def getAlignmentMatrix(self, alignment_id):
sys.stderr.write("Getting alignment matrix for alignment=%s ..." %
(alignment_id))
snp_pos_ls = []
accession_id_ls = []
name_ls = []
data_matrix = []
rows = Sequence.query.filter_by(alignment=alignment_id).order_by(
Sequence.accession).all()
counter = 0
for row in rows:
if counter == 0:
snp_pos_ls = self.get_snp_pos_ls(row.alignment_obj.target,
row.alignment_obj.chromosome,
row.alignment_obj.start)
accession_id_ls.append(row.accession)
name_ls.append(row.accession_obj.name)
data_row = dict_map(nt2number, row.bases)
data_matrix.append(data_row)
counter += 1
data_matrix = num.array(data_matrix, num.int8)
passingdata = PassingData(snp_pos_ls=snp_pos_ls,
accession_id_ls=accession_id_ls,
name_ls=name_ls,
data_matrix=data_matrix)
sys.stderr.write(' %s accessions, %s bases. Done.\n' %
(len(accession_id_ls), len(snp_pos_ls)))
return passingdata
def getAlignmentMatrix(self, alignment_id):
sys.stderr.write("Getting alignment matrix for alignment=%s ..."%(alignment_id))
snp_pos_ls = []
accession_id_ls = []
name_ls = []
data_matrix = []
rows = Sequence.query.filter_by(alignment=alignment_id).order_by(Sequence.accession).all()
counter = 0
for row in rows:
if counter == 0:
for i in range(len(row.alignment_obj.target)):
base_number = nt2number[row.alignment_obj.target[i]]
if base_number!=-1:
if i==0:
snp_pos_ls.append((row.alignment_obj.chromosome, row.alignment_obj.start, 0)) #the 3rd position is insertion offset relative to Column position
else:
snp_pos_ls.append((row.alignment_obj.chromosome, snp_pos_ls[i-1][1]+1, 0))
else: #base is deletion
if i==0:
snp_pos_ls.append((row.alignment_obj.chromosome, row.alignment_obj.start-1, 1)) #this probably doesn't exist in db. it's controversal whether this insertion should be assigned to the previous or alignment's start base
else:
snp_pos_ls.append((row.alignment_obj.chromosome, snp_pos_ls[i-1][1], snp_pos_ls[i-1][2]+1)) #position doesn't change. offset++
accession_id_ls.append(row.accession)
name_ls.append(row.accession_obj.name)
data_row = dict_map(nt2number, row.bases)
data_matrix.append(data_row)
counter += 1
data_matrix = num.array(data_matrix, num.int8)
passingdata = PassingData(snp_pos_ls=snp_pos_ls, accession_id_ls=accession_id_ls, name_ls=name_ls, data_matrix=data_matrix)
sys.stderr.write(' %s accessions, %s bases. Done.\n'%(len(accession_id_ls), len(snp_pos_ls)))
return passingdata
def read_data(cls, input_fname, input_alphabet=0, turn_into_integer=1, double_header=0, delimiter="\t"):
"""
2008-05-18
DEPRECATED. moved to pymodule.SNP
2008-05-12
add delimiter
2008-05-07
add option double_header
2007-03-06
different from the one from SelectStrains.py is map(int, data_row)
2007-05-14
add input_alphabet
2007-10-09
add turn_into_integer
"""
sys.stderr.write("Reading data ...")
reader = csv.reader(open(input_fname), delimiter=delimiter)
header = reader.next()
if double_header:
header = [header, reader.next()]
data_matrix = []
strain_acc_list = []
category_list = []
for row in reader:
strain_acc_list.append(row[0])
category_list.append(row[1])
data_row = row[2:]
no_of_snps = len(data_row)
if input_alphabet:
data_row = dict_map(nt2number, data_row)
if no_of_snps != len(data_row):
print row
else:
if turn_into_integer:
data_row = map(int, data_row)
data_matrix.append(data_row)
del reader
sys.stderr.write("Done.\n")
return header, strain_acc_list, category_list, data_matrix
