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/* subfuse.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: subfuse.c
*
* Author: Jonathan Kans
*
* Version Creation Date: 7/30/01
*
* $Revision: 1.5 $
*
* File Description:
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
*
* ==========================================================================
*/
#include <ncbi.h>
#include <objall.h>
#include <objsset.h>
#include <objsub.h>
#include <objfdef.h>
#include <sqnutils.h>
#include <gather.h>
static SeqSubmitPtr ReadOneSubmission (
CharPtr directory,
CharPtr base,
CharPtr suffix
)
{
AsnIoPtr aip;
Char file [FILENAME_MAX], path [PATH_MAX];
SeqSubmitPtr ssp;
if (base == NULL) {
base = "";
}
if (suffix == NULL) {
suffix = "";
}
StringNCpy_0 (path, directory, sizeof (path));
sprintf (file, "%s%s", base, suffix);
FileBuildPath (path, NULL, file);
aip = AsnIoOpen (path, "r");
if (aip == NULL) return NULL;
ssp = SeqSubmitAsnRead (aip, NULL);
AsnIoClose (aip);
return ssp;
}
static void WriteOneSubmission (
CharPtr path,
SeqSubmitPtr ssp
)
{
AsnIoPtr aip;
aip = AsnIoOpen (path, "w");
if (aip == NULL) return;
SeqSubmitAsnWrite (ssp, aip, NULL);
AsnIoFlush (aip);
AsnIoClose (aip);
}
static void ProcessOneRecord (
SeqSubmitPtr master,
BioseqSetPtr bssp,
CharPtr directory,
CharPtr base,
CharPtr suffix
)
{
SeqEntryPtr sep;
SeqSubmitPtr ssp;
ssp = ReadOneSubmission (directory, base, suffix);
if (ssp == NULL || ssp->datatype != 1) return;
if (master->sub == NULL) {
master->sub = ssp->sub;
ssp->sub = NULL;
}
sep = (SeqEntryPtr) ssp->data;
ssp->data = NULL;
ValNodeLink (&(bssp->seq_set), sep);
}
/* Args structure contains command-line arguments */
#define p_argInputPath 0
#define o_argOutputFile 1
#define x_argSuffix 2
Args myargs [] = {
{"Path to files", NULL, NULL, NULL,
TRUE, 'p', ARG_STRING, 0.0, 0, NULL},
{"Output file", "stdout", NULL, NULL,
TRUE, 'o', ARG_FILE_OUT, 0.0, 0, NULL},
{"Suffix", ".sqn", NULL, NULL,
TRUE, 'x', ARG_STRING, 0.0, 0, NULL},
};
Int2 Main (void)
{
CharPtr base, directory, outfile, suffix, ptr;
BioseqSetPtr bssp;
Int4 count;
Uint2 entityID;
ValNodePtr head, vnp;
Int4 offset = 0;
SeqEntryPtr sep;
SeqSubmitPtr ssp;
SeqEntryPtr tmp;
/* 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 ("subfuse", sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
directory = (CharPtr) myargs [p_argInputPath].strvalue;
outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
suffix = (CharPtr) myargs [x_argSuffix].strvalue;
bssp = BioseqSetNew ();
if (bssp == NULL) return 0;
bssp->_class = BioseqseqSet_class_genbank;
sep = SeqEntryNew ();
if (sep == NULL) return 0;
sep->choice = 2;
sep->data.ptrvalue = (Pointer) bssp;
SeqMgrSeqEntry (SM_BIOSEQSET, (Pointer) bssp, sep);
ssp = SeqSubmitNew ();
if (ssp == NULL) return 0;
ssp->datatype = 1;
ssp->data = (Pointer) sep;
entityID = ObjMgrRegister (OBJ_BIOSEQSET, (Pointer) bssp);
AssignIDsInEntity (entityID, 0, NULL);
/* get list of all files in source directory */
head = DirCatalog (directory);
head = ValNodeSort (head, SortVnpByNaturalCI);
for (vnp = head; vnp != NULL; vnp = vnp->next) {
if (vnp->choice == 0) {
base = (CharPtr) vnp->data.ptrvalue;
if (! StringHasNoText (base)) {
ptr = StringStr (base, suffix);
if (ptr != NULL) {
*ptr = '\0';
Message (MSG_POST, "Processing %s\n", base);
ProcessOneRecord (ssp, bssp, directory, base, suffix);
}
}
}
}
/* clean up file list */
ValNodeFreeData (head);
/* reassign feature IDs, remove nested genbank sets */
for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) {
count = FindHighestFeatureID (tmp);
OffsetFeatureIDs (tmp, offset);
OffsetFeatureIDXrefs (tmp, offset);
offset += count;
}
RemoveDuplicateNestedSetsForEntityID (entityID);
/* write output file */
WriteOneSubmission (outfile, ssp);
return 0;
}
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