obitools/ecopcr
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add a -k option to the ecoPCR binary to substitute superkingdom column by a kingdom column

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@11 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2007-03-27 16:29:20 +00:00
parent b2c307e611
commit 8c91d3d8f3
3 changed files with 34 additions and 4 deletions
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19
src/ecopcr.c
View File

@ -135,6 +135,7 @@ static void ExitUsage(stat)
void printRepeat(ecoseq_t *seq,
PatternPtr o1, PatternPtr o2,
char strand,
char kingdom,
int32_t pos1, int32_t pos2,
int32_t err1, int32_t err2,
ecotaxonomy_t *taxonomy)
@ -204,7 +205,11 @@ void printRepeat(ecoseq_t *seq,
family_name = "###";
}
taxon = eco_getsuperkingdom((taxon) ? taxon:main_taxon,taxonomy);
if (kingdom)
taxon = eco_getkingdom((taxon) ? taxon:main_taxon,taxonomy);
else
taxon = eco_getsuperkingdom((taxon) ? taxon:main_taxon,taxonomy);
if (taxon)
{
superkingdom_taxid = taxon->taxid;
@ -299,6 +304,7 @@ int main(int argc, char **argv)
int32_t lmax=0;
int32_t error_max=0;
int32_t errflag=0;
char kingdom_mode=0;
char *prefix;
@ -325,7 +331,7 @@ int main(int argc, char **argv)
int32_t errj;
while ((carg = getopt(argc, argv, "h1:2:l:L:e:")) != -1) {
while ((carg = getopt(argc, argv, "h1:2:l:L:e:k")) != -1) {
switch (carg) {
/* -------------------- */
@ -368,6 +374,11 @@ int main(int argc, char **argv)
case 'e': /* error max */
/* -------------------- */
sscanf(optarg,"%d",&error_max);
break;
case 'k': /* error max */
/* -------------------- */
kingdom_mode = 1;
break;
/* -------------------- */
@ -462,7 +473,7 @@ int main(int argc, char **argv)
if ((!lmin || (length >= lmin)) &&
(!lmax || (length <= lmax)))
printRepeat(seq,o1,o2c,'D',posi,posj,erri,errj,taxonomy);
printRepeat(seq,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy);
//printf("%s\tD\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o1Hits,o2cHits,posi,posj,scname);
}
}
@ -495,7 +506,7 @@ int main(int argc, char **argv)
if ((!lmin || (length >= lmin)) &&
(!lmax || (length <= lmax)))
printRepeat(seq,o2,o1c,'R',posi,posj,erri,errj,taxonomy);
printRepeat(seq,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy);
//printf("%s\tR\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o2Hits,o1cHits,posi,posj,scname);
}
}

1
src/libecoPCR/ecoPCR.h
View File

@ -224,6 +224,7 @@ char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end);
ecotx_t *eco_getspecies(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getgenus(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getfamily(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
#endif /*ECOPCR_H_*/

18
src/libecoPCR/ecotax.c
View File

@ -215,6 +215,24 @@ ecotx_t *eco_getfamily(ecotx_t *taxon,
return eco_findtaxonatrank(taxon,rankindex,tax);
}
ecotx_t *eco_getkingdom(ecotx_t *taxon,
ecotaxonomy_t *taxonomy)
{
static ecotaxonomy_t *tax=NULL;
static int32_t rankindex=-1;
if (taxonomy && tax!=taxonomy)
{
rankindex = rank_index("kingdom",taxonomy->ranks);
tax=taxonomy;
}
if (!tax || rankindex < 0)
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
return eco_findtaxonatrank(taxon,rankindex,tax);
}
ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
ecotaxonomy_t *taxonomy)
{