ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/bioseg/trunk/README.bioseg
Revision: 35
Committed: Thu Aug 21 16:18:18 2008 UTC (11 years, 1 month ago) by kmr
File size: 6864 byte(s)
Log Message:
Removed redundancy from README.

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     NOTE: The performance of an R-tree index can largely depend on the
161     order of input values. It may be very helpful to sort the input table
162     on the BIOSEG column (see the script sort-segments.pl for an example)
163    
164    
165     INDEXES
166     =======
167    
168     A GiST index can created for bioseg columns that will greatly speed up
169     overlaps and contains queries. For example:
170    
171     CREATE TABLE tt (range bioseg, id integer);
172     CREATE INDEX tt_range_idx ON tt USING gist (range);
173    
174    
175     INTERBASE COORDINATES
176     =====================
177    
178     The standard bioseg type uses the common convention of numbering the bases
179     starting at 1. If you wish to use "interbase" coordinates (also known as "0
180     based" or "half-open intervals") run the build with INTERBASE_COORDS defined
181     in make, ie.:
182    
183 kmr 32 make clean
184 kmr 1 make INTERBASE_COORDS=t
185     make install INTERBASE_COORDS=t
186 kmr 32 (or: sudo make install INTERBASE_COORDS=t)
187 kmr 1
188     This will compile and install the implementation for the "bioseg0" type.
189 kmr 22 The "0" in the name is a mnemonic for "0-based".
190 kmr 1
191 kmr 22 Then read "bioseg0.sql" into your database:
192 kmr 5 psql -d databasename < bioseg0.sql
193 kmr 22 to install the type.
194 kmr 1
195 kmr 22 The bioseg and bioseg0 types can be mixed in the same database.
196    
197 kmr 32 Notes
198     -----
199 kmr 1 In the interbase system '1..10'::bioseg0 and '10..20'::bioseg0 don't overlap,
200     whereas in the 1-based system '1..10'::bioseg and '10..20'::bioseg have a one
201     base overlap. Also note that the length of '1..10'::bioseg0 is 9, whereas the
202     length of '1..10'::bioseg is 10.
203    
204 kmr 32 Unlike the bioseg type the start and/or end of a bioseg0 can be negative, with
205     the expected reults.
206     eg. bioseg0_size('-10..10'::bioseg0) == 20
207    
208 kmr 1 See:
209     http://www.gmod.org/wiki/index.php/Introduction_to_Chado#Interbase_Coordinates
210     for a longer discussion of the differences between the coordinate systems.
211    
212    
213     TESTS
214     =====
215    
216     The installation of bioseg can be checked by running:
217    
218     make installcheck
219    
220    
221     CREDITS
222     =======
223    
224     Note from the author: Most of the code and all of the hard work needed to
225     implement BIOSEG was by Gene Selkov, Jr, author of the SEG type (contrib/seg
226 kmr 7 in the PostgreSQL source). All bugs are due to me (kmr).
227 kmr 1
228    
229 kmr 23 THANKS
230     ======
231    
232     Thanks to bioinformatics.org for hosting the project.
233    
234    
235 kmr 1 AUTHOR
236     ======
237    
238     Kim Rutherford <kmr@flymine.org>
239 kmr 7
240     SEG code by Gene Selkov, Jr.