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/* $Id: readbclhits.c,v 6.2 2002/10/08 15:31:55 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.
*
* ===========================================================================
*
* Author: Ilya Dondoshansky
*
* File Description:
* Program to read the binary hits file from blastclust and produce a text
* hit file in tabular format
*
* $Revision: 6.2 $
*/
#include <ncbi.h>
#ifdef NUMARG
#undef NUMARG
#endif
#define NUMARG (sizeof(myargs)/sizeof(myargs[0]))
typedef struct cluster_log_header
{
Boolean numeric_id_type;
Int4 size;
} ClusterLogHeader, PNTR ClusterLogHeaderPtr;
typedef struct cluster_log_info
{
Int4 id1, id2;
Int4 hsp_length1, hsp_length2;
FloatHi bit_score, perc_identity;
} ClusterLogInfo, PNTR ClusterLogInfoPtr;
static Args myargs [] = {
{ "Binary input file with hits from blastclust run", /* 0 */
"stdin", NULL, NULL, FALSE, 'i', ARG_FILE_IN, 0.0, 0, NULL},
{ "Text output file", /* 1 */
"stdout", NULL, NULL, FALSE, 'o', ARG_FILE_OUT, 0.0, 0, NULL}
};
#define INFO_LIST_SIZE 1000
Int2 Main(void)
{
FILE *hitsfp, *outfp;
ClusterLogInfoPtr info;
Int4 num_queries, num_hits, i, total_id_len;
Int4Ptr gi_list = NULL, seq_len = NULL;
CharPtr PNTR id_list = NULL;
CharPtr ptr, id_string;
ClusterLogHeader header;
if (! GetArgs ("readbclhits", NUMARG, myargs))
return (1);
hitsfp = FileOpen(myargs[0].strvalue, "rb");
outfp = FileOpen(myargs[1].strvalue, "w");
FileRead(&header, sizeof(ClusterLogHeader), 1, hitsfp);
if (header.numeric_id_type) {
num_queries = header.size;
gi_list = (Int4Ptr) MemNew(num_queries*sizeof(Int4));
FileRead(gi_list, sizeof(Int4), num_queries, hitsfp);
} else {
total_id_len = header.size;
num_queries = 0;
id_string = (CharPtr) MemNew(total_id_len+1);
FileRead(id_string, sizeof(Char), total_id_len, hitsfp);
ptr = id_string;
/* Count the ID's and change delimiter from space to null character */
for (i=0; i<total_id_len; i++) {
if (*ptr==' ') {
num_queries++;
*ptr = '\0';
}
ptr++;
}
id_list = (CharPtr PNTR) MemNew(num_queries*sizeof(CharPtr));
for (i=0; i<num_queries; i++) {
/* No need for allocation of new memory */
id_list[i] = id_string;
id_string += StringLen(id_string) + 1;
}
id_string = id_list[0];
}
seq_len = (Int4Ptr) Malloc(num_queries*sizeof(Int4));
FileRead(seq_len, sizeof(Int4), num_queries, hitsfp);
info = (ClusterLogInfoPtr) MemNew(INFO_LIST_SIZE*sizeof(ClusterLogInfo));
fprintf(outfp,
"# Fields: id1, id2, length1, length2, bit score, percent identity\n");
while ((num_hits = FileRead(info, sizeof(ClusterLogInfo), INFO_LIST_SIZE,
hitsfp)) > 0) {
for (i=0; i<num_hits; ++i) {
if (header.numeric_id_type) {
fprintf(outfp, "%ld\t%ld\t%ld\t%ld\t%f\t%f\n",
gi_list[info[i].id1], gi_list[info[i].id2],
info[i].hsp_length1, info[i].hsp_length2,
info[i].bit_score, info[i].perc_identity);
} else {
fprintf(outfp, "%s\t%s\t%ld\t%ld\t%f\t%f\n", id_list[info[i].id1],
id_list[info[i].id2], info[i].hsp_length1,
info[i].hsp_length2, info[i].bit_score,
info[i].perc_identity);
}
}
} /* End loop on chunks of hits */
FileClose(hitsfp);
FileClose(outfp);
}
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