/usr/lib/perl5/pwm_search.h is in libtfbs-perl 0.5.svn.20100421-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 | /*---------------------------------------------------------------
* INCLUDES
*---------------------------------------------------------------*/
#include <stdio.h>
#include <math.h>
/*---------------------------------------------------------------
* DECLARATIONS
*---------------------------------------------------------------*/
/*
extern double atof();
extern double log2();
extern double sqrt();
extern FILE *fopen();
*/
void err_log(), err_show();
/*---------------------------------------------------------------
* DEFINES
*---------------------------------------------------------------*/
#define __DEBUG__ 0 /* put debug messages on */
#define FNAMELEN 1000 /* max allowed length of file name */
#define MAX_LINE 200
#define MAXCOUNTS 1000 /* max number of counts in count matrix */
#define MAXERR 100 /* max number of errors that err_log can handle */
#define MAXHITS 1000
#define SEQLEN 1000000 /* max sequence length allowed */
#define SEQNAMELEN MAX_LINE /* max allowed sequence name length */
/*---------------------------------------------------------------
* GLOBALS
*---------------------------------------------------------------*/
static char PANIC[] = "err_log function failure";
static char *__ERR__[MAXERR];
static int NUM_ERRS=0;
static char SQCOMP[] = /* calculate base on complementary strand */
{ /* ASCII chars; IUPAC conventions */
/* Control characters unchanged */
'\000','\001','\002','\003','\004','\005','\006','\007',
'\010','\011','\012','\013','\014','\015','\016','\017',
'\020','\021','\022','\023','\024','\025','\026','\027',
'\030','\031','\032','\033','\034','\035','\036','\037',
/* Punctuation and digits unchanged */
'\040','\041','\042','\043','\044','\045','\046','\047',
'\050','\051','\052','\053','\054','\055','\056','\057',
'\060','\061','\062','\063','\064','\065','\066','\067',
'\070','\071','\072','\073','\074','\075','\076','\077',
/* Capitals go to capitals */
'\100', 'T', 'V', 'G', 'H', '?', '?', 'C', /* @,A-G */
'D', '?', '?', 'M', '?', 'K', 'N', '?', /* H-O */
'?', '?', 'Y', 'S', 'A', '?', 'B', 'W', /* P-W */
'?', 'R', '?','\133','\134','\135','\136','\137', /* X-Z,etc */
/* Lower case goes to lower case */
'\140', 't', 'v', 'g', 'h', '?', '?', 'c',
'd', '?', '?', 'm', '?', 'k', 'n', '?',
'?', '?', 'y', 's', 'a', '?', 'b', 'w',
'?', 'r', '?','\173','\174','\175','\176','\177'
};
static int TRANS[] = /* translate characters to numbers */
{ /* A=0; C=1; G=2; T=3; other = 4 */
/* Control characters */
4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,
/* Punctuation and digits */
4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,
/* Capitals */
4,0,4,1,4,4,4,2, /* @,A-G */
4,4,4,4,4,4,4,4, /* H-O */
4,4,4,4,3,3,4,4, /* P-W */
4,4,4,4,4,4,4,4, /* X-Z,etc */
/* Lower case */
4,0,4,1,4,4,4,2, /* @,A-G */
4,4,4,4,4,4,4,4, /* H-O */
4,4,4,4,3,3,4,4, /* P-W */
4,4,4,4,4,4,4,4 /* X-Z,etc */
};
/*---------------------------------------------------------------
* STRUCTURE DEFINITIONS
*---------------------------------------------------------------*/
/* ARGUMENTS -- Structure to contain shared arguments */
struct arguments
{
char counts_file[FNAMELEN+1]; /* file name, count matrix */
char mask_file[FNAMELEN+1]; /* file name, masked seq output,
"" means none. */
char seq_file[FNAMELEN+1]; /* file name, sequences */
char name[FNAMELEN+1]; /* TF name */
char class[FNAMELEN+1]; /* TF structural class */
int print_all; /* print scores of all hits */
long best_base; /* base for best score on sequence */
int best_only; /* only show best score on each
sequence */
double best_score; /* best score on this sequence */
int best_strand; /* strand for best score on sequence */
double max_score; /* max score possible (implied
from pwm) */
double min_score; /* min score possible (implied
from pwm) */
double threshold; /* print stuff with log score >
max_possible - threshold */
int width; /* pattern width (implied from
number of counts) */
};
/* HIT - location and score of a site scoring above threshold */
struct HIT
{
long base; /* location */
int strand; /* 0 forward, 1 complement */
double score; /* score */
};
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