def run(self):
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
self.parser_dict[self.type](curs, self.inputfile,
self.output_table_dict[self.type],
self.organism, self.sequence_type)
if self.commit:
curs.execute("end")
def run(self):
"""
2007-02-17
-db_connect()
-get_strain_acc2id()
-get_snp_acc2id()
-parse_file()
-expand_snp_locus_table()
-submit_to_strain_info_table()
-submit_to_snp_table()
"""
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
strain_acc2id = self.get_strain_acc2id(curs, self.strain_info_table, self.tax_id)
snp_acc2id = self.get_snp_acc2id(curs, self.snp_locus_table, self.tax_id)
self.parse_file(self.input_fname, curs, self.output_table, self.tax_id, self.snp_acc_category_pattern, strain_acc2id, snp_acc2id, self.snp_locus_table)
if self.commit:
curs.execute("end")
def run(self):
"""
12-11-05
--db_connect()
--get_gene_symbol2gene_id()
--get_ensembl_id2gene_id()
--parser_dict[]
--harbison2004_parse()
--cisred_parse()
"""
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
if self.type==1:
mapping_dict = get_gene_symbol2gene_id(curs, self.tax_id)
elif self.type==2:
mapping_dict = get_ensembl_id2gene_id(curs, self.tax_id)
else:
mapping_dict = None
self.parser_dict[self.type](curs, self.inputfile, mapping_dict, self.tax_id)
if self.commit:
curs.execute("end")
def run(self):
"""
2007-02-17
-db_connect()
-get_strain_acc2id()
-get_snp_acc2id()
-parse_file()
-expand_snp_locus_table()
-submit_to_strain_info_table()
-submit_to_snp_table()
"""
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
strain_acc2id = self.get_strain_acc2id(curs, self.strain_info_table,
self.tax_id)
snp_acc2id = self.get_snp_acc2id(curs, self.snp_locus_table,
self.tax_id)
self.parse_file(self.input_fname, curs, self.output_table, self.tax_id,
self.snp_acc_category_pattern, strain_acc2id,
snp_acc2id, self.snp_locus_table)
if self.commit:
curs.execute("end")
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)
def run(self):
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
self.parser_dict[self.type](curs, self.inputfile, self.output_table_dict[self.type], self.organism, self.sequence_type)
if self.commit:
curs.execute("end")