def ovarlap_search(self, s2, e2):
array_of_indices = self._search(s2, e2)
all_original_indices_and_length = {}
if array_of_indices is not None:
for indice in array_of_indices:
(s1, e1, set_indices) = self.ranges[indice]
s, e = overlap_boundaries(s1, e1, s2, e2)
if e < s:
print 'ERROR end %s is greater than start %s' % (e, s)
print s1, e1, s2, e2
for original_i in set_indices:
if all_original_indices_and_length.has_key(original_i):
list_range = all_original_indices_and_length.get(
original_i)
list_range.append((s, e))
list_range = merge_ranges(list_range)
all_original_indices_and_length[
original_i] = list_range
else:
all_original_indices_and_length[original_i] = [(s, e)]
list_of_array_value_and_length = []
for indice in all_original_indices_and_length.keys():
list_of_array_value_and_length.append(
(self.array[indice],
all_original_indices_and_length.get(indice)))
return list_of_array_value_and_length
def summarize(all_sites):
for site_name in all_sites.keys():
site_info = all_sites.get(site_name)
contig_span_list = []
for value in site_info.get("contig_span"):
s, e = value.split('-')
contig_span_list.append((int(s), int(e)))
merged_contig_span_list = merge_ranges(contig_span_list)
regions = site_info.get("span_region").split(';')
overlap_ranges = []
pileup = Counter()
#Find overlap between the contigs and the expected position
for start2, end2 in contig_span_list:
tmp_overlap_ranges = []
for i in range(int(start2), int(end2) + 1):
pileup[i] += 1
for region in regions:
if len(region) == 0:
logging.warning("Site %s has no expected regions" %
(site_name))
continue
start1, end1 = region.split('-')
overlap_res = overlap.get_overlap_if_exist(
int(start1), int(end1), int(start2), int(end2))
if overlap_res:
tmp_overlap_ranges.append(overlap_res)
s, e = overlap_res
if len(tmp_overlap_ranges) == 0:
logging.warning(
"%s: No overlap found between expected region %s and contig alignment %s-%s"
% (site_name, site_info.get("span_region"), start2, end2))
else:
max_ol_length = get_length_of_list_range(tmp_overlap_ranges)
if site_info["max_ol_length"] < max_ol_length:
site_info["max_ol_length"] = max_ol_length
overlap_ranges.extend(tmp_overlap_ranges)
for pileup_value in pileup.values():
if pileup_value >= 4:
site_info["contig_coverage4plus"] += 1
else:
site_info["contig_coverage%s" % pileup_value] += 1
site_info["overlap_length"] = get_length_of_list_range(overlap_ranges)
length = get_length_of_list_range(merged_contig_span_list)
site_info["alignment_length"] = length
return all_sites
def summarize(all_sites):
for site_name in all_sites.keys():
site_info=all_sites.get(site_name)
contig_span_list = []
for value in site_info.get("contig_span"):
s,e = value.split('-')
contig_span_list.append((int(s),int(e)))
merged_contig_span_list=merge_ranges(contig_span_list)
regions = site_info.get("span_region").split(';')
overlap_ranges=[]
pileup=Counter()
#Find overlap between the contigs and the expected position
for start2,end2 in contig_span_list:
tmp_overlap_ranges=[]
for i in range(int(start2), int(end2)+1):
pileup[i]+=1
for region in regions:
if len(region)==0:
logging.warning("Site %s has no expected regions"%(site_name))
continue
start1,end1 =region.split('-')
overlap_res = overlap.get_overlap_if_exist(int(start1), int(end1), int(start2), int(end2))
if overlap_res:
tmp_overlap_ranges.append(overlap_res)
s, e = overlap_res
if len(tmp_overlap_ranges)==0:
logging.warning("%s: No overlap found between expected region %s and contig alignment %s-%s"%(site_name, site_info.get("span_region") ,start2, end2))
else:
max_ol_length = get_length_of_list_range(tmp_overlap_ranges)
if site_info["max_ol_length"]<max_ol_length:
site_info["max_ol_length"]=max_ol_length
overlap_ranges.extend(tmp_overlap_ranges)
for pileup_value in pileup.values():
if pileup_value>=4:
site_info["contig_coverage4plus"]+=1
else:
site_info["contig_coverage%s"%pileup_value]+=1
site_info["overlap_length"]=get_length_of_list_range(overlap_ranges)
length=get_length_of_list_range(merged_contig_span_list)
site_info["alignment_length"]=length
return all_sites
def ovarlap_search(self,s2,e2):
array_of_indices=self._search(s2,e2)
all_original_indices_and_length={}
if array_of_indices is not None:
for indice in array_of_indices:
(s1,e1,set_indices)=self.ranges[indice]
s, e = overlap_boundaries(s1, e1, s2, e2)
if e<s:
print 'ERROR end %s is greater than start %s'%(e,s)
print s1, e1, s2, e2
for original_i in set_indices:
if all_original_indices_and_length.has_key(original_i):
list_range=all_original_indices_and_length.get(original_i)
list_range.append((s,e))
list_range=merge_ranges(list_range)
all_original_indices_and_length[original_i]=list_range
else:
all_original_indices_and_length[original_i]=[(s,e)]
list_of_array_value_and_length=[]
for indice in all_original_indices_and_length.keys():
list_of_array_value_and_length.append((self.array[indice],
all_original_indices_and_length.get(indice)))
return list_of_array_value_and_length
