Well, I thought its not to concern wthe query or the database in this instance, I think(may be I am wrong) the issue is the way I go through the loop. (foreach sample and for each snp)
but here it is:

 
$conn = XXXXX::Database::Conn->new('live'); #its the wrapper build aro
+und the actual DBI module to facilitate the ease of fetching the data
+.
$conn->addConnection(DBI->connect('dbi:Oracle:SNP.world','snp','snp', 
+{RaiseError =>1 , AutoCommit=>0}),'snp');
[download]

My queries

select distinct i.id_ind  from dna_plate p,dnaplate_status ps, dna_wel
+l w, individual_name i where p.id_dnaplate = w.id_dnaplate and w.id_c
+ontent = i.id_ind and p.plate_type = 13 and ps.id_dnaplate = p.id_dna
+plate and ps.status = 7 and p.id_study in(6637,7867) and i.name_type 
+= 2 order by i.id_ind 

select ss.id_snp
from well_assay wa, snpassay_snp sas, snp_summary ss
where wa.id_assay = sas.id_assay
and sas.id_snp = ss.id_snp
and wa.id_well in ('W30467', 'W30569', 'W30572')
order by 1

select distinct 'C' as proc_status,nvl(o.abbreviation, substr(translat
+e(o.orgtitle, ' ', '_'), 1, 15)) || ':' || nvl(inm.name, 'NOEXTNAME')
+ as suppname,i.id_ind,i.clonename,g.id_snp,wa.id_well as plex,nvl(dp.
+id_dnaplate, 0) as id_dnaplate,nvl(upper(rm.maprow), '-') || nvl( tri
+m(to_char(rm.mapcol, '09')), '-') as wellrc,nvl(to_char(g.id_dnawell)
+, 'UNKNOWN') as id_dnawell,g.genotype,g.confidence,nvl(dp.plate_name,
+ 'NOPLATENAME') as plate_name from (individual i left outer join indi
+vidual_name inm on i.id_ind = inm.id_ind and inm.name_type = 2),
(genotype g left outer join ((dna_well dw join dna_plate dp on dw.id_d
+naplate = dp.id_dnaplate) join rowcol_map rm on dp.format = rm.format
+ and dw.id_map = rm.id_map) on g.id_dnawell = dw.id_dnawell),
organisation o,
well_assay wa
where nvl(i.supplier, 0) = o.id_org
and i.id_ind = g.id_ind
and g.id_assay = wa.id_assay
and i.id_ind = ?
and g.id_snp = ?
and g.disregard = 0
order by 2, 3, 4, 5, 6
[download]