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static char const rcsid[] = "$Id: formatdb.c,v 6.104 2007/08/21 20:07:49 kans 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: formatdb.c
Author: Sergei B. Shavirin
Version Creation Date: 10/01/96
$Revision: 6.104 $
File Description: formats FASTA databases for use by BLAST
$Log: formatdb.c,v $
Revision 6.104 2007/08/21 20:07:49 kans
made static functions static, added cast of EFDBCleanOpt to fix CodeWarrior complaints
Revision 6.103 2007/04/13 13:21:11 madden
Add call to ErrSetLogLevel
Revision 6.102 2006/09/25 19:56:05 camacho
Added s_SetDBListNameMultiVolDereference to fix bug when creating alias files over est
Revision 6.101 2006/06/19 17:20:14 coulouri
Extend 1GB default volume size to all platforms and impose a hard limit of 4G. rt#15171398
Revision 6.100 2006/05/04 20:07:27 camacho
Report fatal error in case of failure to add sequence to BLAST database because
of zero-length sequence and clean up the datababase that was being created.
Revision 6.99 2006/03/14 14:36:46 camacho
Logging changes
Revision 6.98 2006/03/08 19:06:12 camacho
Moved definition for maximum number of volumes to readdb.[ch], fixes rt ticket 15147600
Revision 6.97 2005/09/30 14:54:32 camacho
Enable recognition of the formatdb configuration file to allow users to set the
membership and link bits in the ASN.1 deflines.
Revision 6.96 2005/07/28 14:52:22 coulouri
remove dead code
Revision 6.95 2005/06/08 19:25:53 camacho
New feature to allow formatdb to add taxonomy ids to BLAST databases
generated from FASTA input
BugzID: 6
Revision 6.94 2004/08/25 14:47:21 camacho
Refactorings to allow formatdb process multiple deflines
Revision 6.93 2004/06/30 19:52:00 camacho
Added #include <blfmtutl.h>
Revision 6.92 2004/01/29 14:56:44 camacho
Removed -A option, FORMATDB_VER_TEXT no longer supported
Revision 6.91 2003/10/01 18:59:56 camacho
Fix to creation of custom databases using a gi list and alias files when the
source database spans multiple volumes.
Revision 6.90 2003/09/12 20:18:55 camacho
This change enables the generation of alias files for multiple ASN.1 inputs.
Revision 6.89 2003/05/30 17:31:09 coulouri
add rcsid
Revision 6.88 2003/05/13 16:02:42 coulouri
make ErrPostEx(SEV_FATAL, ...) exit with nonzero status
Revision 6.87 2003/05/08 16:02:17 camacho
Use conditional compilation for reading .formatdbrc
Revision 6.86 2003/04/03 19:10:59 camacho
Fixed typo
Revision 6.85 2003/03/26 18:51:45 camacho
1. Minor bug fixes.
2. Added eFDBCleanOpt parameter to FDBOptionsNew.
Revision 6.84 2003/03/20 14:03:02 camacho
Allow users to set the membership and link bits
Revision 6.83 2003/03/11 18:27:45 madden
Cast value to Int8 to prevent rollover
Revision 6.82 2003/02/25 15:53:40 beloslyu
final coma is not allowed after the last element of enum (at least AIX compiler barks)
Revision 6.81 2003/01/27 20:17:06 camacho
Bug fix in alias file creation
Revision 6.80 2003/01/23 22:01:29 camacho
Minor change
Revision 6.79 2003/01/22 19:44:51 camacho
1. Added check for number of volumes greater than 100.
2. Fixed bug when creating alias files if multiple FASTA inputs are used.
3. Implemented correct creation of alias files when creating custom
blast databases with a gi list.
Revision 6.78 2003/01/16 19:46:07 kans
changed NULL to 0 to fix Mac compiler error
Revision 6.77 2003/01/07 17:20:26 camacho
Added error message when gi file is not found
Revision 6.76 2002/12/18 15:16:17 camacho
Minor fixes of command-line arguments
Revision 6.75 2002/12/16 20:22:19 camacho
Better error handling when creating alias files
Revision 6.74 2002/12/13 13:44:50 camacho
Use FDBOptionsNew to create options structure
Revision 6.73 2002/12/02 22:43:42 camacho
Added warning message when no sequences are found when creating alias files
Revision 6.72 2002/11/06 21:27:46 ucko
Make 4294967295 explicitly unsigned to avoid warnings.
Revision 6.71 2002/09/26 02:14:43 camacho
Allow limiting the number of sequences per volume
Revision 6.70 2002/09/25 20:14:20 camacho
Fix for multivolume databases with non-parseable seqids
Revision 6.69 2002/08/09 19:41:25 camacho
1) Added blast version number to command-line options
2) Added explanations for some default parameters
Revision 6.68 2002/07/24 20:52:55 coulouri
Change database volume size parameter to megabases
Revision 6.67 2002/04/19 13:10:43 madden
Make new database format the default
Revision 6.66 2002/02/15 22:01:19 beloslyu
fix from HP
Revision 6.65 2001/11/06 15:24:20 dondosha
Roll back previous change - it was not needed
Revision 6.64 2001/11/05 22:14:49 dondosha
Allow stdin as input
Revision 6.63 2001/11/02 19:27:45 camacho
Fixed problem that would corrupt the BlastDefLine structures for the new database format
Revision 6.62 2001/07/12 19:35:51 madden
Set alias_file_name
Revision 6.61 2001/07/06 19:58:57 madden
Add NLM_GENERATED_CODE_PROTO and include for fdlobj.h, remove unused variables
Revision 6.60 2001/06/14 14:18:48 madden
Replace FD_MakeAliasFile with FD_CreateAliasFile
Revision 6.59 2001/06/07 20:52:07 shavirin
Fixed problem with truncation of definition lines when TEXT mode is
chosen for dump.
Revision 6.58 2001/06/07 13:13:02 madden
Set limits for -v arg, set bases_in_volume to UINT4_MAX if not set
Revision 6.57 2001/05/17 20:21:46 dondosha
Do not add .00 extension when only one volume created
Revision 6.56 2001/05/11 20:02:35 madden
Add oidlist and gifile to FD_CreateAliasFileEx
Revision 6.55 2001/05/11 18:19:02 madden
Add option to output binary gifile
Revision 6.54 2001/05/10 17:28:33 madden
Make gifile optional
Revision 6.53 2001/05/10 17:21:11 madden
Add options to produce alias file from a gifile
Revision 6.52 2001/05/08 21:56:43 shavirin
Added possibility to generate tax_id for every definition in Blast FASTA
definition set in ASN.1 structured definition lines.
Revision 6.51 2001/05/02 16:22:04 dondosha
Add NSEQ and LENGTH to alias files in case of multiple inputs to formatdb
Revision 6.50 2001/04/11 21:00:53 dondosha
Made functions FD_CreateAliasFile(Ex) public
Revision 6.49 2001/04/11 20:45:35 dondosha
Moved appending of .00 for the first volume to FormatDBInit function
Revision 6.48 2001/04/11 20:14:41 dondosha
Processing of volumes moved to lower level
Revision 6.47 2001/03/27 21:11:40 dondosha
Allow multiple input files for formatting
Revision 6.46 2001/02/01 22:25:50 shavirin
Added (uncommented) option to create ASN.1 structured deflines in
BLAST databases.
Revision 6.45 2001/01/25 21:08:09 madden
Fix an ABR
Revision 6.44 2000/12/12 23:12:09 shavirin
Fixed some FMR error.
Revision 6.43 2000/12/08 22:34:35 shavirin
Added possibility to create Taxonomy lookup database.
Revision 6.42 2000/11/22 20:53:19 shavirin
Added possibility to use Taxonomy client/server for creation of ASN.1
structured deflines with taxonomy ID (Using define TAX_CS_LOOKUP).
Revision 6.41 2000/11/13 21:37:23 madden
Use ErrPostEx
Revision 6.40 2000/11/03 18:13:22 madden
Print list of bad characters in FASTA input
Revision 6.39 2000/09/29 16:40:16 shavirin
Fixed problem with multivolume database creation.
Revision 6.38 2000/09/18 20:46:36 kans
added back #include <sqnutils.h>, needed for UseLocalAsnloadDataAndErrMsg
Revision 6.37 2000/09/12 15:38:35 shavirin
Error message level set to SEV_WARNING
Revision 6.36 2000/07/18 19:32:28 shavirin
Added new option -V to enable check for non-unique string ids in the
FASTA database. Default is FALSE.
Revision 6.35 2000/02/17 17:20:59 sicotte
Change Calling convention for FastaToSeqEntryForDb
Revision 6.34 2000/02/04 21:52:58 madden
Use FastaToSeqEntryForDb
Revision 6.33 1999/12/21 18:31:38 madden
Fixed bug with writing alias file.
Revision 6.32 1999/12/17 20:48:54 egorov
Fix 'gcc -Wall' warnings and remove old stuff.
Revision 6.31 1999/12/16 15:53:23 egorov
Typo fixed
Revision 6.30 1999/09/10 16:30:35 shavirin
Fixed problems with formating proteins by formatdb
Revision 6.29 1999/09/09 18:25:51 shavirin
Changed way to parse ASN.1. Added possibility to parse
delta sequences.
Revision 6.28 1999/08/25 20:20:27 shavirin
Added -s option to create sparse indexes.
Revision 6.27 1999/08/18 15:00:11 shavirin
If title missing from args *.pal file will have basename as title.
Revision 6.26 1999/08/03 16:38:56 shavirin
Added function FD_CreateAliasFile() for multivolume formating.
Revision 6.24 1999/07/23 18:59:01 shavirin
Added support for creation of multivolume databases.
Revision 6.23 1999/05/13 19:34:19 shavirin
More changes towards dump from ID.
Revision 6.21 1999/05/12 15:46:52 shavirin
Changed parameter in function FDBAddSequence().
Revision 6.20 1999/04/26 21:06:19 shavirin
Fixed minor bug.
Revision 6.19 1999/04/26 19:37:45 shavirin
Dumping info set to FALSE.
Revision 6.18 1999/04/26 14:53:16 shavirin
Fixed memory leaks in FDBAddSequence() function.
Revision 6.17 1999/04/21 21:44:34 shavirin
Many functions were moved to "readdb.c" file.
Revision 6.16 1999/03/21 19:16:59 madden
Fix problem on round numbers
Revision 6.15 1999/03/05 21:34:48 madden
Changes for accession.version
Revision 6.14 1999/02/04 18:01:48 madden
Add -n option for basename
Revision 6.13 1998/11/16 18:34:42 madden
Add return-value checks
Revision 6.12 1998/07/13 15:32:17 egorov
make error message more understandable
Revision 6.10 1998/06/19 21:05:46 egorov
Fix MemFree() bug
Revision 6.9 1998/05/05 13:57:37 madden
Print version number to log file
Revision 6.8 1998/04/20 19:14:05 egorov
Fix just one, but huge MLK
Revision 6.7 1998/02/23 16:49:14 egorov
Changes to make the tofasta.c independent on readdb.h
Revision 6.6 1998/02/18 15:29:31 madden
Added const to prototype for FormatdbCreateStringIndex
Revision 6.5 1998/02/11 18:05:32 madden
Changed program to take ASN.1 as input
Revision 6.3 1997/12/08 21:55:00 madden
Parse naked (no bars) as IDs
Revision 6.2 1997/11/06 18:11:17 madden
Added indices for naked gnl|PID and backbone entries
Revision 6.1 1997/10/30 18:15:08 madden
Changes to SeqIdE2Index to allow lookups by accession strings
Revision 6.0 1997/08/25 18:20:04 madden
Revision changed to 6.0
Revision 1.20 1997/07/28 18:36:55 madden
Replaced printf with ErrPostEx and fprintf
Revision 1.19 1997/07/28 14:35:37 vakatov
Added LIBCALLBACK to the ID_Compare() proto
Revision 1.18 1997/06/10 18:44:11 shavirin
Fixed return value from UpdateLookupInfo()
Revision 1.17 1997/05/19 21:16:30 shavirin
Changed content of string index file due to E2Iindex API logic
Revision 1.16 1997/05/12 19:57:38 shavirin
Added additional dump of Accessions/Locuses into string indexes
Revision 1.15 1997/05/07 21:08:15 madden
flipped parse argument default
Revision 1.14 1997/05/05 17:01:42 shavirin
Added ability to format "non-parced" seqid-deflines
Removed not-used d if#defs with FASTA_ASN
* Revision 1.13 1997/05/01 17:31:32 shavirin
* Added dumping of 2 more files: String ISAM SeqId index
*
* Revision 1.12 1997/02/25 22:20:39 shavirin
* Changes in accordance to ISAM API changes
*
* Revision 1.11 1997/02/24 21:22:57 shavirin
* Added dump of numeric ISAM information.
*
* Revision 1.10 1996/12/20 00:31:19 madden
* Protected ambiguity data against big/little endian changes.
*
* Revision 1.9 1996/12/19 16:30:36 madden
* Changes to eliminate ".nac" file for nucl.
*
* Revision 1.8 1996/11/27 16:40:19 madden
* Save build date, Make "o" argument FALSE by default.
*
* Revision 1.7 1996/11/26 20:08:08 madden
* BioseqRawConvert(bsp, Seq_code_ncbistdaa); only called for protein alphabets.
*
* Revision 1.6 1996/11/26 19:52:10 madden
* Removed FORMATDB_VER and added readdb.h (which contains same);
* Changed phd or nhd to phr or nhr
*
* Revision 1.5 1996/11/18 20:53:58 shavirin
* Forced output protein code to Seq_code_ncbistdaa.
*
* Revision 1.4 1996/11/06 23:15:34 shavirin
* Removed bug with reallocation of index tables
*
*****************************************************************************/
#define NLM_GENERATED_CODE_PROTO
#include <ncbi.h>
#include <tofasta.h>
#include <sequtil.h>
#include <readdb.h>
#include <sqnutils.h>
#include <taxblast.h>
#include <blastdef.h>
#include <mblast.h>
#include <fdlobj.h>
#include <blfmtutl.h>
/* program's arguments */
#define NUMARG (sizeof(dump_args)/sizeof(dump_args[0]))
Args dump_args[] = {
{ "Title for database file",
NULL, NULL, NULL, TRUE, 't', ARG_STRING, 0.0, 0, NULL},
{"Input file(s) for formatting",
NULL, NULL,NULL,TRUE,'i',ARG_FILE_IN, 0.0,0,NULL},
{"Logfile name:",
"formatdb.log", NULL,NULL,TRUE,'l',ARG_FILE_OUT, 0.0,0,NULL},
{"Type of file\n"
" T - protein \n"
" F - nucleotide",
"T", NULL,NULL,TRUE,'p',ARG_BOOLEAN,0.0,0,NULL},
{"Parse options\n"
" T - True: Parse SeqId and create indexes.\n"
" F - False: Do not parse SeqId. Do not create indexes.\n",
"F", NULL,NULL,TRUE,'o',ARG_BOOLEAN,0.0,0,NULL},
{"Input file is database in ASN.1 format (otherwise FASTA is expected)\n"
" T - True, \n"
" F - False.\n",
"F", NULL,NULL,TRUE,'a',ARG_BOOLEAN,0.0,0,NULL},
{"ASN.1 database in binary mode\n"
" T - binary, \n"
" F - text mode.\n",
"F", NULL,NULL,TRUE,'b',ARG_BOOLEAN,0.0,0,NULL},
{"Input is a Seq-entry",
"F", NULL ,NULL ,TRUE,'e',ARG_BOOLEAN,0.0,0,NULL},
{ "Base name for BLAST files",
NULL, NULL, NULL, TRUE, 'n', ARG_STRING, 0.0, 0, NULL},
{ "Database volume size in millions of letters",
"4000", NULL, NULL, TRUE, 'v', ARG_INT, 0.0, 0, NULL},
{ "Create indexes limited only to accessions - sparse",
"F", NULL, NULL, TRUE, 's', ARG_BOOLEAN, 0.0, 0, NULL},
{ "Verbose: check for non-unique string ids in the database",
"F", NULL, NULL, TRUE, 'V', ARG_BOOLEAN, 0.0, 0, NULL},
{ "Create an alias file with this name\n"
" use the gifile arg (below) if set to calculate db size\n"
" use the BLAST db specified with -i (above)",
NULL, NULL, NULL, TRUE, 'L', ARG_FILE_OUT, 0.0, 0, NULL},
{"Gifile (file containing list of gi's)",
NULL, NULL,NULL,TRUE,'F',ARG_FILE_IN, 0.0,0,NULL},
{"Binary Gifile produced from the Gifile specified above",
NULL, NULL,NULL,TRUE,'B',ARG_FILE_OUT, 0.0,0,NULL},
{"Taxid file to set the taxonomy ids in ASN.1 deflines",
NULL, NULL,NULL,TRUE,'T',ARG_FILE_IN, 0.0,0,NULL},
#if 0
/* disabled for this release of the NCBI C toolkit */
{"Clean up options for new blast database generation\n"
" 0 - Never: Do not clean up any 'basename.*' blast db files.\n"
" 1 - Always: Remove all 'basename.*' blast db files.\n"
" 2 - Prompt: If any 'basename.*' blast db files are found,\n"
" prompt user.\n",
"0", "0","2",TRUE,'c',ARG_INT,0.0,0,NULL},
#endif
};
enum {
title_arg,
input_arg,
logfile_arg,
is_prot_arg,
parse_arg,
asn_arg,
asnbin_arg,
seqentry_arg,
basename_arg,
dbsize_arg,
sparse_arg,
nonunique_arg,
alias_fn_arg,
gifile_arg,
bin_gifile_arg,
seqid_taxid_file_arg,
cleanup_arg
};
/* Fasta file delimiters */
#define DELIM " "
static Boolean FDBCheckFastaInputs(CharPtr fasta_files, Int4 is_prot, Int8
bases_per_vol, Int4Ptr num_inputs)
{
Int8 predicted_dblength = 0;
Char *next_file;
next_file = StringTokMT(fasta_files, DELIM, &fasta_files);
predicted_dblength = FileLength(next_file);
*num_inputs = 1;
while ((next_file = StringTokMT(fasta_files, DELIM, &fasta_files))) {
predicted_dblength += FileLength(next_file);
(*num_inputs)++;
}
if (bases_per_vol == 0)
return TRUE;
if (!is_prot)
predicted_dblength /= READDB_COMPRESSION_RATIO;
if ((predicted_dblength/bases_per_vol) > (kFDBMaxNumVolumes - 10)) {
ErrPostEx(SEV_ERROR, 0, 0, "Using %s bases per volume will exceed "
"the maximum number\nof volumes formatdb can create.\n"
"Please increase this value or do not set it at all.\n",
Nlm_Int8tostr(bases_per_vol, 0));
return FALSE;
}
return TRUE;
}
static void SeqEntryGetLength(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent)
{
Int8* length = (Int8*) data;
if (IS_Bioseq(sep)) {
BioseqPtr bsp = (BioseqPtr) sep->data.ptrvalue;
*length += (Int8)bsp->length;
return;
} else {
BioseqSetPtr bssp = (BioseqSetPtr) sep->data.ptrvalue;
SeqEntryGetLength(bssp->seq_set, data, index, indent);
}
return;
}
/** This function ensures that the path listed in the alias file's DBLIST
* contains any (relative) paths specified by the user and also do any
* necessary dereferences of the alias file contents so that they refer to the
* database's underlying name
*/
static void
s_SetDBListNameMultiVolDereference(const ReadDBFILE* rdfp,
CharPtr basename_requested_by_user,
Int4 rdfp_ctr,
Char base_fn[])
{
char* basename_of_volume = FileNameFind(rdfp->filename);
char* basename_predicted = NULL;
/* Calculate the 'predicted' name of the database to go in the DBLIST of
* the alias file */
sprintf(base_fn, "%s.%02d", basename_requested_by_user, rdfp_ctr);
basename_predicted = FileNameFind(base_fn); /* basename thereof */
/* If the basename of the volume is not the same as the 'predicted'
* basename, save the path prefix of the database name provided by the
* user and append the volume's basename */
if (StringCmp(basename_predicted, basename_of_volume)) {
char* dirname = FilePathFind(basename_requested_by_user);
if (StringLen(dirname)) {
sprintf(base_fn, "%s%c%s", dirname, DIRDELIMCHR,
basename_of_volume);
} else {
StringCpy(base_fn, basename_of_volume);
}
MemFree(dirname);
}
}
Int2 Main(void)
{
SeqEntryPtr sep = NULL;
FormatDBPtr fdbp = NULL;
FDB_optionsPtr options = NULL;
BioseqPtr bsp = NULL;
BlastDefLinePtr bdp = NULL;
Int2 id_ctr=1;
Int4 sequence_count=0;
Int4 input_ctr = 0, num_inputfiles = 0;
Int8 total_length, *lengths = NULL;
CharPtr error_msg=NULL;
FILE *fd = NULL;
CharPtr next_db = NULL, file_inputs = NULL, orig_ptr = NULL, tmp = NULL;
Boolean multiple_inputs = FALSE;
Char buf[256] = { '\0' };
Int4Ptr last_oid = NULL;
CharPtr *inputs = NULL;
Char tmpbuf1[PATH_MAX], tmpbuf2[PATH_MAX];
FDBTaxidDeflineTable* taxid_tbl = NULL;
CharPtr seqid_taxid_file = NULL;
/* get arguments */
StringCpy(buf, "formatdb ");
StringNCat(buf, BlastGetVersionNumber(), sizeof(buf)-StringLen(buf));
if (!GetArgs(buf, NUMARG, dump_args))
return 1;
if (!SeqEntryLoad())
return 1;
if (!ErrSetLog(dump_args[logfile_arg].strvalue))
ErrShow();
else
ErrSetOpts(ERR_CONTINUE, ERR_LOG_ON);
UseLocalAsnloadDataAndErrMsg();
ErrSetMessageLevel(SEV_WARNING);
ErrSetLogLevel(SEV_WARNING);
/* Ensure that volume size is within acceptable limits */
if (dump_args[dbsize_arg].intvalue > 16000) {
ErrPostEx(SEV_FATAL, 1, 0, "Volume size may not exceed 16 gigabases.\n");
return 1;
}
/* Parse input string for multiple inputs */
file_inputs = StringSave(dump_args[input_arg].strvalue);
tmp = StringTokMT(file_inputs, DELIM, &next_db);
if (next_db) {
if (!dump_args[basename_arg].strvalue) {
ErrPostEx(SEV_FATAL, 1, 0, "Database base name must be provided "
"with multiple input files\n");
return 1;
}
multiple_inputs = TRUE;
/* When formatdb takes multiple inputs and writes one blast database,
* it also writes alias files for each of the inputs passed in. Make
* sure that none of these inputs has the same name as the basename for
* the new database */
do {
if (!StringCmp(dump_args[basename_arg].strvalue, tmp)) {
ErrPostEx(SEV_FATAL, 1, 0, "Database base name cannot have the "
"same name as one of the input files\n");
return 1;
}
} while ((tmp = StringTokMT(next_db, DELIM, &next_db)));
}
MemFree(file_inputs);
options = FDBOptionsNew(dump_args[input_arg].strvalue,
dump_args[is_prot_arg].intvalue,
dump_args[title_arg].strvalue,
dump_args[asn_arg].intvalue,
dump_args[asnbin_arg].intvalue,
dump_args[seqentry_arg].intvalue,
dump_args[sparse_arg].intvalue,
dump_args[nonunique_arg].intvalue,
dump_args[parse_arg].intvalue,
dump_args[basename_arg].strvalue,
dump_args[alias_fn_arg].strvalue,
((Int8)dump_args[dbsize_arg].intvalue)*1000000, 0,
FORMATDB_VER, FALSE, (EFDBCleanOpt) 0);
if (options == NULL)
return 1;
options->gi_file = StringSave(dump_args[gifile_arg].strvalue);
options->gi_file_bin = StringSave(dump_args[bin_gifile_arg].strvalue);
orig_ptr = options->db_file;
options->db_file = StringTokMT(options->db_file, DELIM, &next_db);
if (options->gi_file && dump_args[alias_fn_arg].strvalue == NULL &&
options->gi_file_bin == NULL) {
ErrPostEx(SEV_FATAL, 1,0,"The -F option must be used with either "
"the -L or -B option\n");
FDBOptionsFree(options);
return 1;
} else if (dump_args[alias_fn_arg].strvalue && options->gi_file_bin) {
ErrPostEx(SEV_FATAL, 1, 0, "The -L and -B options may not be "
"specified together");
FDBOptionsFree(options);
return 1;
} else if (options->gi_file_bin && options->gi_file == NULL) {
ErrPostEx(SEV_FATAL, 1, 0, "The -B option may not be specified "
"without the -F option");
FDBOptionsFree(options);
return 1;
} else if (dump_args[alias_fn_arg].strvalue && options->gi_file == NULL) {
ErrPostEx(SEV_FATAL, 1, 0, "The -L option must be specified "
"with the -F option\n");
FDBOptionsFree(options);
return 1;
}
/*** Write alias file using a gilist ***/
if (options->alias_file_name && options->gi_file) {
Int8 nletters=0, nletters_tot=0;
Int4 nseqs=0, nseqs_tot=0;
CharPtr gifile;
Int4 i, gi_list_total, ordinal_id, rdfp_ctr = 0;
BlastDoubleInt4Ptr gi_list;
ReadDBFILEPtr rdfp, rdfp_tmp;
Char alias_fn[PATH_MAX], base_fn[PATH_MAX];
rdfp = rdfp_tmp = readdb_new(options->db_file, options->is_protein);
if (rdfp == NULL) {
ErrPostEx(SEV_FATAL, 1, 0, "Unable to open BLAST db %s\n",
options->db_file);
FDBOptionsFree(options);
return 1;
}
if ((gifile = FindBlastDBFile(options->gi_file)) == NULL) {
ErrPostEx(SEV_FATAL, 1, 0, "Unable to find %s\n", options->gi_file);
rdfp = readdb_destruct(rdfp);
FDBOptionsFree(options);
return 1;
}
gi_list = GetGisFromFile(gifile, &gi_list_total);
gifile = MemFree(gifile);
/* Iterate through the rdfp's (there might be many) */
for (; rdfp; rdfp = rdfp->next, rdfp_ctr++) {
/* Isolate the current rdfp so that we restrict the search for gis
* to this volume only! */
ReadDBFILEPtr next = rdfp->next;
rdfp->next = NULL;
nseqs = nletters = 0;
for (i = 0; i < gi_list_total; i++) {
ordinal_id = readdb_gi2seq(rdfp, gi_list[i].gi, NULL);
if (ordinal_id >= 0) {
nseqs++;
nletters += readdb_get_sequence_length(rdfp, ordinal_id);
}
}
rdfp->next = next; /* restore the next rdfp */
sprintf(alias_fn, "%s.%02d", options->alias_file_name, rdfp_ctr);
/* For the base name (DBLIST field in alias file) append the
* volume number if there are multiple volumes in this database */
if (rdfp->next || rdfp_ctr != 0) {
s_SetDBListNameMultiVolDereference(rdfp, options->base_name,
rdfp_ctr, base_fn);
} else {
StringCpy(base_fn, options->base_name);
}
FD_CreateAliasFileEx(options->db_title, alias_fn, 0,
options->is_protein, base_fn, 0, 0,
nletters, nseqs, NULL, options->gi_file);
ErrLogPrintf("Created %s alias file with %ld sequences, %s %s\n",
alias_fn, nseqs, Nlm_Int8tostr(nletters,0),
options->is_protein ? "residues" : "bases");
nseqs_tot += nseqs; nletters_tot += nletters;
}
/* Sanity check: Don't write 'ghost' alias files */
if (nletters_tot == 0 || nseqs_tot == 0) {
ErrPostEx(SEV_FATAL, 1, 0, "No gis from %s were found in the %s "
"database", options->gi_file, options->db_file);
for (i = 0; i <= rdfp_ctr; i++) {
sprintf(alias_fn,"%s.%02d.%cal", options->alias_file_name, i,
options->is_protein ? 'p' : 'n');
FileRemove(alias_fn);
}
FDBOptionsFree(options);
gi_list = MemFree(gi_list);
rdfp_tmp = readdb_destruct(rdfp_tmp);
return 1;
}
/* Adjust alias files if necessary */
if (rdfp_ctr == 1) { /* single volume database */
sprintf(tmpbuf1, "%s.%cal", alias_fn,
options->is_protein ? 'p' : 'n');
sprintf(tmpbuf2, "%s.%cal", options->alias_file_name,
options->is_protein ? 'p' : 'n');
FileRename(tmpbuf1, tmpbuf2);
ErrLogPrintf("SUCCESS: Renamed %s to %s\n", tmpbuf1, tmpbuf2);
} else { /* multi-volume database */
Char *p = FD_ConstructMultivolumeDBList(options->alias_file_name,
rdfp_ctr);
/* Create wrapper alias file
* Note that the total number of sequences and letters is not needed
* because these will be calculated by readdb when reading the alias
* files.
*/
FD_CreateAliasFileEx(options->db_title, options->alias_file_name,
0, options->is_protein, p, 0, 0, 0, 0, NULL, NULL);
ErrLogPrintf("SUCCESS: Created wrapper alias file %s for %s\n",
options->alias_file_name, p);
p = MemFree(p);
}
gi_list = MemFree(gi_list);
FDBOptionsFree(options);
rdfp_tmp = readdb_destruct(rdfp_tmp);
return 0;
} else if (options->gi_file_bin && options->gi_file) {
/*** Convert text gi list to binary format ***/
Int4 ngis;
ngis = readdb_MakeGiFileBinary(options->gi_file, options->gi_file_bin);
ErrLogPrintf("SUCCESS: Converted %ld gi(s) to binary format on %s\n",
ngis, options->gi_file_bin);
FDBOptionsFree(options);
return 0;
}
#ifdef TAX_CS_LOOKUP
if(dump_args[12].intvalue && options->parse_mode) {
/* These functions will create taxonomy lookup database */
options->tax_lookup = RDTaxLookupInit();
options->tax_callback = FDBTaxCallback;
}
#endif
/*** Make sure that the inputs will not create too many volumes ***/
if (!FDBCheckFastaInputs(dump_args[input_arg].strvalue,
options->is_protein,
options->bases_in_volume, &num_inputfiles))
return 1;
/* Allocate last_oid to keep track of the last ordinal ids that each
* of the input files had */
if (multiple_inputs) {
ASSERT(num_inputfiles > 0);
last_oid = (Int4Ptr) MemNew(num_inputfiles*sizeof(Int4));
inputs = (CharPtr *) MemNew(num_inputfiles*sizeof(CharPtr));
lengths = (Int8Ptr) MemNew(num_inputfiles*sizeof(Int8));
if (!last_oid || !inputs || !lengths) {
ErrPostEx(SEV_ERROR, 0, 0, "Out of memory");
FDBOptionsFree(options);
return 1;
}
}
/* Initialize formatdb structure */
if ((fdbp = FormatDBInit(options)) == NULL)
return 2;
/* Allow users to set their own membership and link bits using a
* .formatdbrc file. Useful for formatting purposes */
if (options->version >= FORMATDB_VER) {
options->linkbit_listp = FDBLoadLinksTable();
options->memb_tblp = FDBLoadMembershipsTable();
}
/* Process the optional seqid/taxid pair input file */
seqid_taxid_file = dump_args[seqid_taxid_file_arg].strvalue;
taxid_tbl = FDBTaxidDeflineTableNew(seqid_taxid_file);
if ( !taxid_tbl && !StringHasNoText(seqid_taxid_file) ) {
ErrPostEx(SEV_ERROR, 0, 0, "Failed to read taxonomy data from %s",
seqid_taxid_file);
FDBOptionsFree(options);
return 1;
}
/* Loop on input files */
while (options->db_file) {
total_length = 0;
/* Input database file maybe either in ASN.1 or in FASTA format */
if (!options->isASN) {
/* FASTA format of input database */
if((fd = FileOpen(options->db_file, "r")) == NULL) {
ErrPostEx(SEV_ERROR, 0, 0, "Could not open %s\n", options->db_file);
return 3;
}
/* Get sequences */
while ((sep = FastaToSeqEntryForDb(fd,
(Boolean)!options->is_protein,
&error_msg, options->parse_mode, options->base_name, &id_ctr,NULL)) != NULL) {
if(!IS_Bioseq(sep)) { /* Not Bioseq - failure */
ErrLogPrintf("Error in readind Bioseq Formating failed.\n");
return 4;
}
SeqEntrySetScope(sep);
bsp = (BioseqPtr) sep->data.ptrvalue;
total_length += bsp->length;
sequence_count++;
if (error_msg) {
Char buffer[42];
SeqIdWrite(bsp->id, buffer, PRINTID_FASTA_LONG, 41);
ErrPostEx(SEV_WARNING, 0, 0, "Sequence number %ld (%s), %s\n",
sequence_count, buffer, error_msg);
error_msg = MemFree(error_msg);
}
bdp = FDBGetDefAsnFromBioseq(bsp, taxid_tbl);
if ( FDBAddBioseq(fdbp, bsp, bdp) ) {
options->clean_opt = eCleanAlways;
FDBCleanUp(options);
ErrPostEx(SEV_FATAL, 1, 0,
"Fatal error when adding sequence to BLAST database.");
return 1;
}
bdp = BlastDefLineSetFree(bdp);
SeqEntryFree(sep);
}
FileClose(fd);
/* Writing multi-volume pointer file */
FD_MakeAliasFile(options);
} else {
/* ASN.1 format of input database */
AsnTypePtr atp, atp2;
AsnModulePtr amp;
if (! SeqEntryLoad())
ErrShow();
/* get pointer to all loaded ASN.1 modules */
amp = AsnAllModPtr();
if (amp == NULL) {
ErrLogPrintf("Could not load ASN.1 modules.\n");
return 5;
}
/* get the initial type pointers */
atp = AsnFind("Bioseq-set");
if (atp == NULL) {
ErrLogPrintf("Could not get type pointer for Bioseq-set.\n");
return 6;
}
atp2 = AsnFind("Bioseq-set.seq-set.E");
if (atp2 == NULL) {
ErrLogPrintf("Could not get type pointer for Bioseq-set.seq-set.E\n");
return 7;
}
if ((fdbp->aip = AsnIoOpen (options->db_file,
options->asnbin ? "rb":"r")) == NULL) {
ErrLogPrintf("Cannot open input database file. Formating failed...\n");
return 8;
}
if (options->is_seqentry) {
Int8 len = 0;
/* Seq entry */
sep = SeqEntryAsnRead(fdbp->aip, NULL);
FDBAddSeqEntry(fdbp, sep);
SeqEntryExplore(sep, (Pointer)&len, SeqEntryGetLength);
SeqEntryFree(sep);
sequence_count++;
total_length += len;
} else {
/* Bioseq-set */
while ((atp = AsnReadId(fdbp->aip, amp, atp)) != NULL) {
if (atp == atp2) { /* top level Seq-entry */
Int8 len = 0;
sep = SeqEntryAsnRead(fdbp->aip, atp);
FDBAddSeqEntry(fdbp, sep);
SeqEntryExplore(sep, (Pointer)&len, SeqEntryGetLength);
SeqEntryFree(sep);
sequence_count++;
total_length += len;
} else {
AsnReadVal(fdbp->aip, atp, NULL);
}
}
} /* end "if Bioseq or Bioseq-set */
} /* end "if FASTA or ASN.1" */
if (multiple_inputs) {
/* record the ordinal ids, input file names and input file lengths
* in the following arrays. This will be used later to
* create the multiple alias files in case that the multiple input
* results in a multi-volume database */
inputs[input_ctr] = options->db_file;
lengths[input_ctr] = total_length;
last_oid[input_ctr++] = sequence_count;
}
options->db_file = StringTokMT(next_db, DELIM, &next_db);
} /* Loop on input files */
/* Dump indexes, deallocate structure, arrays, etc. */
if(FormatDBClose(fdbp))
return 9;
options->db_file = orig_ptr;
/* If multiple inputs were given, create an alias file for each of the
* fasta file inputs */
if (multiple_inputs) {
ReadDBFILEPtr rdfp, rdfp_tmp;
Boolean span_multiple_rdfp = FALSE, first_time = TRUE;
Int4 start_oid = 1, stop_oid, vol_ctr = 0;
Char basename[PATH_MAX]; /* save the name of individual alias files */
Char dblist[PATH_MAX]; /* save the name(s) of all alias files when an
input spans multiple volumes */
ASSERT(input_ctr == num_inputfiles);
rdfp = rdfp_tmp = readdb_new(dump_args[basename_arg].strvalue,
options->is_protein);
if (rdfp == NULL) {
ErrPostEx(SEV_FATAL, 1, 0,
"Cannot create alias files for multiple inputs");
FDBOptionsFree(options);
return 1;
}
/* For each rdfp write the corresponding alias file(s) */
ErrLogPrintf("\nCreating alias files for multiple FASTA inputs...\n");
input_ctr = 0;
MemSet(dblist, 0, sizeof(dblist));
MemSet(basename, 0, sizeof(basename));
for (; input_ctr < num_inputfiles; input_ctr++) {
while (rdfp) {
sprintf(basename, "%s.%02d", inputs[input_ctr], vol_ctr);
if (first_time || span_multiple_rdfp) {
start_oid = 1;
first_time = FALSE;
} else
start_oid = last_oid[input_ctr-1] - rdfp->start+1;
if (last_oid[input_ctr] > (rdfp->stop+1)) {
stop_oid = rdfp->stop+1;
span_multiple_rdfp = TRUE;
StringCat(dblist, basename); StringCat(dblist, " ");
} else if (span_multiple_rdfp) {
StringCat(dblist, basename); StringCat(dblist, " ");
stop_oid = last_oid[input_ctr] - rdfp->start;
} else {
stop_oid = last_oid[input_ctr] - rdfp->start;
}
ErrLogPrintf("Input %s (up to %ld) alias file %s (%ld-%ld)\n",
inputs[input_ctr], last_oid[input_ctr], basename,
start_oid, stop_oid);
FD_CreateAliasFileEx(NULL, basename, 0,
options->is_protein, rdfp->filename,
start_oid, stop_oid, lengths[input_ctr],
0, NULL, NULL);
if (last_oid[input_ctr] > rdfp->stop) {
rdfp = rdfp->next;
vol_ctr++;
} else
break;
}
if (span_multiple_rdfp) {
/* Create wrapper alias file for the corresponding volumes */
FD_CreateAliasFileEx(NULL, inputs[input_ctr], 0,
options->is_protein, dblist, 0, 0, lengths[input_ctr],
0, NULL, NULL);
span_multiple_rdfp = FALSE;
ErrLogPrintf("Created wrapper alias file %s for %s\n",
inputs[input_ctr], dblist);
} else {
/* Rename the alias file just created */
sprintf(tmpbuf1, "%s.%cal", basename,
options->is_protein ? 'p' : 'n');
sprintf(tmpbuf2, "%s.%cal", inputs[input_ctr],
options->is_protein ? 'p' : 'n');
FileRename(tmpbuf1, tmpbuf2);
ErrLogPrintf("Renamed %s to %s\n", tmpbuf1, tmpbuf2);
}
MemSet(dblist, 0, sizeof(dblist));
}
rdfp_tmp = readdb_destruct(rdfp_tmp);
MemFree(last_oid);
MemFree(inputs);
MemFree(lengths);
}
#ifdef TAX_CS_LOOKUP
if(dump_args[12].intvalue && options->parse_mode) {
RDTaxLookupClose(options->tax_lookup);
}
#endif
taxid_tbl = FDBTaxidDeflineTableFree(taxid_tbl);
if (options->version >= FORMATDB_VER) {
options->linkbit_listp = FDBDestroyLinksTable(options->linkbit_listp);
options->memb_tblp = FDBDestroyMembershipsTable(options->memb_tblp);
}
ErrLogPrintf("SUCCESS: formatted database %s\n",
options->alias_file_name ?
options->alias_file_name : options->base_name);
options = FDBOptionsFree(options);
return 0;
} /* main()*/
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