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/*****************************************************************************
*
* getseq.c
* entrez version
*
*****************************************************************************/
#include <accentr.h>
#include <tofasta.h>
#define NUMARGS 9
Args myargs[NUMARGS] = {
/*0*/ { "Input string id", "M65051", NULL, NULL, FALSE, 'i', ARG_STRING, 0.0,0,NULL},
/*1*/ { "Output Seq-entry", "T", NULL, NULL, TRUE , 's', ARG_BOOLEAN, 0.0,0,NULL},
/*2*/ { "Output File Name", "stdout", NULL, NULL, FALSE, 'o', ARG_FILE_OUT, 0.0,0,NULL},
/*3*/ { "GenInfo Import id", "0", NULL, NULL, TRUE , 'g', ARG_INT, 0.0,0,NULL},
/*4*/ { "Id is GenBank accession", "T", NULL, NULL, TRUE , 'a', ARG_BOOLEAN, 0.0,0,NULL},
/*5*/ { "Id is GenBank locus", "F", NULL, NULL, TRUE , 'l', ARG_BOOLEAN, 0.0,0,NULL},
/*6*/ { "Id is PIR accession", "F", NULL, NULL, TRUE , 'b', ARG_BOOLEAN, 0.0,0,NULL},
/*7*/ { "Id is PIR locus", "F", NULL, NULL, TRUE , 'p', ARG_BOOLEAN, 0.0,0,NULL},
/*8*/ { "Return type 1=Bioseq,2=seg-set,3=nuc-prot,4=pub-set", "1", "1", "4", TRUE , 'r', ARG_INT, 0.0,0,NULL}};
Int2 Main(void)
{
Boolean seqentry; /* Arg 1 should always be TRUE */
Int2 retcode; /* Default is nuc-prot */
TextSeqIdPtr tsip; /* Text object, name, locus, or release */
SeqIdPtr sip; /* Same as a ValNodePtr, generic data ptr implemented */
/* as a choice and a union. Used to pass "tsip" data */
GiimPtr giim; /* GenInfo structure passed via "sip" in the special case */
/* of accessing a by GenInfo Id */
Int4 uid;
SeqEntryPtr sep;
FILE * output;
/*
** Get program arguments
*/
if ( !GetArgs("GetSeq 1.1", NUMARGS, myargs) ) return 1;
/*
** Set parameters from the command line
*/
seqentry = (Boolean)myargs[1].intvalue;
retcode = (Int2)myargs[8].intvalue;
/*
** Instantiate ASN stream pointers and data.
** "sip" is used to pass the information in "tsip".
*/
tsip = TextSeqIdNew();
sip = ValNodeNew(NULL);
sip->data.ptrvalue = tsip;
/*
** From the command line, set either the name or accession field
** and the choice field of SeqIdPtr, this structure will be used
** to return an ASN stream from the CD-ROM
*/
if (myargs[3].intvalue) { /* GenInfo import ID */
giim = GiimNew();
giim->id = myargs[3].intvalue;
sip->data.ptrvalue = giim;
sip->choice = SEQID_GIIM;
} else if (myargs[4].intvalue) { /* GenBank accession */
tsip->accession = myargs[0].strvalue;
sip->choice = SEQID_GENBANK;
} else if (myargs[5].intvalue) { /* GenBank locus */
tsip->name = myargs[0].strvalue;
sip->choice = SEQID_GENBANK;
} else if (myargs[6].intvalue) { /* PIR accession */
tsip->accession = myargs[0].strvalue;
sip->choice = SEQID_PIR;
} else if (myargs[7].intvalue) { /* PIR locus name */
tsip->name = myargs[0].strvalue;
sip->choice = SEQID_PIR;
}
/*
** Initialize, open and otherwise prepare for CD-ROM or Network access.
*/
if ( !EntrezInit("getfasta", FALSE, NULL) ) {
Message(MSG_ERROR, "Init failed");
return 1;
}
/*
** Using the SeqEntryPtr structure query the access routines
** and get the internal access number for this SeqEntry
**
** If the SeqEntryPtr comes up without a hit, report the error and
** and exit.
**
** Otherwise, use the internal access number, uid, and retrieve a
** a sequence entry ASN pointer, sep. If for some strange reason
** that it is NULL report the error and exit.
**
** Write a (nucleic acid) sequence to output in FASTA format
**
** Close the ASN file stream, free up memory create which was
** allocated elsewhere, sep.
*/
if (seqentry) {
uid = EntrezFindSeqId(sip);
if (! uid)
Message(MSG_ERROR, "Couldn't find uid");
else {
sep = EntrezSeqEntryGet(uid, retcode);
if (sep == NULL)
Message(MSG_ERROR, "sep was NULL");
else {
output = FileOpen(myargs[2].strvalue, "w");
SeqEntryToFasta(sep, output, TRUE); /* nucleic acid output */
FileClose(output);
SeqEntryFree(sep);
}
}
} else {
Message(MSG_ERROR, "Oops");
}
/*
** Close down the CD-ROM or Network access.
** Return OK to Operating system.
*/
EntrezFini();
return 0;
}
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