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/* trna2tbl.c
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information (NCBI)
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government do not place any restriction on its use or reproduction.
* We would, however, appreciate having the NCBI and the author cited in
* any work or product based on this material
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* ===========================================================================
*
* File Name: trna2tbl.c
*
* Author: Jonathan Kans
*
* Version Creation Date: 5/31/05
*
* $Revision: 1.1 $
*
* File Description:
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
*
* ==========================================================================
*/
/*
* To compile on Linux:
*
* gcc -o trna2tbl trna2tbl.c -lm
*
* To compile on Solaris:
*
* cc -xildoff -o trna2tbl trna2tbl.c -lgen -lm
*
* To compile on SGI:
*
* cc -mips1 -o trna2tbl trna2tbl.c -lm -lPW -lsun
*
* To compile on Darwin:
*
* cc -pipe -o trna2tbl trna2tbl.c -lc
*
*/
#include <stddef.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
/* convenient defines and typedefs from NCBI toolkit */
#ifndef NULL
#define NULL ((void *)0)
#endif
#ifndef Pointer
typedef void * Pointer;
#endif
#ifndef Char
typedef char Char, * CharPtr;
#endif
#ifndef Bool
typedef unsigned char Bool, * BoolPtr;
#endif
#ifndef TRUE
#define TRUE ((Bool)1)
#endif
#ifndef FALSE
#define FALSE ((Bool)0)
#endif
#ifndef Int2
typedef short Int2, * Int2Ptr;
#endif
#ifndef Int4
typedef long Int4, * Int4Ptr;
#endif
#ifndef MIN
#define MIN(a,b) ((a)>(b)?(b):(a))
#endif
/* useful portable character macros from NCBI toolkit (assumes ASCII) */
#define IS_DIGIT(c) ('0'<=(c) && (c)<='9')
#define IS_UPPER(c) ('A'<=(c) && (c)<='Z')
#define IS_LOWER(c) ('a'<=(c) && (c)<='z')
#define IS_ALPHA(c) (IS_UPPER(c) || IS_LOWER(c))
#define TO_LOWER(c) ((Char)(IS_UPPER(c) ? (c)+' ' : (c)))
#define TO_UPPER(c) ((Char)(IS_LOWER(c) ? (c)-' ' : (c)))
#define IS_WHITESP(c) (((c) == ' ') || ((c) == '\n') || ((c) == '\r') || ((c) == '\t'))
#define IS_ALPHANUM(c) (IS_ALPHA(c) || IS_DIGIT(c))
#define IS_PRINT(c) (' '<=(c) && (c)<='~')
#define MAX_FIELDS 9
static void RunTrnaScan (void)
{
CharPtr aa;
CharPtr beg;
Char buf [256];
Char cmmd [256];
CharPtr end;
CharPtr field [MAX_FIELDS];
CharPtr id;
Int2 idNotSent = TRUE;
Int2 inBody = FALSE;
CharPtr intronBeg;
CharPtr intronEnd;
long int intronStart;
long int intronStop;
Int2 numFields = 0;
CharPtr ptr;
CharPtr speed;
long int start;
long int stop;
Char str [80];
/* line by line processing of tRNAscan-SE output table */
while (fgets (buf, sizeof (buf), stdin) != NULL) {
if (inBody) {
memset (field, 0, sizeof (field));
/*
* parse tab-delimited output line into array of fields, avoiding use of
* strtok so that empty columns (adjacent tabs) are properly assigned to
* field array
*/
ptr = buf;
for (numFields = 0; numFields < MAX_FIELDS && ptr != NULL; numFields++) {
field [numFields] = ptr;
ptr = strchr (ptr, '\t');
if (ptr != NULL) {
*ptr = '\0';
ptr++;
}
}
/* interested in ID, start, stop, amino acid, and intron start and stop */
id = field [0];
beg = field [2];
end = field [3];
aa = field [4];
intronBeg = field [6];
intronEnd = field [7];
if (numFields > 7 &&
sscanf (beg, "%ld", &start) == 1 &&
sscanf (end, "%ld", &stop) == 1 &&
sscanf (intronBeg, "%ld", &intronStart) == 1 &&
sscanf (intronEnd, "%ld", &intronStop) == 1) {
/* first line of output gives SeqId from FASTA definition line */
if (idNotSent) {
fprintf (stdout, ">Features %s\n", id);
fflush (stdout);
idNotSent = FALSE;
}
/* first line of feature has start (tab) stop (tab) feature key */
/* multiple intervals would have lines of start (tab) stop */
if (intronStart == 0 && intronStop == 0) {
fprintf (stdout, "%ld\t%ld\ttRNA\n", (long) start, (long) stop);
fflush (stdout);
} else {
fprintf (stdout, "%ld\t%ld\ttRNA\n", (long) start, (long) (intronStart - 1));
fprintf (stdout, "%ld\t%ld\t\n", (long) (intronStop + 1), (long) stop);
fflush (stdout);
}
/* qualifier lines are (tab) (tab) (tab) qualifier key (tab) value */
if (strstr (aa, "Pseudo") != NULL) {
fprintf (stdout, "\t\t\tnote\ttRNA-Pseudo\n");
fflush (stdout);
} else {
fprintf (stdout, "\t\t\tproduct\t%s\n", aa);
fflush (stdout);
}
/* dash (formerly empty) gene qualifier to suppress /gene (e.g., if tRNA is in an intron) */
fprintf (stdout, "\t\t\tgene\t-\n");
fflush (stdout);
}
}
/* detect last line of table header, ignoring everything before data section */
if (strstr (buf, "-----") != NULL) {
inBody = TRUE;
}
}
if (idNotSent) {
fprintf (stdout, ">Message\ntRNAscan-SE found no tRNA genes in this sequence\n");
fflush (stdout);
}
}
main (int argc, char *argv[])
{
RunTrnaScan ();
return 0;
}
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