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static char const rcsid[] = "$Id: blast_input.c,v 1.10 2003/12/03 17:30:25 dondosha 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: blast_input.c
Author: Ilya Dondoshansky
Contents: Reading FASTA sequences for BLAST
$Revision: 1.10 $
******************************************************************************/
#include <objloc.h>
#include <tofasta.h>
#include <algo/blast/api/blast_input.h>
#include <algo/blast/api/blast_seq.h>
#define MAX_NUM_QUERIES 16383 /* == 1/2 INT2_MAX */
#define MAX_TOTAL_LENGTH 20000000
Boolean
BLAST_GetQuerySeqLoc(FILE *infp, Boolean query_is_na, Uint1 strand,
Int4 start, Int4 end, BlastMaskLoc** lcase_mask, SeqLocPtr* query_slp,
Int4 ctr_start, Int4* num_queries)
{
Int8 total_length;
BioseqPtr query_bsp;
SeqLocPtr mask_slp, last_slp;
BlastMaskLoc* last_mask;
char prefix[2]; /* for FastaToSeqEntryForDb */
Int2 ctr = ctr_start + 1; /* Counter for FastaToSeqEntryForDb */
Int4 query_index = 0;
BlastMaskLoc* new_mask;
SeqEntryPtr sep;
Boolean done = TRUE;
Int4 from, to;
if (!query_slp)
return -1;
total_length = 0;
*query_slp = NULL;
last_slp = NULL;
if (query_is_na && strand == Seq_strand_unknown)
strand = Seq_strand_both;
SeqMgrHoldIndexing(TRUE);
mask_slp = NULL;
last_mask = NULL;
StrCpy(prefix, "");
while ((sep=FastaToSeqEntryForDb(infp, query_is_na, NULL, FALSE, prefix,
&ctr, (lcase_mask ? &mask_slp : NULL))) != NULL)
{
if (mask_slp) {
new_mask = BlastMaskLocFromSeqLoc(mask_slp, query_index);
if (!last_mask)
*lcase_mask = last_mask = new_mask;
else {
last_mask->next = new_mask;
last_mask = last_mask->next;
}
/* Masking locations in a SeqLoc form are no longer needed */
mask_slp = SeqLocSetFree(mask_slp);
}
++query_index;
query_bsp = NULL;
if (query_is_na) {
SeqEntryExplore(sep, &query_bsp, FindNuc);
} else {
SeqEntryExplore(sep, &query_bsp, FindProt);
}
if (query_bsp == NULL) {
ErrPostEx(SEV_FATAL, 0, 0, "Unable to obtain bioseq\n");
return 2;
}
/* Original from and to are 1-offsets, except when they are 0's,
in which case they are start and end of sequence respectively */
from = ((start > 0) ? start - 1 : 0);
to = ((end > 0) ? end - 1 : query_bsp->length - 1);
from = MIN(from, query_bsp->length - 1);
to = MIN(to, query_bsp->length - 1);
if ((strand == Seq_strand_plus) || (strand == Seq_strand_minus) ||
(from > 0) || (to < query_bsp->length - 1))
{
SeqLocPtr new_slp = SeqLocIntNew(from, to, strand,
SeqIdFindBest(query_bsp->id, SEQID_GI));
if (last_slp) {
last_slp->next = new_slp;
last_slp = last_slp->next;
} else {
*query_slp = last_slp = new_slp;
}
} else {
last_slp = ValNodeAddPointer(&last_slp, SEQLOC_WHOLE,
SeqIdDup(SeqIdFindBest(query_bsp->id, SEQID_GI)));
if (*query_slp == NULL)
*query_slp = last_slp;
}
total_length += query_bsp->length;
if (total_length > MAX_TOTAL_LENGTH ||
query_index >= MAX_NUM_QUERIES) {
done = FALSE;
if (total_length > MAX_TOTAL_LENGTH) {
ErrPostEx(SEV_INFO, 0, 0,
"Total length of queries has exceeded %ld\n",
MAX_TOTAL_LENGTH);
} else {
ErrPostEx(SEV_INFO, 0, 0,
"Number of query sequences has exceeded the limit of %ld\n",
MAX_NUM_QUERIES);
}
break;
}
}
SeqMgrHoldIndexing(FALSE);
if (num_queries)
*num_queries = query_index;
return done;
}
/** Probably can be removed */
Int4 MakeBlastSequenceBlkFromFasta(FILE *fasta_fp, BLAST_SequenceBlk* seq)
{
BioseqPtr query_bsp;
SeqEntryPtr query_sep;
Boolean is_na = FALSE;
Boolean believe_defline = TRUE;
SeqLocPtr mask_slp = NULL;
Int2 ctr=1;
Uint1* sequence = NULL;
query_sep=FastaToSeqEntryForDb(fasta_fp,
is_na, /* query is nucleotide? */
NULL, /* error message */
believe_defline, /* believe query defline? */
"", /* prefix for localid if not parseable */
&ctr, /* starting point for constructing a unique id */
&mask_slp);
if (query_sep == NULL)
return 1;
SeqEntryExplore(query_sep, &query_bsp, FindProt);
if (query_bsp == NULL)
return 1;
/* allocate contiguous space for the sequence */
sequence = (Uint1 *) malloc(query_bsp->length);
if (sequence == NULL)
return 1;
/* convert to ncbistdaa encoding */
BioseqRawConvert(query_bsp, Seq_code_ncbistdaa);
/* read the sequence */
BSSeek(query_bsp->seq_data, 0, SEEK_SET);
BSRead(query_bsp->seq_data, sequence, query_bsp->length);
seq->length = query_bsp->length;
seq->sequence = sequence;
return 0;
}
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