Mercurial > repos > nick > duplex

annotate mafft/core/dndblast.c @ 18:e4d75f9efb90 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1 #include "mltaln.h"
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2 #include <sys/types.h>
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
3 #include <unistd.h>
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
4 #define DEBUG 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
5 #define TEST 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
6
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
7
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
8 int howmanyx( char *s )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
9 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
10 int val = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
11 if( scoremtx == -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
12 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
13 do
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
14 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
15 if( !strchr( "atgcuATGCU", *s ) ) val++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
16 } while( *++s );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
17 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
18 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
19 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
20 do
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
21 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
22 if( !strchr( "ARNDCQEGHILKMFPSTWYV", *s ) ) val++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
23 } while( *++s );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
24 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
25 return( val );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
26 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
27
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
28 void arguments( int argc, char *argv[] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
29 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
30 int c;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
31
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
32 inputfile = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
33 disopt = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
34 divpairscore = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
35
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
36 while( --argc > 0 && (*++argv)[0] == '-' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
37 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
38 while ( (c = *++argv[0]) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
39 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
40 switch( c )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
41 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
42 case 'i':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
43 inputfile = *++argv;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
44 fprintf( stderr, "inputfile = %s\n", inputfile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
45 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
46 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
47 case 'I':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
48 disopt = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
49 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
50 default:
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
51 fprintf( stderr, "illegal option %c\n", c );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
52 argc = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
53 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
54 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
55 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
56 nextoption:
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
57 ;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
58
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
59 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
60 if( argc != 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
61 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
62 fprintf( stderr, "options: -i\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
63 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
64 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
65 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
66
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
67 int main( int argc, char *argv[] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
68 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
69 int ktuple;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
70 int i, j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
71 FILE *infp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
72 FILE *hat2p;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
73 FILE *hat3p;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
74 char **seq = NULL; // by D.Mathog
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
75 char **seq1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
76 static char **name;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
77 static char **name1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
78 static int nlen1[M];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
79 double **mtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
80 double **mtx2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
81 static int nlen[M];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
82 char b[B];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
83 double max;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
84 char com[1000];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
85 int opt[M];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
86 int res;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
87 char *home;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
88 char queryfile[B];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
89 char datafile[B];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
90 char fastafile[B];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
91 char hat2file[B];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
92 int pid = (int)getpid();
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
93 LocalHom **localhomtable, *tmpptr;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
94 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
95 home = getenv( "HOME" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
96 #else /* $HOME wo tsukau to fasta ni watasu hikisuu ga afureru */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
97 home = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
98 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
99
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
100 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
101 if( home ) fprintf( stderr, "home = %s\n", home );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
102 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
103 if( !home ) home = "";
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
104 sprintf( queryfile, "%s/tmp/query-%d", home, pid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
105 sprintf( datafile, "%s/tmp/data-%d", home, pid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
106 sprintf( fastafile, "%s/tmp/fasta-%d", home, pid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
107 sprintf( hat2file, "hat2-%d", pid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
108
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
109
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
110 arguments( argc, argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
111
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
112 if( inputfile )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
113 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
114 infp = fopen( inputfile, "r" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
115 if( !infp )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
116 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
117 fprintf( stderr, "Cannot open %s\n", inputfile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
118 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
119 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
120 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
121 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
122 infp = stdin;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
123 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
124 PreRead( infp, &njob, &nlenmax );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
125 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
126 dorp = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
127 getnumlen( infp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
128 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
129
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
130 if( dorp == 'd' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
131 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
132 scoremtx = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
133 pamN = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
134 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
135 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
136 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
137 nblosum = 62;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
138 scoremtx = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
139 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
140 constants( njob, seq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
141
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
142 rewind( infp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
143
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
144 name = AllocateCharMtx( njob, B+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
145 name1 = AllocateCharMtx( njob, B+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
146 seq = AllocateCharMtx( njob, nlenmax+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
147 seq1 = AllocateCharMtx( 2, nlenmax+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
148 mtx = AllocateDoubleMtx( njob, njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
149 mtx2 = AllocateDoubleMtx( njob, njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
150 localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
151 for( i=0; i<njob; i++)
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
152 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
153 localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
154 for( j=0; j<njob; j++)
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
155 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
156 localhomtable[i][j].start1 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
157 localhomtable[i][j].end1 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
158 localhomtable[i][j].start2 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
159 localhomtable[i][j].end2 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
160 localhomtable[i][j].opt = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
161 localhomtable[i][j].next = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
162
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
163 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
164 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
165
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
166 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
167 FRead( infp, name, nlen, seq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
168 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
169 readData_pointer( infp, name, nlen, seq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
170 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
171 fclose( infp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
172
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
173 if( scoremtx == -1 ) ktuple = 6;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
174 else ktuple = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
175
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
176 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
177 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
178 gappick0( seq1[0], seq[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
179 strcpy( seq[i], seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
180 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
181 for( j=0; j<njob; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
182 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
183 sprintf( name1[j], "+==========+%d ", j );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
184 nlen1[j] = nlen[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
185 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
186
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
187 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
188 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
189 // fprintf( stderr, "### i = %d\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
190
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
191 if( i % 10 == 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
192 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
193 fprintf( stderr, "formatting .. " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
194 hat2p = fopen( datafile, "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
195 if( !hat2p ) ErrorExit( "Cannot open datafile." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
196 WriteForFasta( hat2p, njob-i, name1+i, nlen1+i, seq+i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
197 fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
198
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
199 if( scoremtx == -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
200 sprintf( com, "formatdb -p f -i %s -o F", datafile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
201 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
202 sprintf( com, "formatdb -i %s -o F", datafile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
203 system( com );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
204 fprintf( stderr, "done.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
205 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
206
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
207 hat2p = fopen( queryfile, "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
208 if( !hat2p ) ErrorExit( "Cannot open queryfile." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
209 WriteForFasta( hat2p, 1, name1+i, nlen+i, seq+i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
210 fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
211
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
212
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
213 if( scoremtx == -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
214 sprintf( com, "blastall -e 1e10 -p blastn -m 7 -i %s -d %s > %s", queryfile, datafile, fastafile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
215 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
216 sprintf( com, "blastall -G 10 -E 1 -e 1e10 -p blastp -m 7 -i %s -d %s > %s", queryfile, datafile, fastafile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
217 res = system( com );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
218 if( res ) ErrorExit( "error in fasta" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
219
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
220
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
221 hat2p = fopen( fastafile, "r" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
222 if( hat2p == NULL )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
223 ErrorExit( "file 'fasta.$$' does not exist\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
224 res = ReadBlastm7( hat2p, mtx[i], i, name1, localhomtable[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
225 fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
226
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
227 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
228 for( j=0; j<njob; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
229 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
230 for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
231 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
232 if( tmpptr->opt == -1.0 ) continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
233 // fprintf( stderr, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
234 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
235 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
236 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
237
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
238 if( res < njob-i+i%10 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
239 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
240 fprintf( stderr, "WARNING: count (blast) = %d < %d\n", res, njob-i+i%10 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
241 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
242
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
243
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
244 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
245 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
246 int ii, jj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
247 if( i < njob-1 ) for( jj=i; jj<i+5; jj++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
248 fprintf( stdout, "mtx[%d][%d] = %f\n", i+1, jj+1, mtx[i][jj] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
249 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
250 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
251 fprintf( stderr, "query : %4d / %d\n", i+1, njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
252 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
253
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
254 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
255 fprintf( stderr, "##### writing hat3\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
256 hat3p = fopen( "hat3", "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
257 if( !hat3p ) ErrorExit( "Cannot open hat3." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
258 for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
259 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
260 // fprintf( stderr, "mtx[%d][%d] = %f, mtx[%d][%d] = %f\n", i, j, mtx[i][j], j, i, mtx[j][i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
261 if( i == j ) continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
262 if( mtx[i][j] == mtx[j][i] && i > j ) continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
263 if( mtx[j][i] > mtx[i][j] ) continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
264 for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
265 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
266 if( tmpptr->opt == -1.0 ) continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
267 fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
268 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
269 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
270 fclose( hat3p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
271 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
272
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
273 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
274 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
275 // fprintf( stderr, "### i = %d\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
276 hat2p = fopen( datafile, "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
277 if( !hat2p ) ErrorExit( "Cannot open datafile." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
278 WriteForFasta( hat2p, njob-i, name1+i, nlen1+i, seq+i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
279 fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
280
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
281 // seq1[0] = seq[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
282 // nlen1[0] = nlen[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
283
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
284 hat2p = fopen( queryfile, "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
285 if( !hat2p ) ErrorExit( "Cannot open queryfile." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
286 WriteForFasta( hat2p, 1, name1+i, nlen+i, seq+i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
287 fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
288
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
289
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
290 if( scoremtx == -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
291 sprintf( com, "fasta34 -z3 -m10 -n -Q -b%d -E%d -d%d %s %s %d > %s", M, M, 0, queryfile, datafile, ktuple, fastafile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
292 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
293 sprintf( com, "fasta34 -z3 -m10 -Q -b%d -E%d -d%d %s %s %d > %s", M, M, 0, queryfile, datafile, ktuple, fastafile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
294 res = system( com );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
295 if( res ) ErrorExit( "error in fasta" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
296
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
297
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
298 hat2p = fopen( fastafile, "r" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
299 if( hat2p == NULL )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
300 ErrorExit( "file 'fasta.$$' does not exist\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
301 res = ReadFasta34noalign( hat2p, mtx[i], i, name1, localhomtable[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
302 fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
303 if( res < njob - i )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
304 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
305 fprintf( stderr, "count (fasta34 -z 3) = %d\n", res );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
306 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
307 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
308
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
309
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
310 if( i == 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
311 for( j=0; j<njob; j++ ) opt[j] = (int)mtx[0][j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
312
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
313
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
314 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
315 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
316 int ii, jj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
317 if( i < njob-1 ) for( jj=i; jj<i+5; jj++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
318 fprintf( stdout, "mtx[%d][%d] = %f\n", i+1, jj+1, mtx[i][jj] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
319 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
320 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
321 fprintf( stderr, "query : %4d\r", i+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
322 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
323
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
324
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
325
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
326
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
327 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
328 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
329 max = mtx[i][i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
330 if( max == 0.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
331 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
332 for( j=0; j<njob; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
333 mtx2[i][j] = 2.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
334 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
335 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
336 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
337 for( j=0; j<njob; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
338 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
339 mtx2[i][j] = ( max - mtx[MIN(i,j)][MAX(i,j)] ) / max * 2.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
340 // fprintf( stdout, "max = %f, mtx[%d][%d] = %f -> %f\n", max, i+1, j+1, mtx[i][j], mtx2[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
341 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
342 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
343 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
344 for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
345 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
346 // fprintf( stdout, "mtx2[%d][%d] = %f, %f\n", i+1, j+1, mtx2[i][j], mtx2[j][i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
347 mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
348 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
349
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
350 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
351 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
352 int ii, jj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
353 if( i < njob-1 ) for( jj=i+1; jj<njob; jj++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
354 fprintf( stderr, "mtx2[][] = %f\n", mtx2[i][jj] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
355 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
356 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
357
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
358 for( i=0; i<njob; i++ ) name[i][0] = '=';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
359
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
360 if( disopt )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
361 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
362 strcpy( b, name[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
363 sprintf( name[0], "=query====lgth=%04d-%04d %.*s", nlen[0], howmanyx( seq[0] ), B-30, b );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
364 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
365 strins( b, name[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
366 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
367 for( i=1; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
368 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
369 strcpy( b, name[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
370 sprintf( name[i], "=opt=%04d=lgth=%04d-%04d %.*s", opt[i], nlen[i], howmanyx( seq[i] ), B-30, b );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
371 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
372 strins( b, name[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
373 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
374 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
375 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
376
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
377 hat2p = fopen( hat2file, "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
378 if( !hat2p ) ErrorExit( "Cannot open hat2." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
379 WriteHat2_pointer( hat2p, njob, name, mtx2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
380 fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
381
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
382
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
383 sprintf( com, "/bin/rm %s %s %s", queryfile, datafile, fastafile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
384 system( com );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
385
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
386 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
387 sprintf( com, ALNDIR "/supgsdl < %s", hat2file );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
388 res = system( com );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
389 if( res ) ErrorExit( "error in spgsdl" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
390 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
391
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
392 sprintf( com, "mv %s hat2", hat2file );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
393 res = system( com );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
394 if( res ) ErrorExit( "error in mv" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
395
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
396 SHOWVERSION;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
397 exit( 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
398 }