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/**************************************************************************
* *
* COPYRIGHT NOTICE *
* *
* This software/database is categorized as "United States Government *
* Work" under the terms of the United States Copyright Act. It was *
* produced as part of the author's official duties as a Government *
* employee and thus can not be copyrighted. This software/database is *
* freely available to the public for use without a copyright notice. *
* Restrictions can not be placed on its present or future use. *
* *
* Although all reasonable efforts have been taken to ensure the accuracy *
* and reliability of the software and data, the National Library of *
* Medicine (NLM) and the U.S. Government do not and can not warrant the *
* performance or results that may be obtained by using this software, *
* data, or derivative works thereof. The NLM and the U.S. Government *
* disclaim any and all warranties, expressed or implied, as to the *
* performance, merchantability or fitness for any particular purpose or *
* use. *
* *
* In any work or product derived from this material, proper attribution *
* of the author(s) as the source of the software or data would be *
* appreciated. *
* *
**************************************************************************/
/* Author Hugues Sicotte 8/14/99
Stand-alone program to dust one sequence.
future improvements are to take a whole fasta library as input.
*/
#include <ncbi.h>
#include <objseq.h>
#include <objsset.h>
#include <sequtil.h>
#include <seqport.h>
#include <tofasta.h>
#include <blast.h>
#include <blastpri.h>
#include <txalign.h>
#include <objloc.h>
#include <dust.h>
#define NUMARG 6
static Args myargs [NUMARG] = {
{ "sequence",
NULL, NULL, NULL, FALSE, 'i', ARG_FILE_IN, 0.0, 0, NULL},
{ "Lowercase Masked letters (default is N)",
"F", NULL, NULL, FALSE, 'l', ARG_BOOLEAN, 0.0, 0, NULL},
{ "is nucleotide)",
"T", NULL, NULL, FALSE, 'N', ARG_BOOLEAN, 0.0, 0, NULL},
{ "level",
"20", NULL, NULL, FALSE, 'L', ARG_INT, 0.0, 0, NULL},
{ "window size",
"16", NULL, NULL, FALSE, 'W', ARG_INT, 0.0, 0, NULL},
{ "Number of iterations of dusting (for timing purposes)",
"1", NULL, NULL, FALSE, 'I', ARG_INT, 0.0, 0, NULL}
};
Int2 Main (void)
{
CharPtr inputfile;
FILE* infp, *outfp;
Boolean is_na,UseN;
BioseqPtr query;
SeqEntryPtr sep;
Int4 loop,i,start,stop,last;
SeqLocPtr slp,slp_dust;
Char c;
SeqPortPtr spp;
Int2 level,window;
if (! GetArgs ("testdust", NUMARG, myargs))
{
return (1);
}
if (! SeqEntryLoad())
return 1;
ErrSetMessageLevel(SEV_WARNING);
inputfile = myargs [0].strvalue;
if ((infp = FileOpen(inputfile, "r")) == NULL)
{
ErrPostEx(SEV_FATAL, 1, 0, "blast: Unable to open input file %s\n", inputfile);
return (1);
}
is_na = (Boolean) myargs [2].intvalue;
UseN = (Boolean) myargs [1].intvalue;
level = (Int2) myargs[3].intvalue;
window = (Int2) myargs[4].intvalue;
loop = (Int2) myargs[5].intvalue;
sep = FastaToSeqEntry(infp, is_na);
FileClose(infp);
if (sep != NULL)
{
query = NULL;
if (is_na)
{
SeqEntryExplore(sep, &query, FindNuc);
}
else
{
SeqEntryExplore(sep, &query, FindProt);
}
if (query == NULL)
{
ErrPostEx(SEV_FATAL, 1, 0, "Unable to obtain bioseq\n");
return 2;
}
}
for(i=0;i<loop;i++) {
slp_dust = BioseqDust (query, (Int4)0, query->length-1,
level, window, (Int2)5, (Int2) 1);
if(i!=loop-1 && slp_dust)
slp_dust = SeqLocFree(slp_dust);
}
outfp = stdout;
if(slp_dust==NULL) {
BioseqRawToFasta(query, outfp, is_na);
} else {
SeqEntrysToDefline(sep,outfp,is_na,TRUE);
start = SeqLocStart(slp_dust);
stop = SeqLocStop(slp_dust);
spp = SeqPortNew(query,0,query->length-1,Seq_strand_plus,Seq_code_iupacna);
last =-1;
slp=NULL;
last = -1;
while((slp=SeqLocFindNext(slp_dust,slp))!=NULL) {
start = SeqLocStart(slp);
stop = SeqLocStop(slp);
for(i=last+1;i<start;) {
c= SeqPortGetResidue(spp);
fprintf(outfp,"%c",c);
i++;
if(!(i%80))
fprintf(outfp,"\n");
}
for(i=start;i<=stop;) {
c= SeqPortGetResidue(spp);
if(UseN)
c= 'N';
else
c = TO_LOWER(c);
fprintf(outfp,"%c",c);
i++;
if(!(i%80))
fprintf(outfp,"\n");
}
last = stop;
}
for(i=stop+1;i<query->length;) {
c= SeqPortGetResidue(spp);
fprintf(outfp,"%c",c);
i++;
if(!(i%80))
fprintf(outfp,"\n");
}
if(i%80)
fprintf(outfp,"\n");
SeqPortFree(spp);
slp_dust = SeqLocFree(slp_dust);
}
SeqEntryFree(sep);
return 0;
}
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