Codebase list tigr-glimmer / 3d066a8
[svn-inject] Installing original source of tigr-glimmer Charles Plessy 16 years ago
3 changed file(s) with 210 addition(s) and 0 deletion(s). Raw diff Collapse all Expand all
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Makefile less more
0 # -*- makefile -*-
1 # just make headings for each thing and put the headings
2 # on the line for ALL
3 PROJECTDIR = .
4 BINDIR = $(PROJECTDIR)
5
6 CC = gcc
7 CPPC = g++
8 CFLAGS = -O3 -g -Wall
9 LDFLAGS = -lm
10
11 DEPEND_FILES = *.cc *.c *.h
12 CLEANABLE_FILES = *.o *~
13
14 ALL = adjust anomaly build-icm check codon-usage compare-lists \
15 extract generate get-len get-putative glimmer2 long-orfs
16
17 .SUFFIXES: .cc .c
18
19 .c.o:
20 $(CC) $(CFLAGS) -c $*.c -o $*.o
21
22 .cc.o:
23 $(CPPC) $(CFLAGS) -c $*.cc -o $*.o
24
25 all: $(ALL)
26
27 adjust: adjust.o delcher.o
28 $(CPPC) -o $(BINDIR)/$@ adjust.o delcher.o $(LDFLAGS)
29
30 anomaly: anomaly.o delcher.o gene.o
31 $(CPPC) -o $(BINDIR)/$@ anomaly.o delcher.o gene.o $(LDFLAGS)
32
33 build-icm: build-icm.o misc.o
34 $(CC) -o $(BINDIR)/$@ build-icm.o misc.o $(LDFLAGS)
35
36 check: check.o delcher.o
37 $(CPPC) -o $(BINDIR)/$@ check.o delcher.o $(LDFLAGS)
38
39 codon-usage: codon-usage.o delcher.o gene.o
40 $(CPPC) -o $(BINDIR)/$@ codon-usage.o delcher.o gene.o $(LDFLAGS)
41
42 compare-lists: compare-lists.o delcher.o
43 $(CPPC) -o $(BINDIR)/$@ compare-lists.o delcher.o $(LDFLAGS)
44
45 extract: extract.o delcher.o
46 $(CPPC) -o $(BINDIR)/$@ extract.o delcher.o $(LDFLAGS)
47
48 generate: generate.o delcher.o gene.o
49 $(CPPC) -o $(BINDIR)/$@ generate.o delcher.o gene.o $(LDFLAGS)
50
51 get-len: get-len.o delcher.o
52 $(CPPC) -o $(BINDIR)/$@ get-len.o delcher.o $(LDFLAGS)
53
54 get-putative: get-putative.o delcher.o
55 $(CPPC) -o $(BINDIR)/$@ get-putative.o delcher.o $(LDFLAGS)
56
57 glimmer2: glimmer2.o delcher.o gene.o rnabin.o
58 $(CPPC) -o $(BINDIR)/$@ glimmer2.o delcher.o gene.o rnabin.o $(LDFLAGS)
59
60 long-orfs: long-orfs.o delcher.o gene.o
61 $(CPPC) -o $(BINDIR)/$@ long-orfs.o delcher.o gene.o $(LDFLAGS)
62
63 rnabin: rnabin.o delcher.o
64 $(CPPC) -o $(BINDIR)/$@ rnabin.o delcher.o $(LDFLAGS)
65
66 depend:
67 makedepend $(DEPEND_FILES)
68
69 clean:
70 /bin/rm -f $(CLEANABLE_FILES)
71
72 # DO NOT DELETE THIS LINE -- make depend depends on it.
73
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delcher.h less more
0 // A. L. Delcher
1 //
2 // File: ANNOTATION/Glimmer/delcher.h
3 // Version: 2.03 3 Dec 2002
4 //
5 // Copyright (c) 2002 by Arthur Delcher, Steven Salzberg, Simon
6 // Kasif, and Owen White. All rights reserved. Redistribution
7 // is not permitted without the express written permission of
8 // the authors.
9 //
10 // Common generic routines.
11 //
12
13
14 #ifndef __DELCHER_H_INCLUDED
15 #define __DELCHER_H_INCLUDED
16
17
18 #include <stdio.h>
19 #include <stdlib.h>
20 #include <iostream.h>
21 #include <iomanip.h>
22 #include <fstream.h>
23 #include <math.h>
24 #include <string.h>
25 #include <ctype.h>
26 #include <limits.h>
27 #include <float.h>
28 #include <time.h>
29 #include <assert.h>
30 #include <errno.h>
31 #include <unistd.h>
32
33
34 #define TRUE 1
35 #define FALSE 0
36 #ifndef EXIT_FAILURE
37 #define EXIT_FAILURE -1
38 #endif
39 #ifndef EXIT_SUCCESS
40 #define EXIT_SUCCESS 0
41 #endif
42
43
44 const int FASTA_WIDTH = 60;
45 // Max number of characters to print on a FASTA data line
46
47
48 const char * Commatize
49 (long int n);
50 void Fasta_Print
51 (FILE * fp, char * s, char * hdr);
52 void Fasta_Print_N
53 (FILE * fp, char * s, int n, char * hdr);
54 FILE * File_Open
55 (const char *, const char *);
56 double Percent
57 (double a, double b);
58 void * Safe_calloc
59 (size_t N, size_t Len, size_t line_num = 0);
60 void * Safe_malloc
61 (size_t Len, size_t line_num = 0);
62 void * Safe_realloc
63 (void * Q, size_t Len, size_t line_num = 0);
64
65
66 template <class DT>
67 DT Max (DT, DT);
68 template <class DT>
69 DT Min (DT, DT);
70 template <class DT>
71 void Swap (DT &, DT &);
72
73
74 template <class DT>
75 DT Max (DT A, DT B)
76
77 // Return the larger of A and B .
78
79 {
80 if (A > B)
81 return A;
82 else
83 return B;
84 }
85
86
87
88 template <class DT>
89 DT Min (DT A, DT B)
90
91 // Return the smaller of A and B .
92
93 {
94 if (A < B)
95 return A;
96 else
97 return B;
98 }
99
100
101
102 template <class DT>
103 void Swap (DT & A, DT & B)
104
105 // Swap the values in A and B .
106
107 {
108 DT Save;
109
110 Save = A;
111 A = B;
112 B = Save;
113
114 return;
115 }
116
117
118
119 #endif
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run-glimmer2 less more
0 echo "run Glimmer2"
1 clear
2 echo "Genome is " $1
3 echo "Find non-overlapping orfs in tmp.coord"
4 rm -f tmp.coord
5 long-orfs $1 | get-putative >tmp.coord
6 echo "Extract training sequences to tmp.train"
7 rm -f tmp.train
8 extract $1 tmp.coord >tmp.train
9 wc tmp.train
10 echo "Build interpolated context model in tmp.model"
11 rm -f tmp.model
12 build-icm <tmp.train >tmp.model
13 echo "Predict genes with Glimmer2 with coordinates in g2.coord"
14 rm -f g2.coord
15 glimmer2 $1 tmp.model | get-putative >g2.coord