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/* sugint.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: sugint.c
*
* Author: Jonathan Kans
*
* Version Creation Date: 10/31/08
*
* $Revision: 1.4 $
*
* File Description:
*
* 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>
#include <suggslp.h>
static SeqEntryPtr ReadSep (
FILE *fp,
Boolean forceNuc,
Boolean forcePrt
)
{
Pointer dataptr;
Uint2 datatype, entityID;
dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, forceNuc, forcePrt, TRUE, FALSE);
if (dataptr == NULL) return NULL;
entityID = ObjMgrRegister (datatype, dataptr);
return GetTopSeqEntryForEntityID (entityID);
}
static Int2 ProcessSuggest (
FILE *nfp,
FILE *pfp,
AsnIoPtr ofp,
Int2 gencode
)
{
BioseqPtr nbsp = NULL, pbsp = NULL;
SeqEntryPtr nsep, psep, sep;
Int2 rsult = 0;
SeqAnnotPtr sap;
SeqFeatPtr sfp;
SeqLocPtr slp;
nsep = ReadSep (nfp, TRUE, FALSE);
psep = ReadSep (pfp, FALSE, TRUE);
if (nsep != NULL && psep != NULL) {
sep = FindNthBioseq (nsep, 1);
if (sep != NULL && IS_Bioseq (sep)) {
nbsp = (BioseqPtr) sep->data.ptrvalue;
}
sep = FindNthBioseq (psep, 1);
if (sep != NULL && IS_Bioseq (sep)) {
pbsp = (BioseqPtr) sep->data.ptrvalue;
}
if (nbsp != NULL && pbsp != NULL) {
if (ISA_na (nbsp->mol) && ISA_aa (pbsp->mol)) {
sap = SuggestCodingRegionEx (nbsp, pbsp, gencode, &rsult);
if (sap != NULL && sap->type == 1) {
sfp = (SeqFeatPtr) sap->data;
if (sfp != NULL && sfp->data.choice == SEQFEAT_CDREGION) {
slp = sfp->location;
if (slp != NULL) {
SeqLocAsnWrite (slp, ofp, NULL);
rsult = 0;
}
}
}
SeqAnnotFree (sap);
}
}
}
SeqEntryFree (nsep);
SeqEntryFree (psep);
return rsult;
}
#define n_argNucInputFile 0
#define p_argPrtInputFile 1
#define o_argOutputFile 2
#define g_argGeneticCode 3
Args myargs [] = {
{"Nucleotide Input File", NULL, NULL, NULL,
FALSE, 'n', ARG_FILE_IN, 0.0, 0, NULL},
{"Protein Input File", NULL, NULL, NULL,
FALSE, 'p', ARG_FILE_IN, 0.0, 0, NULL},
{"Output File", NULL, NULL, NULL,
FALSE, 'o', ARG_FILE_OUT, 0.0, 0, NULL},
{"Genetic Code", "1", "0", "20",
TRUE, 'g', ARG_INT, 0.0, 0, NULL},
};
Int2 Main (void)
{
Int2 gencode;
FILE *nfp, *pfp;
AsnIoPtr ofp;
CharPtr nucfile, prtfile, outfile;
Int2 rsult = 0;
/* standard setup */
ErrSetFatalLevel (SEV_MAX);
ErrClearOptFlags (EO_SHOW_USERSTR);
UseLocalAsnloadDataAndErrMsg ();
ErrPathReset ();
/* finish resolving internal connections in ASN.1 parse tables */
if (! AllObjLoad ()) {
Message (MSG_FATAL, "AllObjLoad failed");
return 1;
}
if (! SubmitAsnLoad ()) {
Message (MSG_FATAL, "SubmitAsnLoad failed");
return 1;
}
if (! FeatDefSetLoad ()) {
Message (MSG_FATAL, "FeatDefSetLoad failed");
return 1;
}
if (! SeqCodeSetLoad ()) {
Message (MSG_FATAL, "SeqCodeSetLoad failed");
return 1;
}
if (! GeneticCodeTableLoad ()) {
Message (MSG_FATAL, "GeneticCodeTableLoad failed");
return 1;
}
/* process command line arguments */
if (! GetArgs ("sugint", sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
nucfile = (CharPtr) myargs [n_argNucInputFile].strvalue;
prtfile = (CharPtr) myargs [p_argPrtInputFile].strvalue;
outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
gencode = (Int2) myargs [g_argGeneticCode].intvalue;
nfp = FileOpen (nucfile, "r");
if (nfp == NULL) {
Message (MSG_FATAL, "Unable to open nucleotide input file");
return 1;
}
pfp = FileOpen (prtfile, "r");
if (pfp == NULL) {
Message (MSG_FATAL, "Unable to open protein input file");
return 1;
}
ofp = AsnIoOpen (outfile, "w");
if (ofp == NULL) {
Message (MSG_FATAL, "Unable to open output file");
return 1;
}
rsult = ProcessSuggest (nfp, pfp, ofp, gencode);
AsnIoClose (ofp);
FileClose (pfp);
FileClose (nfp);
return rsult;
}
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