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/* findspl.c
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* 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 have not placed any restriction on its use or reproduction.
*
* 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.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* File Name: findspl.c
*
* Author: Epstein, Weisemann
*
* Version Creation Date: 1/4/94
*
* $Revision: 6.2 $
*
* File Description:
* Find protein splice sites
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
* $Log: findspl.c,v $
* Revision 6.2 1998/08/26 18:41:09 kans
* fixed remaining -v -fd warning
*
* Revision 6.1 1998/08/24 20:43:43 kans
* fixed -v -fd warnings
*
* Revision 6.0 1997/08/25 18:20:00 madden
* Revision changed to 6.0
*
* Revision 1.2 1996/06/24 18:37:50 epstein
* move splicing functionality to sequtil.c
*
* Revision 1.1 1996/06/19 15:23:21 epstein
* Initial revision
*
*
* ==========================================================================
*/
#include <accentr.h>
#include <sequtil.h>
#include <connect/ncbi_gnutls.h>
#define NUMARGS 3
Args myargs[NUMARGS] = {
{"Gi number of protein","0","1","99999999",FALSE,'g',ARG_INT,0.0,0,NULL},
{"Input file containing protein GIs","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}};
static void FindAndPrint(FILE *ofp, Int4 gi)
{
SeqLocPtr slp, current;
SeqEntryPtr sep;
if ((sep = EntrezSeqEntryGet(gi, 0)) != NULL)
{
fprintf (ofp, "%ld", (long) gi);
slp = FindSpliceSites(sep, /* find on protein */ TRUE);
for (current = SeqLocFindNext(slp, NULL); current != NULL;
current = SeqLocFindNext(slp, current))
{
fprintf (ofp, " %ld", (long) SeqLocStart(current) + 1);
}
fprintf (ofp, "\n");
SeqEntryFree(sep);
SeqLocFree(slp);
}
}
Int2 Main(void)
{
long longgi;
char line[9];
Int4 gi;
FILE *ofp;
FILE *ifp = NULL;
SOCK_SetupSSL(NcbiSetupGnuTls);
if ( !GetArgs("findspl", NUMARGS, myargs) ) return 1;
gi = myargs[0].intvalue;
if (gi <= 0)
{
if ((ifp = FileOpen(myargs[1].strvalue, "r")) == NULL)
{
Message(MSG_FATAL, "Unable to open input file %s",
myargs[1].strvalue);
return 1;
}
}
if ((ofp = FileOpen(myargs[2].strvalue, "w")) == NULL)
{
Message(MSG_FATAL, "Unable to open output file %s",
myargs[2].strvalue);
return 1;
}
if (! EntrezInit("findspl", FALSE, NULL))
{
Message(MSG_FATAL, "Unable to open Entrez database");
FileClose(ofp);
return 1;
}
if (gi > 0)
{
FindAndPrint(ofp, gi);
} else {
while (fgets(line,sizeof(line),ifp) != NULL) {
sscanf(line, "%ld", &longgi);
gi = (Int4) longgi;
FindAndPrint(ofp, gi);
}
FileClose(ifp);
}
FileClose(ofp);
EntrezFini();
return 0;
}
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