def run(self):
"""
2007-03-20
2007-04-03
"""
from FilterStrainSNPMatrix import FilterStrainSNPMatrix
FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
if self.draw_only:
header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix_instance.read_data(self.output_fname)
data_matrix = Numeric.array(data_matrix)
else:
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix_instance.read_data(self.input_fname)
snp_acc_ls = header[2:]
strain_id2index = self.get_id2index(curs, self.strain_info_table, strain_acc_list)
snp_id2index = self.get_id2index(curs, self.snp_locus_table, snp_acc_ls)
from dbSNP2data import dbSNP2data
dbSNP2data_instance = dbSNP2data(report=self.report)
data_matrix = dbSNP2data_instance.get_data_matrix(curs, strain_id2index, snp_id2index, nt2number, self.data_table, need_heterozygous_call=1)
FilterStrainSNPMatrix_instance.write_data_matrix(data_matrix, self.output_fname, header, strain_acc_list, category_list)
heterozygous_data_matrix, coarse_data_matrix = self.get_heterozygous_and_coarse_data_matrix(data_matrix)
self.displayDataMatrix(heterozygous_data_matrix, title='heterozygous_data_matrix, 5-10=hetero, else=0')
self.displayDataMatrix(coarse_data_matrix, title='coarse_data_matrix, 0=NA, 1=h**o, 2=hetero')
raw_input("enter")
def run(self): """ 2007-07-12 2007-07-17 """ from dbSNP2data import dbSNP2data dbSNP2data_instance = dbSNP2data(user=self.user, passwd=self.passwd, output_fname='whatever') import MySQLdb conn = MySQLdb.connect(db=self.dbname,host=self.hostname, user = self.user, passwd = self.passwd) curs = conn.cursor() #snp_id2index, snp_id_list, snp_acc_list, snp_id2acc = self.get_snp_struc(curs, self.snpacc_fname, self.snp_locus_table) snp_id2index, snp_id_list, snp_id2info = dbSNP2data_instance.get_snp_id2index_m(curs, self.input_table, self.snp_locus_table) #snp_id2acc = dbSNP2data_instance.get_snp_id_info_m(curs, snp_id_list, self.snp_locus_table) snp_acc_list = [] for snp_id in snp_id_list: snp_acc_list.append(snp_id2info[snp_id][0]) #popid2ecotypeid_ls = self.get_popid2ecotypeid_ls(curs, self.population_table) popid2strain_id_snp_id_ls = self.get_popid2strain_id_snp_id_ls(curs, self.population_table, self.popid2snpid_table) strain_id2index, strain_id_list = self.get_strain_id2index(popid2strain_id_snp_id_ls, self.min_no_of_strains_per_pop) #strain_id2index, strain_id_list, nativename2strain_id, strain_id2acc, strain_id2category = dbSNP2data_instance.get_strain_id2index_m(curs, self.input_table, self.strain_info_table) strain_id2acc, strain_id2category = dbSNP2data_instance.get_strain_id_info_m(curs, strain_id_list, self.strain_info_table) data_matrix = dbSNP2data_instance.get_data_matrix_m(curs, strain_id2index, snp_id2index, nt2number, self.input_table, need_heterozygous_call=1) self.OutputPop_dict[self.output_type](data_matrix, popid2strain_id_snp_id_ls, strain_id2index, self.output_fname, snp_id2index, strain_id2acc,\ strain_id2category, snp_acc_list, self.with_header_line, self.nt_alphabet)
def remove_identity_strains(self, data_matrix, rows_to_be_checked, cols_to_be_checked):
"""
2009-2-18
class "dbSNP2data" has a few non-null arguments. feed it during initialization
2007-04-16
the similarity graph structure complicated the issue
bug found by Chris Toomajian
Now use the greedy graph algorithm to remove identity strains.
2007-09-13
remove parameter strain_index2no_of_NAs
"""
sys.stderr.write("Searching for identity strains ...")
rows_to_be_checked_ls = list(rows_to_be_checked)
rows_to_be_checked_ls.sort() #from small to big
if self.debug:
import pdb
pdb.set_trace()
no_of_total_cols_to_be_checked = len(cols_to_be_checked)
identity_pair_ls = [] #2007-04-16
for i in range(len(rows_to_be_checked_ls)):
row1_index = rows_to_be_checked_ls[i] #watch this
for j in rows_to_be_checked_ls[i+1:]:
no_of_same_cols = 0
for k in cols_to_be_checked:
if data_matrix[row1_index][k] == data_matrix[j][k] or data_matrix[row1_index][k]==0 or data_matrix[j][k]==0:
no_of_same_cols += 1
if no_of_same_cols == no_of_total_cols_to_be_checked:
identity_pair_ls.append([row1_index, j])
if self.debug:
import pdb
pdb.set_trace()
sys.stderr.write("done.\n")
sys.stderr.write("Removing identity strains ...")
import networkx as nx
g = nx.Graph()
g.add_edges_from(identity_pair_ls)
from dbSNP2data import dbSNP2data
dbSNP2data_instance = dbSNP2data(user='******', passwd='secret', output_fname='/tmp/nothing') #dbSNP2data has a few non-null arguments.
vertex_list_to_be_deleted = dbSNP2data_instance.find_smallest_vertex_set_to_remove_all_edges(g)
identity_strains_to_be_removed = set(vertex_list_to_be_deleted)
"""
#2007-04-16 useless
identity_strains_to_be_removed = set()
for src, tg_list in src2tg_list.iteritems():
strain_with_least_NA = src
least_no_of_NAs = strain_index2no_of_NAs[src]
identity_strains_to_be_removed.add(src) #add in src
for tg in tg_list:
identity_strains_to_be_removed.add(tg) #add in tg
if strain_index2no_of_NAs[tg] < least_no_of_NAs:
strain_with_least_NA = tg
least_no_of_NAs = strain_index2no_of_NAs[tg]
identity_strains_to_be_removed.remove(strain_with_least_NA) #remove the one with least NAs
"""
if self.debug:
print
print 'identity_strains_to_be_removed'
print identity_strains_to_be_removed
sys.stderr.write("%s identity strains, done.\n"%(len(identity_strains_to_be_removed)))
return identity_strains_to_be_removed
def test_find_smallest_vertex_set_to_remove_all_edges(self): from dbSNP2data import dbSNP2data identity_pair_ls = [[1,2],[2,3],[2,4],[4,5]] import networkx as nx g = nx.Graph() g.add_edges_from(identity_pair_ls) from dbSNP2data import dbSNP2data dbSNP2data_instance = dbSNP2data() #import pdb #pdb.set_trace() vertex_list_to_be_deleted = dbSNP2data_instance.find_smallest_vertex_set_to_remove_all_edges(g) print 'graph' print identity_pair_ls print 'vertex_list_to_be_deleted' print vertex_list_to_be_deleted
def test_find_smallest_vertex_set_to_remove_all_edges(self):
from dbSNP2data import dbSNP2data
identity_pair_ls = [[1, 2], [2, 3], [2, 4], [4, 5]]
import networkx as nx
g = nx.Graph()
g.add_edges_from(identity_pair_ls)
from dbSNP2data import dbSNP2data
dbSNP2data_instance = dbSNP2data()
#import pdb
#pdb.set_trace()
vertex_list_to_be_deleted = dbSNP2data_instance.find_smallest_vertex_set_to_remove_all_edges(
g)
print 'graph'
print identity_pair_ls
print 'vertex_list_to_be_deleted'
print vertex_list_to_be_deleted
def run(self):
"""
2007-07-12
2007-07-17
"""
from dbSNP2data import dbSNP2data
dbSNP2data_instance = dbSNP2data(user=self.user,
passwd=self.passwd,
output_fname='whatever')
import MySQLdb
conn = MySQLdb.connect(db=self.dbname,
host=self.hostname,
user=self.user,
passwd=self.passwd)
curs = conn.cursor()
#snp_id2index, snp_id_list, snp_acc_list, snp_id2acc = self.get_snp_struc(curs, self.snpacc_fname, self.snp_locus_table)
snp_id2index, snp_id_list, snp_id2info = dbSNP2data_instance.get_snp_id2index_m(
curs, self.input_table, self.snp_locus_table)
#snp_id2acc = dbSNP2data_instance.get_snp_id_info_m(curs, snp_id_list, self.snp_locus_table)
snp_acc_list = []
for snp_id in snp_id_list:
snp_acc_list.append(snp_id2info[snp_id][0])
#popid2ecotypeid_ls = self.get_popid2ecotypeid_ls(curs, self.population_table)
popid2strain_id_snp_id_ls = self.get_popid2strain_id_snp_id_ls(
curs, self.population_table, self.popid2snpid_table)
strain_id2index, strain_id_list = self.get_strain_id2index(
popid2strain_id_snp_id_ls, self.min_no_of_strains_per_pop)
#strain_id2index, strain_id_list, nativename2strain_id, strain_id2acc, strain_id2category = dbSNP2data_instance.get_strain_id2index_m(curs, self.input_table, self.strain_info_table)
strain_id2acc, strain_id2category = dbSNP2data_instance.get_strain_id_info_m(
curs, strain_id_list, self.strain_info_table)
data_matrix = dbSNP2data_instance.get_data_matrix_m(
curs,
strain_id2index,
snp_id2index,
nt2number,
self.input_table,
need_heterozygous_call=1)
self.OutputPop_dict[self.output_type](data_matrix, popid2strain_id_snp_id_ls, strain_id2index, self.output_fname, snp_id2index, strain_id2acc,\
strain_id2category, snp_acc_list, self.with_header_line, self.nt_alphabet)
def run(self):
import MySQLdb
conn = MySQLdb.connect(db=self.dbname,host=self.hostname, user = self.user, passwd = self.passwd)
curs = conn.cursor()
from dbSNP2data import dbSNP2data
dbSNP2data_instance = dbSNP2data(user=self.user, passwd=self.passwd, output_fname='whatever')
snp_id2index, snp_id_list, snp_id2info = dbSNP2data_instance.get_snp_id2index_m(curs, self.input_table, self.snp_locus_table)
#strain_id2index, strain_id_list
strain_id2index, strain_id_list, nativename2strain_id, strain_id2acc, strain_id2category = dbSNP2data_instance.get_strain_id2index_m(curs, self.input_table, self.strain_info_table)
#2008-06-02 stuff returned by get_strain_id2index_m is totally changed.
ecotype_id2row_index = {}
for strain_id, acc in strain_id2acc.iteritems():
row_index = strain_id2index[strain_id]
ecotype_id2row_index[acc] = row_index
#strain_id2acc, strain_id2category = dbSNP2data_instance.get_strain_id_info_m(curs, strain_id_list, self.strain_info_table)
snp_id2acc = dbSNP2data_instance.get_snp_id_info_m(curs, snp_id_list, self.snp_locus_table)
data_matrix = dbSNP2data_instance.get_data_matrix_m(curs, strain_id2index, snp_id2index, nt2number, self.input_table, need_heterozygous_call=1)
from OutputPopulation import OutputPopulation
popid2ecotypeid_ls = OutputPopulation.get_popid2ecotypeid_ls(curs, self.population_table)
from FilterStrainSNPMatrix import FilterStrainSNPMatrix
FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
from RemoveBadSNPs import RemoveBadSNPs
RemoveBadSNPs_instance = RemoveBadSNPs()
popid2strain_id_snp_id_ls = {}
for popid, ecotypeid_ls in popid2ecotypeid_ls.iteritems():
if len(ecotypeid_ls)>=self.min_no_of_strains_per_pop:
sys.stderr.write("Population %s\n"%popid)
sub_data_matrix, new_ecotypeid_ls = self.create_sub_data_matrix(popid, data_matrix, ecotypeid_ls, ecotype_id2row_index)
if len(new_ecotypeid_ls)>=self.min_no_of_strains_per_pop:
sys.stderr.write("\tPopulation %s has %s strains\n"%(popid, len(new_ecotypeid_ls)))
strain_id_selected, snp_id_selected = self.cleanup_one_population(FilterStrainSNPMatrix_instance, RemoveBadSNPs_instance, sub_data_matrix, new_ecotypeid_ls, snp_id_list, self.min_no_of_strains_per_pop, self.row_cutoff, self.col_cutoff, self.min_log_prob)
if strain_id_selected and snp_id_selected:
popid2strain_id_snp_id_ls[popid] = [strain_id_selected, snp_id_selected]
if self.commit:
self.create_popid2snpid_table(curs, self.output_table)
self.mark_strain_id_selected(curs, popid2strain_id_snp_id_ls, self.population_table)
self.submit_popid2snpid_list(curs, popid2strain_id_snp_id_ls, self.population_table, self.output_table)
conn.commit()
def run(self):
"""
2007-03-20
2007-04-03
"""
from FilterStrainSNPMatrix import FilterStrainSNPMatrix
FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
if self.draw_only:
header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix_instance.read_data(
self.output_fname)
data_matrix = Numeric.array(data_matrix)
else:
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix_instance.read_data(
self.input_fname)
snp_acc_ls = header[2:]
strain_id2index = self.get_id2index(curs, self.strain_info_table,
strain_acc_list)
snp_id2index = self.get_id2index(curs, self.snp_locus_table,
snp_acc_ls)
from dbSNP2data import dbSNP2data
dbSNP2data_instance = dbSNP2data(report=self.report)
data_matrix = dbSNP2data_instance.get_data_matrix(
curs,
strain_id2index,
snp_id2index,
nt2number,
self.data_table,
need_heterozygous_call=1)
FilterStrainSNPMatrix_instance.write_data_matrix(
data_matrix, self.output_fname, header, strain_acc_list,
category_list)
heterozygous_data_matrix, coarse_data_matrix = self.get_heterozygous_and_coarse_data_matrix(
data_matrix)
self.displayDataMatrix(
heterozygous_data_matrix,
title='heterozygous_data_matrix, 5-10=hetero, else=0')
self.displayDataMatrix(
coarse_data_matrix,
title='coarse_data_matrix, 0=NA, 1=h**o, 2=hetero')
raw_input("enter")
def remove_identity_strains(self, data_matrix, rows_to_be_checked, cols_to_be_checked):
"""
2009-2-18
class "dbSNP2data" has a few non-null arguments. feed it during initialization
2007-04-16
the similarity graph structure complicated the issue
bug found by Chris Toomajian
Now use the greedy graph algorithm to remove identity strains.
2007-09-13
remove parameter strain_index2no_of_NAs
"""
sys.stderr.write("Searching for identity strains ...")
rows_to_be_checked_ls = list(rows_to_be_checked)
rows_to_be_checked_ls.sort() # from small to big
if self.debug:
import pdb
pdb.set_trace()
no_of_total_cols_to_be_checked = len(cols_to_be_checked)
identity_pair_ls = [] # 2007-04-16
for i in range(len(rows_to_be_checked_ls)):
row1_index = rows_to_be_checked_ls[i] # watch this
for j in rows_to_be_checked_ls[i + 1 :]:
no_of_same_cols = 0
for k in cols_to_be_checked:
if (
data_matrix[row1_index][k] == data_matrix[j][k]
or data_matrix[row1_index][k] == 0
or data_matrix[j][k] == 0
):
no_of_same_cols += 1
if no_of_same_cols == no_of_total_cols_to_be_checked:
identity_pair_ls.append([row1_index, j])
if self.debug:
import pdb
pdb.set_trace()
sys.stderr.write("done.\n")
sys.stderr.write("Removing identity strains ...")
import networkx as nx
g = nx.Graph()
g.add_edges_from(identity_pair_ls)
from dbSNP2data import dbSNP2data
dbSNP2data_instance = dbSNP2data(
user="******", passwd="secret", output_fname="/tmp/nothing"
) # dbSNP2data has a few non-null arguments.
vertex_list_to_be_deleted = dbSNP2data_instance.find_smallest_vertex_set_to_remove_all_edges(g)
identity_strains_to_be_removed = Set(vertex_list_to_be_deleted)
"""
#2007-04-16 useless
identity_strains_to_be_removed = Set()
for src, tg_list in src2tg_list.iteritems():
strain_with_least_NA = src
least_no_of_NAs = strain_index2no_of_NAs[src]
identity_strains_to_be_removed.add(src) #add in src
for tg in tg_list:
identity_strains_to_be_removed.add(tg) #add in tg
if strain_index2no_of_NAs[tg] < least_no_of_NAs:
strain_with_least_NA = tg
least_no_of_NAs = strain_index2no_of_NAs[tg]
identity_strains_to_be_removed.remove(strain_with_least_NA) #remove the one with least NAs
"""
if self.debug:
print
print "identity_strains_to_be_removed"
print identity_strains_to_be_removed
sys.stderr.write("%s identity strains, done.\n" % (len(identity_strains_to_be_removed)))
return identity_strains_to_be_removed