def on_button_filechooserdialog_save_ok_clicked(self, widget, data=None):
"""
2008-02-12
to update the no_of_selected rows (have to double click a row to change a cursor if it's multiple selection)
2008-02-05
"""
output_fname = self.filechooserdialog_save.get_filename()
self.filechooserdialog_save.hide()
pathlist_strains1 = []
self.treeselection.selected_foreach(yh_gnome.foreach_cb, pathlist_strains1)
self.app1_appbar1.push("%s rows selected."%len(pathlist_strains1))
if self.header and self.strain_acc_list and self.category_list and self.data_matrix:
selected_index_set = Set()
for path in pathlist_strains1:
row = self.liststore[path[0]]
id = row[0]
index_in_data_matrix = row[-1]
selected_index_set.add(index_in_data_matrix)
if self.id_is_strain:
id = id[1:-1].split(',') #id is a tuple of (ecotypeid,duplicate)
self.strain_acc_list[index_in_data_matrix] = id[0].strip() #remove extra space
self.category_list[index_in_data_matrix] = id[1].strip()
#else:
# self.header[index_in_data_matrix+2] = id
from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
if self.id_is_strain:
rows_to_be_tossed_out = Set(range(len(self.strain_acc_list))) - selected_index_set
FilterStrainSNPMatrix_instance.write_data_matrix(self.data_matrix, output_fname, self.header, self.strain_acc_list, self.category_list,\
rows_to_be_tossed_out, cols_to_be_tossed_out=Set(), nt_alphabet=0)
else:
cols_to_be_tossed_out = Set(range(len(self.header)-2)) - selected_index_set
FilterStrainSNPMatrix_instance.write_data_matrix(self.data_matrix, output_fname, self.header, self.strain_acc_list, self.category_list,\
rows_to_be_tossed_out=Set(), cols_to_be_tossed_out=cols_to_be_tossed_out, nt_alphabet=0)
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 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 run(self):
"""
2008-08-11
the database interface changed in variation.src.dbsnp
2008-05-06
"""
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()
db = DBSNP(username=self.user,
password=self.passwd,
hostname=self.hostname,
database=self.dbname)
session = db.session
session.begin()
#transaction = session.create_transaction()
snps_name2possible_mappings, snps_name2snps_id = self.get_snps_name2possible_mappings(
db)
from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix.read_data(
self.input_fname1)
snpData1 = SNPData(header=header, strain_acc_list=strain_acc_list, category_list=category_list, data_matrix=data_matrix, \
col_id2id=snps_name2snps_id, snps_table='dbsnp.snps')
header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix.read_data(
self.input_fname2)
snpData2 = SNPData(header=header, strain_acc_list=strain_acc_list, category_list=category_list, data_matrix=data_matrix,\
snps_table='stock_250k.snps')
twoSNPData = TwoSNPData384(SNPData1=snpData1,
SNPData2=snpData2,
curs=curs,
user=self.user)
readme = formReadmeObj(sys.argv, self.ad, README)
session.save(readme)
session.flush()
twoSNPData.figureOutABMapping(session, readme,
snps_name2possible_mappings)
if self.commit:
curs.execute("commit")
session.commit()
else:
session.rollback()
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):
"""
2008-08-11
the database interface changed in variation.src.dbsnp
2008-05-06
"""
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()
db = DBSNP(username=self.user,
password=self.passwd, hostname=self.hostname, database=self.dbname)
session = db.session
session.begin()
#transaction = session.create_transaction()
snps_name2possible_mappings, snps_name2snps_id = self.get_snps_name2possible_mappings(db)
from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix.read_data(self.input_fname1)
snpData1 = SNPData(header=header, strain_acc_list=strain_acc_list, category_list=category_list, data_matrix=data_matrix, \
col_id2id=snps_name2snps_id, snps_table='dbsnp.snps')
header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix.read_data(self.input_fname2)
snpData2 = SNPData(header=header, strain_acc_list=strain_acc_list, category_list=category_list, data_matrix=data_matrix,\
snps_table='stock_250k.snps')
twoSNPData = TwoSNPData384(SNPData1=snpData1, SNPData2=snpData2, curs=curs, user=self.user)
readme = formReadmeObj(sys.argv, self.ad, README)
session.save(readme)
session.flush()
twoSNPData.figureOutABMapping(session, readme, snps_name2possible_mappings)
if self.commit:
curs.execute("commit")
session.commit()
else:
session.rollback()
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 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)
def run(self):
"""
2008-05-08
transpose everything if output_matrix_type=1 (bjarni's SNP matrix format)
2007-02-19
--db_connect
--get_snp_id2index()
--get_strain_id2index()
--get_strain_id_info()
--get_snp_id_info()
--get_data_matrix()
if self.toss_out_rows:
--toss_rows_to_make_distance_matrix_NA_free()
--find_smallest_vertex_set_to_remove_all_edges()
--write_data_matrix()
#--sort_file()
2007-09-22
for mysql_connection
add get_nativename_snpid2call_m()
add fill_in_resolved_duplicated_calls()
"""
if self.debug:
import pdb
pdb.set_trace()
if self.db_connection_type == 1:
import MySQLdb
#conn = MySQLdb.connect(db="stock",host='natural.uchicago.edu', user='******', passwd='iamhereatusc')
conn = MySQLdb.connect(db=self.dbname,
host=self.hostname,
user=self.user,
passwd=self.passwd)
curs = conn.cursor()
snp_id2index, snp_id_list, snp_id2info = self.get_snp_id2index_m(
curs, self.input_table, self.snp_locus_table)
strain_id2index, strain_id_list, nativename2strain_id, strain_id2acc, strain_id2category = self.get_strain_id2index_m(curs, \
self.input_table, self.strain_info_table, self.only_include_strains_with_GPS, \
self.resolve_duplicated_calls, toss_contaminants=self.toss_contaminants)
#strain_id2acc, strain_id2category = self.get_strain_id_info_m(curs, strain_id_list, self.strain_info_table)
#snp_id2info = self.get_snp_id_info_m(curs, snp_id_list, self.snp_locus_table)
if self.input_table == 'dbsnp.calls':
from variation.src.FigureOut384IlluminaABMapping import get_snps_id2mapping
snps_id2mapping = get_snps_id2mapping(self.hostname,
dbname='dbsnp',
user=self.user,
passwd=self.passwd)
else:
snps_id2mapping = None
data_matrix = self.get_data_matrix_m(curs, strain_id2index,
snp_id2index, nt2number,
self.input_table,
self.need_heterozygous_call,
snps_id2mapping)
"""
if self.resolve_duplicated_calls:
nativename_snpid2call = self.get_nativename_snpid2call_m(curs, self.strain_info_table, self.input_table)
data_matrix = self.fill_in_resolved_duplicated_calls(data_matrix, strain_id2index, snp_id2index, nativename2strain_id, nativename_snpid2call)
"""
if self.include_other_strain_info:
strain_id2other_info = self.get_strain_id2other_info(
curs, strain_id_list, self.strain_info_table,
self.input_table)
else:
strain_id2other_info = {}
elif self.db_connection_type == 2:
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
snp_id2index, snp_id_list = self.get_snp_id2index(
curs, self.input_table, self.snp_locus_table)
strain_id2index, strain_id_list = self.get_strain_id2index(
curs, self.input_table)
strain_id2acc, strain_id2category = self.get_strain_id_info(
curs, strain_id_list, self.strain_info_table)
snp_id2info = self.get_snp_id_info(curs, snp_id_list,
self.snp_locus_table)
data_matrix = self.get_data_matrix(curs, strain_id2index,
snp_id2index, nt2number,
self.input_table,
self.need_heterozygous_call)
strain_id2other_info = {}
if self.toss_out_rows:
rows_to_be_tossed_out = self.toss_rows_to_make_distance_matrix_NA_free(
data_matrix)
rows_to_be_tossed_out = Set(rows_to_be_tossed_out)
else:
rows_to_be_tossed_out = Set()
#05/08/08
if self.discard_all_NA_strain:
from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
remove_rows_data = FilterStrainSNPMatrix.remove_rows_with_too_many_NAs(
data_matrix, row_cutoff=1)
rows_with_too_many_NAs_set = remove_rows_data.rows_with_too_many_NAs_set
#row_index2no_of_NAs = remove_rows_data.row_index2no_of_NAs
rows_to_be_tossed_out.update(rows_with_too_many_NAs_set)
strain_acc_list = [
strain_id2acc[strain_id] for strain_id in strain_id_list
]
category_list = [
strain_id2category[strain_id] for strain_id in strain_id_list
]
strain_acc2other_info = {}
for strain_id in strain_id2other_info:
strain_acc2other_info[
strain_id2acc[strain_id]] = strain_id2other_info[strain_id]
if self.output_matrix_type == 1:
#transpose everything
data_matrix = num.array(data_matrix)
data_matrix = num.transpose(data_matrix)
header = ['Chromosomes', 'Positions'] + strain_acc_list
chromosome_ls = []
position_ls = []
for snp_id in snp_id_list:
snp_name, chromosome, position = snp_id2info[snp_id]
chromosome_ls.append(chromosome)
position_ls.append(position)
strain_acc_list = chromosome_ls
category_list = position_ls
cols_to_be_tossed_out = rows_to_be_tossed_out
rows_to_be_tossed_out = None
strain_id2other_info = None #make up one
else:
header = ['strain', 'category']
for snp_id in snp_id_list:
snp_name, chromosome, position = snp_id2info[snp_id]
header.append(snp_name)
cols_to_be_tossed_out = None
write_data_matrix(data_matrix, self.output_fname, header, strain_acc_list, category_list, rows_to_be_tossed_out=rows_to_be_tossed_out, \
cols_to_be_tossed_out=cols_to_be_tossed_out, nt_alphabet=self.nt_alphabet,\
strain_acc2other_info=strain_acc2other_info, delimiter=self.delimiter)
def run(self):
"""
2008-05-08
transpose everything if output_matrix_type=1 (bjarni's SNP matrix format)
2007-02-19
--db_connect
--get_snp_id2index()
--get_strain_id2index()
--get_strain_id_info()
--get_snp_id_info()
--get_data_matrix()
if self.toss_out_rows:
--toss_rows_to_make_distance_matrix_NA_free()
--find_smallest_vertex_set_to_remove_all_edges()
--write_data_matrix()
#--sort_file()
2007-09-22
for mysql_connection
add get_nativename_snpid2call_m()
add fill_in_resolved_duplicated_calls()
"""
if self.debug:
import pdb
pdb.set_trace()
if self.db_connection_type==1:
import MySQLdb
#conn = MySQLdb.connect(db="stock",host='natural.uchicago.edu', user='******', passwd='iamhereatusc')
conn = MySQLdb.connect(db=self.dbname,host=self.hostname, user=self.user, passwd = self.passwd)
curs = conn.cursor()
snp_id2index, snp_id_list, snp_id2info = self.get_snp_id2index_m(curs, self.input_table, self.snp_locus_table)
strain_id2index, strain_id_list, nativename2strain_id, strain_id2acc, strain_id2category = self.get_strain_id2index_m(curs, \
self.input_table, self.strain_info_table, self.only_include_strains_with_GPS, \
self.resolve_duplicated_calls, toss_contaminants=self.toss_contaminants)
#strain_id2acc, strain_id2category = self.get_strain_id_info_m(curs, strain_id_list, self.strain_info_table)
#snp_id2info = self.get_snp_id_info_m(curs, snp_id_list, self.snp_locus_table)
if self.input_table == 'dbsnp.calls':
from variation.src.FigureOut384IlluminaABMapping import get_snps_id2mapping
snps_id2mapping = get_snps_id2mapping(self.hostname, dbname='dbsnp', user=self.user, passwd=self.passwd)
else:
snps_id2mapping = None
data_matrix = self.get_data_matrix_m(curs, strain_id2index, snp_id2index, nt2number, self.input_table, self.need_heterozygous_call, snps_id2mapping)
"""
if self.resolve_duplicated_calls:
nativename_snpid2call = self.get_nativename_snpid2call_m(curs, self.strain_info_table, self.input_table)
data_matrix = self.fill_in_resolved_duplicated_calls(data_matrix, strain_id2index, snp_id2index, nativename2strain_id, nativename_snpid2call)
"""
if self.include_other_strain_info:
strain_id2other_info = self.get_strain_id2other_info(curs, strain_id_list, self.strain_info_table, self.input_table)
else:
strain_id2other_info = {}
elif self.db_connection_type==2:
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
snp_id2index, snp_id_list = self.get_snp_id2index(curs, self.input_table, self.snp_locus_table)
strain_id2index, strain_id_list = self.get_strain_id2index(curs, self.input_table)
strain_id2acc, strain_id2category = self.get_strain_id_info(curs, strain_id_list, self.strain_info_table)
snp_id2info = self.get_snp_id_info(curs, snp_id_list, self.snp_locus_table)
data_matrix = self.get_data_matrix(curs, strain_id2index, snp_id2index, nt2number, self.input_table, self.need_heterozygous_call)
strain_id2other_info = {}
if self.toss_out_rows:
rows_to_be_tossed_out = self.toss_rows_to_make_distance_matrix_NA_free(data_matrix)
rows_to_be_tossed_out = Set(rows_to_be_tossed_out)
else:
rows_to_be_tossed_out = Set()
#05/08/08
if self.discard_all_NA_strain:
from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
remove_rows_data = FilterStrainSNPMatrix.remove_rows_with_too_many_NAs(data_matrix, row_cutoff=1)
rows_with_too_many_NAs_set = remove_rows_data.rows_with_too_many_NAs_set
#row_index2no_of_NAs = remove_rows_data.row_index2no_of_NAs
rows_to_be_tossed_out.update(rows_with_too_many_NAs_set)
strain_acc_list = [strain_id2acc[strain_id] for strain_id in strain_id_list]
category_list = [strain_id2category[strain_id] for strain_id in strain_id_list]
strain_acc2other_info = {}
for strain_id in strain_id2other_info:
strain_acc2other_info[strain_id2acc[strain_id]] = strain_id2other_info[strain_id]
if self.output_matrix_type==1:
#transpose everything
data_matrix = num.array(data_matrix)
data_matrix = num.transpose(data_matrix)
header = ['Chromosomes', 'Positions'] + strain_acc_list
chromosome_ls = []
position_ls = []
for snp_id in snp_id_list:
snp_name, chromosome, position = snp_id2info[snp_id]
chromosome_ls.append(chromosome)
position_ls.append(position)
strain_acc_list = chromosome_ls
category_list = position_ls
cols_to_be_tossed_out = rows_to_be_tossed_out
rows_to_be_tossed_out = None
strain_id2other_info = None #make up one
else:
header = ['strain', 'category']
for snp_id in snp_id_list:
snp_name, chromosome, position = snp_id2info[snp_id]
header.append(snp_name)
cols_to_be_tossed_out = None
write_data_matrix(data_matrix, self.output_fname, header, strain_acc_list, category_list, rows_to_be_tossed_out=rows_to_be_tossed_out, \
cols_to_be_tossed_out=cols_to_be_tossed_out, nt_alphabet=self.nt_alphabet,\
strain_acc2other_info=strain_acc2other_info, delimiter=self.delimiter)
