def get_correlated_name(name, correlations):
'It return the name fixed by the correlation'
# it looks in the marker_correlations_file
marker_ = get_marker_from_correlations(name, correlations)
if marker_ is not None:
name = marker_['name']
return name
def read_markers(fhand, cmap, marker_corr=None):
'''It reads the Monforte marker data. It uses the correlations file to
adjust data'''
map_reader = csv.reader(fhand, delimiter='\t')
markers = cmap['features']
for row in map_reader:
name = row[0].lower()
name = name.strip()
kind = row[1].strip()
reference = row[2]
correlation = get_marker_from_correlations(name, marker_corr)
if correlation is not None:
name = correlation['name']
if correlation['type'] is None:
kind = correlation['sofa']
else:
kind = correlation['type']
reference = correlation['publication']
if not kind:
kind = 'unknown'
markers[name] = {'name':name,
'type':kind,
'publication':reference}
def read_bin_map(fhand, cmap, correlations):
'It loads the bin map '
map_reader = csv.reader(fhand, delimiter='\t')
map_reader.next() #ignore fist line
map_data = []
for row in map_reader:
group = row[1]
marker = row[2].lower().strip()
marker_type = row[3]
bin_ = row[5]
if not group and not bin_:
continue
marker_name = get_correlated_name(marker, correlations)
marker_ = get_marker_from_correlations(marker_name, correlations)
feature_type = marker_['sofa']
data = { 'group': group.lower(), 'marker':marker_name,
'marker_type': marker_type, 'bin': bin_,
'feature_type':feature_type}
map_data.append(data)
all_bins = []
list_bins = []
ref = None
group = None
for marker in map_data:
kind = marker['marker_type']
marker_name = marker['marker']
if group is None or group != marker['group']:
for bin_marker in list_bins:
bin_marker['end_marker'] = ref
all_bins.append(bin_marker)
list_bins = []
ref = None
group = marker['group']
if kind in ('bin', 'binint'):
bin_marker = {'start_marker': None, 'end_marker': None,
'type':kind, 'name':marker_name, 'map': group,
'feature_type':marker['feature_type']}
if ref is None:
bin_marker['start_marker'] = None
else:
bin_marker['start_marker'] = ref
list_bins.append(bin_marker)
elif kind == 'ref':
for bin_marker in list_bins:
bin_marker['end_marker'] = marker_name
all_bins.append(bin_marker)
list_bins = []
ref = marker_name
cmap_ = Cmap(cmap)
# now put the positions
for bin in all_bins:
if bin['start_marker'] is None:
bin['start_position'] = 0
else:
try:
start = cmap_.feature_location(feature=bin['start_marker'],
mapset='icugi',
map_=bin['map'])[2]
except KeyError:
print "bin start not found, reference: %s group : %s " % \
(bin['start_marker'], bin['map'])
start = 0 # this is to be able to work, this is unreal
bin['start_position'] = start
if bin['end_marker'] is None:
bin['end_postion'] = bin['start_position']
else:
try:
start = cmap_.feature_location(feature=bin['end_marker'],
mapset='icugi',
map_=bin['map'])[2]
except KeyError:
print "bin end not found, reference: %s group : %s " % \
(bin['end_marker'], bin['map'])
start = 0 # this is to be able to work, this is unreal
bin['end_position'] = start
# now look at the start position of the bininit
for bin in all_bins:
if bin['type'] == 'binint':
half = (bin['end_position'] - bin['start_position']) / float(2)
bin['start_position'] += half
bin['start_position'] = int(round(bin['start_position']))
#add to cmap
for bin in all_bins:
#add to markers
marker_name = bin['name']
sofa = bin['feature_type']
cmap['features'][marker_name] = {'type':sofa, 'name':marker_name}
# add to mapset(icugi)
feat_loc = {'feature':marker_name, 'start':bin['start_position'],
'end':bin['end_position']}
# Now we need to guess where is this feature_loc adding.
# first traduce from icugi to map number
for index, mapset in enumerate(cmap['map_sets']):
if mapset['name'] == 'icugi':
icugi_index = index
for index2, map_ in enumerate(mapset['maps']):
if map_['accession'] == bin['map']:
map_index = index2
cmap['map_sets'][icugi_index]['maps'][map_index]['feature_locations'].append(feat_loc)
