42     assert(rec.contig == "X");
43     assert(rec.coordinates == ZBHO(1200, 1300));
44     assert(rec.name == "X2");
45     assert(rec.score == 500);
46     assert(rec.strand == '+');
47     assert(rec.thickStart == 1200);
48     assert(rec.thickEnd == 1300);
49     assert(rec.itemRGB == RGB(255,0,0));
50 
51     rec.contig = "X1";
52     rec.coordinates = ZBHO(1201, 1301);
53     rec.name = "X21";
54     rec.score = 501;
55     rec.strand = '-';
56     rec.thickStart = 1201;
57     rec.thickEnd = 1301;
58     rec.itemRGB = RGB(255,0,1);
59 
60     assert(rec.contig == "X1");
61     assert(rec.coordinates == ZBHO(1201, 1301));
62     assert(rec.name == "X21");
63     assert(rec.score == 501);
64     assert(rec.strand == '-');
65     assert(rec.thickStart == 1201);
66     assert(rec.thickEnd == 1301);
67     assert(rec.itemRGB == RGB(255,0,1));
68 
69     assert(rec.toString == "X1\t1201\t1301\tX21\t501\t-\t1201\t1301\t255,0,1");
70 
71 }
72 
73 debug(dhtslib_unittest) unittest
74 {
75     import dhtslib.coordinates;
76     import dhtslib.util;
77     import std.stdio;
78     import htslib.hts_log;
79     import htslib.tbx : tbx_index_build2, tbx_conf_gff;
80     import std.algorithm : map;
81     import std.array : array;
82     import std.path : buildPath, dirName;
83     import std.utf : toUTFz;
84     import std.array : array;
85 
86     hts_set_log_level(htsLogLevel.HTS_LOG_INFO);
87     hts_log_info(__FUNCTION__, "Testing BedReader (Tabix)");
88     hts_log_info(__FUNCTION__, "Loading test file");
89     
90     auto reg = getIntervalFromString("X:1000-1400");
91     auto bed = BedReader(
92         buildPath(dirName(dirName(dirName(dirName(__FILE__)))),"htslib","test","tabix","bed_file.bed.gz"),
93         reg.contig, reg.interval
94         );
95 
96     assert(bed.array.length == 2);
97 
98 }