obitools/ecopcr
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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@37 60f365c0-8329-0410-b2a4-ec073aeeaa1d

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This commit is contained in:
Eric Coissac
2007-06-05 13:40:06 +00:00
parent d36821796f
commit 45f27e8c87
1 changed files with 65 additions and 15 deletions
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80
src/ecopcr.c
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@ -17,7 +17,7 @@ static void PrintHelp()
PP "------------------------------------------\n");
PP " ecoPCR Version %s\n", VERSION);
PP "------------------------------------------\n");
PP "synopsis : searching for sequence and taxonomy hybridingwith given primers\n");
PP "synopsis : searching for sequence and taxonomy hybriding with given primers\n");
PP "usage: ecoPCR [options] datafile\n");
PP "------------------------------------------\n");
PP "options:\n");
@ -51,6 +51,27 @@ static void PrintHelp()
PP "ecoPCR needs all the file type. As a result, you have to write the\n");
PP "datafile radical without any extension. For example /database/gbmam\n");
PP "------------------------------------------\n");
PP "Table result description : \n");
PP "column 1 : \n");
PP "column 2 : sequence length\n");
PP "column 3 : taxonomic id\n");
PP "column 4 : rank\n");
PP "column 5 : species taxonomic id\n");
PP "column 6 : scientific name\n");
PP "column 7 : genus taxonomic id\n");
PP "column 8 : genus name\n");
PP "column 9 : family taxonomic id\n");
PP "column 10 : family name\n");
PP "column 11 : super kingdom taxonomic id\n");
PP "column 11 : super kingdom name\n");
PP "column 13 : strand (direct or reverse)\n");
PP "column 14 : first oligonucleotide\n");
PP "column 15 : number of errors for the first strand\n");
PP "column 16 : second oligonucleotide\n");
PP "column 17 : number of errors for the second strand\n");
PP "column 18 : amplification length\n");
PP "column 19 : \n");
PP "------------------------------------------\n");
PP "\n");
}
@ -273,12 +294,17 @@ int main(int argc, char **argv)
int32_t erri;
int32_t errj;
int32_t *restricted_taxid = NULL;
int32_t *excluded_taxid = NULL;
int32_t r=0;
int32_t g=0;
while ((carg = getopt(argc, argv, "h1:2:l:L:e:k")) != -1) {
while ((carg = getopt(argc, argv, "h1:2:l:L:e:E:r:k")) != -1) {
switch (carg) {
/* -------------------- */
case '1': /* first primer */
case '1': /* first primer */
/* -------------------- */
oligo1 = ECOMALLOC(strlen(optarg)+1,
"Error on oligo 1 allocation");
@ -286,7 +312,7 @@ int main(int argc, char **argv)
break;
/* -------------------- */
case '2': /* second primer */
case '2': /* second primer */
/* -------------------- */
oligo2 = ECOMALLOC(strlen(optarg)+1,
"Error on oligo 1 allocation");
@ -296,7 +322,6 @@ int main(int argc, char **argv)
/* -------------------- */
case 'h': /* help */
/* -------------------- */
PrintHelp();
exit(0);
break;
@ -308,7 +333,7 @@ int main(int argc, char **argv)
break;
/* -------------------------- */
case 'L': /* max amplification lenght */
case 'L': /* max amplification lenght */
/* -------------------------- */
sscanf(optarg,"%d",&lmax);
break;
@ -321,8 +346,25 @@ int main(int argc, char **argv)
/* -------------------- */
case 'k': /* set the kingdom mode */
/* -------------------- */
kingdom_mode = 1;
kingdom_mode = 1; /* -------------------- */
break;
/* ------------------------------------------ */
case 'r': /* stores the restricting search taxonomic id */
/* ------------------------------------------ */
restricted_taxid = ECOREALLOC(restricted_taxid,sizeof(int32_t)*(r+1),
"Error on restricted_taxid reallocation");
sscanf(optarg,"%d",&restricted_taxid[r]);
r++;
break;
/* --------------------------------- */
case 'E': /* stores the taxonomic id to ignore */
/* --------------------------------- */
excluded_taxid = ECOREALLOC(excluded_taxid,sizeof(int32_t)*(g+1),
"Error on excluded_taxid reallocation");
sscanf(optarg,"%d",&excluded_taxid[g]);
g++;
break;
/* -------------------- */
@ -332,6 +374,7 @@ int main(int argc, char **argv)
}
}
/**
* check the path to the database is given as last argument
*/
@ -352,9 +395,7 @@ int main(int argc, char **argv)
o1c = complementPattern(o1);
o2c = complementPattern(o2);
printf("########\n");
printf("#\n");
printf("# ecoPCR version %s\n",VERSION);
printf("# direct strand oligo1 : %-32s ; oligo2c : %32s\n", o1->cpat,o2c->cpat);
printf("# reverse strand oligo2 : %-32s ; oligo1c : %32s\n", o2->cpat,o1c->cpat);
@ -385,20 +426,29 @@ int main(int argc, char **argv)
while(seq)
{
checkedSequence++;
/**
* check if the sequence should be ignored
**/
if ( (g > 0) && (eco_is_taxid_ignored(excluded_taxid, g, taxonomy->taxons->taxon[seq->taxid].taxid)) )
goto next;
/**
* check the sequence is included
**/
if ( (r > 0) && (!eco_is_taxid_included(taxonomy, restricted_taxid, r, taxonomy->taxons->taxon[seq->taxid].taxid)) )
goto next;
scname = taxonomy->taxons->taxon[seq->taxid].name;
strncpy(head,seq->SQ,10);
head[10]=0;
strncpy(tail,seq->SQ+seq->SQ_length-10,10);
tail[10]=0;
apatseq=ecoseq2apatseq(seq,apatseq);
o1Hits = ManberAll(apatseq,o1,0,0,apatseq->seqlen);
o2cHits= 0;
if (o1Hits)
{
stktmp = apatseq->hitpos[0];
@ -463,7 +513,7 @@ int main(int argc, char **argv)
}
}
next:
delete_ecoseq(seq);