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root/bioseg/trunk/README.bioseg
Revision: 39
Committed: Thu Aug 21 16:42:35 2008 UTC (10 years, 9 months ago) by kmr
File size: 7171 byte(s)
Log Message:
Give an example in the README of using a function index with bioseg_create().

Line User Rev File contents
1 kmr 1 This directory contains the code for the user-defined type,
2     BIOSEG, representing contiguous intervals in biological sequence.
3    
4     (Most of this documentation is copied from contrib/seg/README.seg in the
5     PostgreSQL source).
6    
7    
8     FILES
9     =====
10    
11     Makefile building instructions for the shared library
12    
13     README.bioseg the file you are now reading
14    
15     bioseg.c the implementation of this data type in C
16    
17     bioseg.sql.in SQL code needed to register this type with PostgreSQL
18     (transformed to bioseg.sql by make)
19    
20     INSTALLATION
21     ============
22    
23     Change into the contrib directory in PostgreSQL and unpack the bioseg tar
24     file:
25     gzip -d < bioseg-x.y.tar.gz | tar xf -
26    
27 kmr 23 (Or check-out from subversion with:
28     svn checkout svn://bioinformatics.org/svnroot/bioseg/trunk bioseg
29     in the contrib directory)
30    
31 kmr 1 To install the type, change to the bioseg directory and run
32    
33     make
34     make install
35    
36     The user running "make install" may need root access; depending on the
37 kmr 22 configuration of PostgreSQL. If so this may work:
38 kmr 1
39 kmr 22 sudo make install
40    
41 kmr 1 This only installs the type implementation and documentation. To make the
42     type available in any particular database, do
43    
44     psql -d databasename < bioseg.sql
45    
46     If you install the type in the template1 database, all subsequently created
47     databases will inherit it.
48    
49     To test the new type, after "make install" do
50    
51     make installcheck
52    
53     If it fails, examine the file regression.diffs to find out the reason (the
54     test code is a direct adaptation of the regression tests from the main
55     source tree).
56    
57     If you have a full installation of PostgreSQL, including the pg_config
58     program, bioseg can be unpacked anywhere and built like:
59    
60 kmr 32 make USE_PGXS=t clean
61 kmr 22 make USE_PGXS=t
62     make install USE_PGXS=t
63 kmr 23 (or: sudo make install USE_PGXS=t)
64 kmr 1
65     and the type can then be installed in a particular database by any user with:
66    
67     psql -d databasename < `pg_config --sharedir`/contrib/bioseg.sql
68    
69    
70     SYNTAX
71     ======
72    
73 kmr 7 The user visible representation of an interval is formed using one or two
74 kmr 1 integers greater than 0 joined by the range operator ('..' or '...').
75     The first integer must be less than or equal to the second.
76    
77 kmr 27 11..22 An interval from 11 to 22 inclusive - length 12 (= 22-11+1)
78 kmr 1
79 kmr 7 1...2 The same as 1..2
80 kmr 1
81 kmr 7 50 The same as 50..50
82 kmr 1
83 kmr 7 In a statement, bioseg values have the form:
84     '<start>..<end>'::bioseg
85     or can be created with:
86     bioseg_create(start, end)
87 kmr 1
88 kmr 7 For example:
89     CREATE TABLE test_bioseg (id integer, seg bioseg);
90     insert into test_bioseg values (1, '1000..2000'::bioseg);
91     or, equivalently
92     insert into test_bioseg values (1, bioseg_create(1000, 2000));
93    
94    
95 kmr 1 USAGE
96     =====
97    
98 kmr 18 See http://www.bioinformatics.org/bioseg/wiki/Main/BiosegUsage for usage
99     examples.
100    
101 kmr 7 The following is a list of the available operators. The [a, b] should be
102 kmr 18 replaced in a statement with 'a..b'::bioseg or bioseg_create(a, b).
103 kmr 1
104     [a, b] && [c, d] Overlaps
105    
106     Returns true if and only if segments [a, b] and [c, d] overlap
107    
108     [a, b] << [c, d] Is left of
109    
110     The left operand, [a, b], occurs entirely to the left of the
111     right operand, [c, d]. It means, [a, b] << [c, d] is true if b
112     < c and false otherwise
113    
114     [a, b] >> [c, d] Is right of
115    
116     [a, b] is occurs entirely to the right of [c, d].
117     [a, b] >> [c, d] is true if a > d and false otherwise
118    
119     [a, b] &< [c, d] Overlaps or is left of
120    
121     This might be better read as "does not extend to right of".
122     It is true when b <= d.
123    
124     [a, b] &> [c, d] Overlaps or is right of
125    
126     This might be better read as "does not extend to left of".
127     It is true when a >= c.
128    
129     [a, b] = [c, d] Same as
130    
131     The segments [a, b] and [c, d] are identical, that is, a == b
132     and c == d
133    
134     [a, b] @> [c, d] Contains
135    
136     The segment [a, b] contains the segment [c, d], that is,
137     a <= c and b >= d
138    
139     [a, b] <@ [c, d] Contained in
140    
141     The segment [a, b] is contained in [c, d], that is,
142     a >= c and b <= d
143    
144     Although the mnemonics of the following operators is questionable, I
145     preserved them to maintain visual consistency with other geometric
146     data types defined in PostgreSQL.
147    
148     Other operators:
149    
150     [a, b] < [c, d] Less than
151     [a, b] > [c, d] Greater than
152    
153     These operators do not make a lot of sense for any practical
154     purpose but sorting. These operators first compare (a) to (c),
155     and if these are equal, compare (b) to (d). That accounts for
156     reasonably good sorting in most cases, which is useful if
157     you want to use ORDER BY with this type
158    
159    
160 kmr 38 NOTE: The performance of an R-tree index can largely depend on the order of
161     input values. It may be helpful to sort the input table on the BIOSEG column.
162 kmr 1
163    
164     INDEXES
165     =======
166    
167     A GiST index can created for bioseg columns that will greatly speed up
168     overlaps and contains queries. For example:
169    
170     CREATE TABLE tt (range bioseg, id integer);
171     CREATE INDEX tt_range_idx ON tt USING gist (range);
172    
173 kmr 39 Or for an existing table a function index can be used. For example on a
174     feature table with fmin and fmax:
175 kmr 1
176 kmr 39 CREATE INDEX bioseg_index ON feature USING gist (bioseg_create(fmin, fmax));
177    
178     This query will then find features that overlap 2000..3000, using the index:
179    
180     SELECT * FROM feature
181     WHERE '2000..3000'::bioseg && bioseg_create(fmin, fmax);
182    
183    
184 kmr 1 INTERBASE COORDINATES
185     =====================
186    
187     The standard bioseg type uses the common convention of numbering the bases
188     starting at 1. If you wish to use "interbase" coordinates (also known as "0
189     based" or "half-open intervals") run the build with INTERBASE_COORDS defined
190     in make, ie.:
191    
192 kmr 32 make clean
193 kmr 1 make INTERBASE_COORDS=t
194     make install INTERBASE_COORDS=t
195 kmr 32 (or: sudo make install INTERBASE_COORDS=t)
196 kmr 1
197     This will compile and install the implementation for the "bioseg0" type.
198 kmr 22 The "0" in the name is a mnemonic for "0-based".
199 kmr 1
200 kmr 22 Then read "bioseg0.sql" into your database:
201 kmr 5 psql -d databasename < bioseg0.sql
202 kmr 22 to install the type.
203 kmr 1
204 kmr 22 The bioseg and bioseg0 types can be mixed in the same database.
205    
206 kmr 32 Notes
207     -----
208 kmr 1 In the interbase system '1..10'::bioseg0 and '10..20'::bioseg0 don't overlap,
209     whereas in the 1-based system '1..10'::bioseg and '10..20'::bioseg have a one
210     base overlap. Also note that the length of '1..10'::bioseg0 is 9, whereas the
211     length of '1..10'::bioseg is 10.
212    
213 kmr 32 Unlike the bioseg type the start and/or end of a bioseg0 can be negative, with
214     the expected reults.
215     eg. bioseg0_size('-10..10'::bioseg0) == 20
216    
217 kmr 1 See:
218     http://www.gmod.org/wiki/index.php/Introduction_to_Chado#Interbase_Coordinates
219     for a longer discussion of the differences between the coordinate systems.
220    
221    
222     TESTS
223     =====
224    
225     The installation of bioseg can be checked by running:
226    
227     make installcheck
228    
229    
230     CREDITS
231     =======
232    
233     Note from the author: Most of the code and all of the hard work needed to
234     implement BIOSEG was by Gene Selkov, Jr, author of the SEG type (contrib/seg
235 kmr 7 in the PostgreSQL source). All bugs are due to me (kmr).
236 kmr 1
237    
238 kmr 23 THANKS
239     ======
240    
241     Thanks to bioinformatics.org for hosting the project.
242    
243    
244 kmr 1 AUTHOR
245     ======
246    
247     Kim Rutherford <kmr@flymine.org>
248 kmr 7
249     SEG code by Gene Selkov, Jr.