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/* flint.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: flint.c
*
* Author: Jonathan Kans
*
* Version Creation Date: 4/19/04
*
* $Revision: 1.4 $
*
* File Description:
*
* Lint for FASTA - reformats to desired line length
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
*
* ==========================================================================
*/
#include <ncbi.h>
#include <objall.h>
#include <objsset.h>
#include <objsub.h>
#include <objfdef.h>
#include <seqport.h>
#include <sequtil.h>
#include <sqnutils.h>
#include <subutil.h>
#include <tofasta.h>
#include <gather.h>
#include <explore.h>
static void ProcessFasta (
FILE *ifp,
FILE *ofp,
Int2 linelen,
Int2 blocklen,
Int2 grouplen
)
{
Int2 blk;
Char buf [512];
Char ch;
Int2 grp;
Int2 idx;
Boolean in_defline;
Int2 lin;
Char line [4004];
CharPtr ptr;
CharPtr str;
size_t total;
in_defline = FALSE;
idx = 0;
blk = 0;
lin = 0;
grp = 0;
total = FileRead (line, sizeof (Char), 4000, ifp);
while (total > 0) {
line [total] = '\0';
str = line;
ch = *str;
while (ch != '\0') {
/* look for defline start character */
if (ch == '>') {
/* flush any sequence remaining in buffer */
if (lin > 0) {
buf [idx] = '\0';
fprintf (ofp, "%s\n", buf);
idx = 0;
blk = 0;
lin = 0;
grp = 0;
}
/* and set in_defline state flag */
in_defline = TRUE;
}
if (in_defline) {
/* look for carriage return, line feed, or end of input buffer */
ptr = str;
ch = *ptr;
while (ch != '\0' && ch != '\n' && ch != '\r') {
ptr++;
ch = *ptr;
}
*ptr = '\0';
if (ch == '\0') {
/* defline continues on next block */
fprintf (ofp, "%s", str);
/* ch == '\0' will cause new buffer to be read */
} else {
/* found newline within input buffer */
fprintf (ofp, "%s\n", str);
/* clear state flag */
in_defline = FALSE;
str = ptr;
str++;
ch = *str;
}
} else {
if (IS_ALPHA (ch)) {
/* optionally separate blocks with space */
if (blk >= blocklen && blocklen > 0) {
buf [idx] = ' ';
idx++;
blk = 0;
}
/* save sequence character to buffer */
buf [idx] = ch;
idx++;
blk++;
lin++;
}
/* write sequence as soon as we have line of characters */
if (lin >= linelen) {
buf [idx] = '\0';
/* optionally separate groups with blank line */
if (grp >= grouplen && grouplen > 0) {
fprintf (ofp, "\n");
grp = 0;
}
/* print actual sequence line here */
fprintf (ofp, "%s\n", buf);
idx = 0;
blk = 0;
lin = 0;
grp++;
}
str++;
ch = *str;
}
}
total = FileRead (line, sizeof (Char), 4000, ifp);
}
/* print any remaining sequence */
if (lin > 0) {
buf [idx] = '\0';
if (grp >= grouplen && grouplen > 0) {
fprintf (ofp, "\n");
}
fprintf (ofp, "%s\n", buf);
}
}
#define i_argInputFile 0
#define o_argOutputFile 1
#define e_argLineLength 2
#define b_argBlockLength 3
#define g_argGroupLength 4
Args myargs [] = {
{"Input File", "stdin", NULL, NULL,
FALSE, 'i', ARG_FILE_IN, 0.0, 0, NULL},
{"Output File", "stdout", NULL, NULL,
FALSE, 'o', ARG_FILE_OUT, 0.0, 0, NULL},
{"Line Length", "60", "10", "200",
TRUE, 'e', ARG_INT, 0.0, 0, NULL},
{"Block Length", "0", "0", "100",
TRUE, 'b', ARG_INT, 0.0, 0, NULL},
{"Group Length", "0", "0", "100",
TRUE, 'g', ARG_INT, 0.0, 0, NULL},
};
Int2 Main (void)
{
Int2 blocklen, grouplen, linelen;
FILE *ifp, *ofp;
CharPtr infile, outfile;
/* standard setup */
ErrSetFatalLevel (SEV_MAX);
ErrClearOptFlags (EO_SHOW_USERSTR);
ErrPathReset ();
if (! GetArgs ("flint", sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
infile = (CharPtr) myargs [i_argInputFile].strvalue;
outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
linelen = (Int2) myargs [e_argLineLength].intvalue;
blocklen = (Int2) myargs [b_argBlockLength].intvalue;
grouplen = (Int2) myargs [g_argGroupLength].intvalue;
ifp = FileOpen (infile, "r");
if (ifp == NULL) {
Message (MSG_FATAL, "Unable to open input file");
return 1;
}
ofp = FileOpen (outfile, "w");
if (ofp == NULL) {
Message (MSG_FATAL, "Unable to open output file");
return 1;
}
ProcessFasta (ifp, ofp, linelen, blocklen, grouplen);
FileClose (ofp);
FileClose (ifp);
return 0;
}
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