def fetchIntensityInGWAWithinRBDictGivenArrayIDFromTilingIntensity(tilingIntensityData, array_id, rbDict, gwr_name=None,\
min_reciprocal_overlap=0.6):
"""
2010-3-18
tilingIntensityData is of type SNPData.
"""
sys.stderr.write("Getting intensity data within the chosen segments for array %s ..."%array_id)
col_index = tilingIntensityData.col_id2col_index.get(array_id)
if col_index is None:
sys.stderr.write("Error: No tiling intensity.\n")
return None
from SNP import GenomeWideResult, DataObject
gwr = GenomeWideResult(name=gwr_name)
# 2010-3-18 custom
gwr.array_id = array_id
#gwr.ecotype_id = array.maternal_ecotype_id
#gwr.nativename = ecotype_nativename
genome_wide_result_id = id(gwr)
no_of_rows = len(tilingIntensityData.row_id_ls)
for i in range(no_of_rows):
chr_pos = tilingIntensityData.row_id_ls[i]
chr, pos = map(int, chr_pos)
cnvSegmentKey = CNVSegmentBinarySearchTreeKey(chromosome=chr, span_ls=[pos],\
min_reciprocal_overlap=min_reciprocal_overlap)
if cnvSegmentKey in rbDict:
probeIntensity = tilingIntensityData.data_matrix[i][col_index]
data_obj = DataObject(chromosome=chr, position=pos, value=probeIntensity)
data_obj.comment = ''
data_obj.genome_wide_result_name = gwr_name
data_obj.genome_wide_result_id = genome_wide_result_id
gwr.add_one_data_obj(data_obj)
sys.stderr.write(" %s probes. Done.\n"%(len(gwr.data_obj_ls)))
return gwr
def getCNVDataFromFileInGWA(input_fname_ls, array_id, max_amp=-0.33, min_amp=-0.33, min_size=50, min_no_of_probes=None, \
report=False):
"""
2009-10-31
get deletion (below max_amp) or duplication (above min_amp) from files (output by RunGADA.py)
"""
sys.stderr.write("Getting CNV calls for array %s, min_size %s, min_no_of_probes %s from %s ..."%\
(array_id, min_size, min_no_of_probes, repr(input_fname_ls)))
gwr_name = "(a-id %s)"%(array_id)
gwr = GenomeWideResult(name=gwr_name)
gwr.data_obj_ls = [] #list and dictionary are crazy references.
gwr.data_obj_id2index = {}
genome_wide_result_id = id(gwr)
amp_ls = []
array_id2array = {}
counter = 0
real_counter = 0
no_of_segments = 0
input_handler = fileinput.input(input_fname_ls)
header = input_handler.readline().strip().split('\t')
col_name2index = getColName2IndexFromHeader(header)
ecotype_id = None
for line in input_handler:
if line.find("array_id")!=-1:
continue
line = line.strip()
row = line.split('\t')
cnv_array_id = int(row[col_name2index['array_id']])
cnv_ecotype_id = int(row[col_name2index.get('ecotype_id', col_name2index['array_id'])])
counter += 1
if cnv_array_id==array_id:
no_of_segments += 1
if ecotype_id is None:
ecotype_id = cnv_ecotype_id
start_probe = row[col_name2index['start_probe']].split('_') # split chr_pos
start_probe = map(int, start_probe)
start_probe_id = row[col_name2index.get('start_probe_id', col_name2index['start_probe'])]
stop_probe = row[col_name2index['end_probe']].split('_')
stop_probe = map(int, stop_probe)
end_probe_id = row[col_name2index.get('end_probe_id', col_name2index['end_probe'])]
no_of_probes = int(row[col_name2index['length']])
if min_no_of_probes is not None and no_of_probes<min_no_of_probes:
continue
amplitude = float(row[col_name2index['amplitude']])
segment_chromosome = start_probe[0]
segment_start_pos = start_probe[1]-12
segment_stop_pos = stop_probe[1]+12
segment_length = abs(segment_stop_pos-segment_start_pos)
if min_size is not None and segment_length<min_size:
continue
if amplitude<=max_amp or amplitude>=min_amp:
real_counter += 1
data_obj = DataObject(chromosome=segment_chromosome, position=segment_start_pos, stop_position=segment_stop_pos, \
value=amplitude)
data_obj.comment = 'start probe-id %s, end probe-id %s, no of probes %s'%\
(start_probe_id, end_probe_id, no_of_probes)
data_obj.genome_wide_result_id = genome_wide_result_id
gwr.add_one_data_obj(data_obj)
if report and counter%10000==0:
sys.stderr.write('%s%s\t%s\t%s'%('\x08'*80, counter, no_of_segments, real_counter))
sys.stderr.write("\n")
if gwr.max_value<3: # insertion at y=3
gwr.max_value=3
if gwr.min_value>-1: # deletion at y = -1
gwr.min_value = -1
gwr.name = '%s '%ecotype_id + gwr.name
setattr(gwr, 'ecotype_id', ecotype_id)
sys.stderr.write(" %s segments. Done.\n"%(len(gwr.data_obj_ls)))
return gwr
