def read_2010_x_149SNP(input_fname): """ 2007-12-30 """ from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix() header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix_instance.read_data(input_fname) snp_acc_ls = header[2:] snp_acc2col_index = dict(zip(snp_acc_ls, range(len(snp_acc_ls)))) accession_id_ls = map(int, strain_acc_list) accession_id2row_index = dict(zip(accession_id_ls, range(len(accession_id_ls)))) return snp_acc2col_index, accession_id2row_index, data_matrix
def load_dstruc(self):
if self.debug:
import pdb
pdb.set_trace()
QualityControl.load_dstruc(self)
from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
self.header1, self.strain_acc_list1, self.category_list1, self.data_matrix1 = self.readTina2010In250kSNPs(
self.input_fname1)
self.header2, self.strain_acc_list2, self.category_list2, self.data_matrix2 = FilterStrainSNPMatrix_instance.read_data(
self.input_fname2)
self.col_id2col_index1, self.col_id2col_index2, self.col_id12col_id2 = self.get_col_matching_dstruc(
self.header1, self.header2)
self.row_id2row_index1, self.row_id2row_index2, self.row_id12row_id2 = self.get_row_matching_dstruc(
self.curs, self.strain_acc_list1, self.strain_acc_list2)
def load_dstruc(self):
if self.debug:
import pdb
pdb.set_trace()
QualityControl.load_dstruc(self)
from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
self.header1, self.strain_acc_list1, self.category_list1, self.data_matrix1 = FilterStrainSNPMatrix_instance.read_data(
self.input_fname1)
self.header2, self.strain_acc_list2, self.category_list2, self.data_matrix2 = FilterStrainSNPMatrix_instance.read_data(
self.input_fname2)
self.col_id2col_index1, self.col_id2col_index2, self.col_id12col_id2 = self.get_col_matching_dstruc(
self.header1, self.header2, self.curs, self.snp_locus_table_250k,
self.snp_locus_table_149snp)
self.row_id2row_index1, self.row_id2row_index2, self.row_id12row_id2 = self.get_row_matching_dstruc(
self.strain_acc_list1, self.category_list1, self.strain_acc_list2,
self.curs, self.ecotype_duplicate2tg_ecotypeid_table)
def run(self):
import MySQLdb
conn = MySQLdb.connect(db=self.dbname, host=self.hostname, user=self.user, passwd = self.passwd)
curs = conn.cursor()
if self.debug:
import pdb
pdb.set_trace()
"""
#2008-02-08 old way to get 2010 data is from raw alignments. didn't realize all SNPs are put into db.
alignment_id2positions_to_be_checked_ls, alignment_id2chr_start_end = self.get_alignment_id2positions_to_be_checked_ls(curs, self.alignment_table)
SNPpos_snpacc_ls = self.get_SNPpos_snpacc_ls(curs, self.snp_locus_table)
SNPpos2col_index, snp_acc_ls = self.setup_SNP_dstruc(SNPpos_snpacc_ls, alignment_id2chr_start_end)
ecotype_id2accession_id, ecotype_id2row_index, ecotype_id2info_ls, ecotype_id_ls, accession_id2row_index, accession_id_ls, nativename_ls = self.setup_accession_ecotype_dstruc(curs, self.accession2ecotype_table, self.ecotype_table)
accession_X_snp_matrix, accession_X_snp_matrix_touched, snp_index2alignment_id = self.get_accession_X_snp_matrix(curs, accession_id2row_index, SNPpos2col_index, self.sequence_table, self.alignment_table, alignment_id2positions_to_be_checked_ls)
"""
if self.processing_bits[3]==0:
#2009-2-12 will be a problem if snp_locus_table doesn't have field offset
SNPpos2col_index, snp_acc_ls = self.setup_SNP_dstruc2(curs, self.snp_locus_table, offset=self.offset)
elif self.processing_bits[3]==1:
SNPpos2col_index, snp_acc_ls = self.setup_SNP_dstruc2(curs, self.snp_locus_table, \
cross_linking_table=self.data_type2data_table[self.processing_bits[1]], \
offset=self.offset)
elif self.processing_bits[3]==2:
SNPpos2col_index, snp_acc_ls = self.setup_SNP_dstruc2(curs, self.data_type2data_table[self.processing_bits[1]], \
offset=self.offset)
else:
sys.stderr.write("Error: unsupported 3rd bit in processing_bits %s.\n"%self.processing_bits[3])
sys.exit(3)
from variation.src.common import get_accession_id2name
accession_id2name = get_accession_id2name(curs)
if self.processing_bits[1]==0:
row_id2dstruc = self.setup_row_dstruc(curs, SNPpos2col_index, accession_id2name, offset=self.offset, version=self.version)
elif self.processing_bits[1]==1:
from variation.src.common import map_perlegen_ecotype_name2accession_id
ecotype_name2accession_id = map_perlegen_ecotype_name2accession_id(curs)
row_id2dstruc = self.setup_row_dstruc(curs, SNPpos2col_index, accession_id2name, data_type=self.processing_bits[1], \
ecotype_name2accession_id=ecotype_name2accession_id,\
offset=self.offset, version=self.version)
else:
sys.stderr("Unsupported data type: %s or no ecotype_name2accession_id specified.\n"%self.processing_bits[1])
sys.exit(2)
accession_id_ls, accession_name_ls, data_matrix = self.transform_row_id2dstruc_2_matrix(row_id2dstruc)
from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
#2008-02-08 which type of row id/1st column
if self.processing_bits[0]==0:
from variation.src.common import map_accession_id2ecotype_id
accession_id2ecotype_id = map_accession_id2ecotype_id(curs, accession2ecotype_table=self.accession2ecotype_table)
accession_id2ecotype_id[99] = 6909 #accession 99 is the reference genome, which col-0 (ecotype_id=6909)
ecotype_id_ls = []
rows_to_be_tossed_out=Set()
for i in range(len(accession_id_ls)):
ecotype_id = accession_id2ecotype_id.get(accession_id_ls[i])
if not ecotype_id: #mapping failed
rows_to_be_tossed_out.add(i)
ecotype_id_ls.append(ecotype_id)
strain_acc_list = ecotype_id_ls
header = ['ecotype_id'] #1st column in the header
else:
rows_to_be_tossed_out=Set()
strain_acc_list = accession_id_ls
header = ['accession_id']
#2008-02-08 which type of 2nd column
if self.processing_bits[2]==0:
category_list = [1]*len(accession_name_ls)
header.append('duplicate') #2nd column in the header
elif self.processing_bits[2]==1:
category_list = accession_name_ls
header.append('accession_name')
else:
category_list = accession_name_ls
header.append('accession_name')
header += snp_acc_ls
FilterStrainSNPMatrix_instance.write_data_matrix(data_matrix, self.output_fname, header, strain_acc_list, category_list, rows_to_be_tossed_out=rows_to_be_tossed_out)
