static char const rcsid[] = "$Id: fastacmd.c,v 6.36 2005/06/22 13:55:22 coulouri Exp $";

/* $Id: fastacmd.c,v 6.36 2005/06/22 13:55:22 coulouri Exp $
* ===========================================================================
*
*                            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:  $RCSfile: fastacmd.c,v $
*
* Author:  Sergei Shavirin
*
* Initial Version Creation Date: 05/20/1997
*
* $Revision: 6.36 $
*
* File Description:
*        FASTA retrievel system using ISAM indexes
*
* $Log: fastacmd.c,v $
* Revision 6.36  2005/06/22 13:55:22  coulouri
* add support for dumping accessions
*
* Revision 6.35  2005/05/05 15:54:06  dondosha
* Enhanced comment for the -s option and fixed typo in -i option description
*
* Revision 6.34  2004/12/04 03:39:48  camacho
* Set range of data on -D option
*
* Revision 6.33  2004/12/03 04:58:06  camacho
* Fix name conflict in enumeration for fastacmd dump types
*
* Revision 6.32  2004/12/02 20:37:40  camacho
* + fastacmd feature to dump list of gis
*
* Revision 6.31  2004/06/30 19:52:00  camacho
* Added #include <blfmtutl.h>
*
* Revision 6.30  2004/05/13 20:54:45  coulouri
* spell 'loci' correctly
*
* Revision 6.29  2003/05/30 17:31:09  coulouri
* add rcsid
*
* Revision 6.28  2003/04/15 19:09:41  camacho
* Added option to retrieve sequences by PIG
*
* Revision 6.27  2002/11/21 21:35:54  camacho
* Make sure the proper exit code is returned
*
* Revision 6.26  2002/08/12 12:40:55  camacho
* Fix for unresolved symbol in Win32 build
*
* Revision 6.25  2002/08/09 19:41:25  camacho
* 1) Added blast version number to command-line options
* 2) Added explanations for some default parameters
*
* Revision 6.24  2002/07/30 21:02:17  camacho
* Added explanation for -T option
*
* Revision 6.23  2002/07/30 15:30:47  camacho
* 1. Added explanation for -L option
* 2. Moved function to parse SeqLocs to readdb.c
*
* Revision 6.22  2002/07/18 22:17:49  madden
* Revert last change
*
* Revision 6.21  2002/07/18 18:49:43  madden
* Set SeqLoc to NULL always
*
* Revision 6.20  2002/07/14 21:02:08  camacho
* Added extra features to fastacmd
*
* Revision 6.19  2002/05/02 21:59:31  camacho
* Clarified database parameter default
*
* Revision 6.18  2001/12/18 13:01:52  camacho
* Added new flag -D to dump blast database in FASTA format
*
* Revision 6.17  2001/12/10 19:17:32  camacho
* Added option to allow fastacmd to use Ctrl-As as defline separators.
*
* Revision 6.16  2001/10/19 19:46:26  camacho
* Added new feature to dump FASTA files from blast databases, added support for the new database format
*
* Revision 6.15  2000/10/16 20:47:35  madden
* Add -o option to write output to file
*
* Revision 6.14  2000/06/28 16:56:52  madden
* Call Fastacmd_Search_ex, Boolean for target gi only
*
* Revision 6.13  2000/03/08 15:26:03  madden
* Add return statement to Main fct, purify nit
*
* Revision 6.12  2000/01/12 21:05:00  egorov
* Use Fastacmd API
*
* Revision 6.11  1999/12/21 21:26:22  egorov
* Use new parameter of readdb_gi2seq function
*
* Revision 6.10  1999/12/17 20:48:54  egorov
* Fix 'gcc -Wall' warnings and remove old stuff.
*
* Revision 6.9  1999/09/28 19:02:47  egorov
* In the new version of the 'fastacmd' there is not need to
* specify database name if search a GI.
*
* Revision 6.8  1999/02/23 17:17:32  madden
* Remove unused static _accession functions
*
* Revision 6.7  1998/02/11 18:06:43  madden
* Fix for reading IDs in from a file
*
* Revision 6.6  1998/02/06 18:26:35  madden
* Removed stripping of white spaces
*
* Revision 6.5  1998/01/29 19:47:02  madden
* Changed second call from BioseqRawToFasta to BioseqRawToFastaExtra
*
* Revision 6.4  1998/01/27 20:27:03  madden
* Added option to specify sequence line length
*
* Revision 6.3  1998/01/23 21:56:16  madden
* Error messages sent to stderr
*
* Revision 6.2  1998/01/16 22:04:20  madden
* Call to readdb_new_ex, fixed FUM
*
* Revision 6.1  1997/11/07 16:19:15  shavirin
* Added possibility to retrieve redundant accessions
*
* Revision 6.0  1997/08/25 18:19:56  madden
* Revision changed to 6.0
*
* Revision 5.2  1997/05/20 21:00:45  shavirin
* Remove spurious error message in accession/locus retrieval
*
* Revision 5.1  1997/05/20 15:47:30  shavirin
* Initial revision
*
*
* ==========================================================================
*/

#include <ncbi.h>
#include <objseq.h>
#include <objsset.h>
#include <sequtil.h>
#include <seqport.h>
#include <tofasta.h>
#include <readdb.h>
#include <blast.h>
#include <blfmtutl.h>

static Args myargs [] = {
    { "Database",                                               /* 0 */
      "nr", NULL, NULL, TRUE, 'd', ARG_STRING, 0.0, 0, NULL},
    { "Type of file\n"                                          /* 1 */
      "         G - guess mode (look for protein, then nucleotide)\n"
      "         T - protein   \n"
      "         F - nucleotide", 
      "G", NULL,NULL,TRUE,'p',ARG_STRING,0.0,0,NULL},
    { "Comma-delimited search string(s).\n"
      "      GIs, accessions, loci, or fullSeq-id strings may be used,\n"
      "      e.g. 555, AC147927, 'gnl|dbname|tag'",             /* 2 */
      NULL, NULL, NULL, TRUE, 's', ARG_STRING, 0.0, 0, NULL},
    { "Input file with GIs/accessions/loci for batch\n"
      "      retrieval",                                        /* 3 */
      NULL, NULL, NULL, TRUE, 'i', ARG_STRING, 0.0, 0, NULL},
    { "Retrieve duplicate accessions",                          /* 4 */
      "F", NULL, NULL, TRUE, 'a', ARG_BOOLEAN, 0.0, 0, NULL},
    { "Line length for sequence",                               /* 5 */
      "80", NULL, NULL, TRUE, 'l', ARG_INT, 0.0, 0, NULL},
    { "Definition line should contain target gi only",          /* 6 */
      "F", NULL, NULL, TRUE, 't', ARG_BOOLEAN, 0.0, 0, NULL},
    { "Output file",                                            /* 7 */ 
      "stdout", NULL, NULL, TRUE, 'o', ARG_FILE_OUT, 0.0, 0, NULL},
    { "Use Ctrl-A's as non-redundant defline separator",        /* 8 */
      "F", NULL, NULL, TRUE, 'c', ARG_BOOLEAN, 0.0, 0, NULL},
    { "Dump the entire database as (default is not to dump anything):\n"
      "      1 FASTA\n"
      "      2 Gi list\n"
      "      3 Accession.version list\n",                       /* 9 */
      "0", "0", "3", TRUE, 'D', ARG_INT, 0.0, 0, NULL},
    { "Range of sequence to extract (Format: start,stop)\n"
      "      0 in 'start' refers to the beginning of the sequence\n"
      "      0 in 'stop' refers to the end of the sequence",
      "0,0", NULL, NULL, TRUE, 'L', ARG_STRING, 0.0, 0, NULL},  /* 10 */
    { "Strand on subsequence (nucleotide only): 1 is top, 2 is bottom",
      "1", NULL, NULL, FALSE, 'S', ARG_INT, 0.0, 0, NULL},      /* 11 */
    { "Print taxonomic information for requested sequence(s)",
      "F", NULL, NULL, FALSE, 'T', ARG_BOOLEAN, 0.0, 0, NULL},  /* 12 */
    { "Print database information only (overrides all other options)",
      "F", NULL, NULL, FALSE, 'I', ARG_BOOLEAN, 0.0, 0, NULL},  /* 13 */
    { "Retrieve sequences with this PIG",
      NULL, NULL, NULL, TRUE, 'P', ARG_INT, 0.0, 0, NULL},     /* 14 */
};

Int2 Main (void)
{
    CharPtr	database, searchstr, batchfile;
    Int4	linelen, pig;
    Boolean	dupl, target, use_ctrlAs, taxonomy_info, dbinfo_only;
    EBlastDbDumpType dump_db = eNoDump;
    Uint1 is_prot;
    FILE *outfp = NULL;
    CharPtr seqlocstr;
    Uint1 strand;
    Char buf[256] = { '\0' };
    Int2 rv;

    StringCpy(buf, "fastacmd ");
    StringNCat(buf, BlastGetVersionNumber(), sizeof(buf)-StringLen(buf));
    if (! GetArgs (buf, DIM(myargs), myargs)) {
	     return (1);
    }

    if( !ErrSetLogfile ("stderr", ELOG_APPEND) ) {
	     exit(1);
    }

    database = myargs[0].strvalue;
    if (!StringICmp(myargs[1].strvalue, "T"))
        is_prot = READDB_DB_IS_PROT;
    else if (!StringICmp(myargs[1].strvalue, "F"))
        is_prot = READDB_DB_IS_NUC;
    else
        is_prot = READDB_DB_UNKNOWN;

    searchstr     = myargs[2].strvalue;
    batchfile     = myargs[3].strvalue;
    dupl          = myargs[4].intvalue;
    linelen       = myargs[5].intvalue;
    target        = myargs[6].intvalue;
    use_ctrlAs    = myargs[8].intvalue;
    dump_db       = myargs[9].intvalue;
    seqlocstr     = myargs[10].strvalue;
    strand        = myargs[11].intvalue;
    taxonomy_info = myargs[12].intvalue;
    dbinfo_only   = myargs[13].intvalue;
    pig           = myargs[14].intvalue == 0 ? PIG_NONE : myargs[14].intvalue;

    if ((outfp = FileOpen(myargs[7].strvalue, "w")) == NULL) {
        ErrPostEx(SEV_ERROR, 0, 0,"Could not open %s", myargs[7].strvalue);
        return 1;
    }

    rv = Fastacmd_Search_ex (searchstr, database, is_prot, batchfile, dupl,
            linelen, outfp, target, use_ctrlAs, dump_db, seqlocstr, strand,
            taxonomy_info, dbinfo_only, pig);

    FileClose(outfp);

    return rv;
}