def run(self):
"""
2007-04-30
2007-05-14
add nt_alphabet_bits
"""
header, strain_acc_list, category_list, data_matrix = read_data(
self.input_fname, int(self.nt_alphabet_bits[0]))
data_matrix = num.array(data_matrix)
strain_homo_perc_vector = self.cal_strain_homo_perc_vector(data_matrix)
snp_locus_log_prob = self.cal_snp_locus_log_prob(
data_matrix, strain_homo_perc_vector)
from sets import Set
cols_to_be_tossed_out_set = Set()
for i in range(len(snp_locus_log_prob)):
if snp_locus_log_prob[i] <= min_log_prob:
cols_to_be_tossed_out_set.add(i)
print "%sSNPs removed:" % (len(cols_to_be_tossed_out_set))
for col_index in cols_to_be_tossed_out_set:
print '\t%s\t%s' % (col_index, header[2 + col_index])
write_data_matrix(data_matrix,
self.output_fname,
header,
strain_acc_list,
category_list,
cols_to_be_tossed_out=cols_to_be_tossed_out_set,
nt_alphabet=int(self.nt_alphabet_bits[1]))
import pylab
pylab.title("histogram of snp locus log probability")
pylab.hist(snp_locus_log_prob, 20)
pylab.show()
def run(self):
"""
2008-05-20 read_call_matrix returns PassingData object
"""
if self.debug:
import pdb
pdb.set_trace()
db = self.db_250k
session = db.session
QC_method_id = 0 #just for QC_250k.get_call_info_id2fname()
call_data = QC_250k.get_call_info_id2fname(db, QC_method_id, self.call_method_id, filter_calls_QCed=0, \
max_call_info_mismatch_rate=self.max_array_mismatch_rate, input_dir=self.input_dir,\
take_unique_ecotype=self.take_unique_ecotype)
#snps_with_best_QC_ls = self.get_snps_with_best_QC_ls(db, self.call_method_id)
if self.max_snp_mismatch_rate < 1 or self.max_snp_NA_rate < 1: #2008-05-18 only do this when it's necessary
snps_name_set = self.get_snps_name_set_given_criteria(
db, self.call_method_id, self.max_snp_mismatch_rate,
self.max_snp_NA_rate)
else:
snps_name_set = None
db_id2chr_pos = db.getSNPID2ChrPos()
if len(call_data.call_info_id2fname) > 0:
db_id2index = self.getSNPID2index(
call_data.call_info_id2fname.values()[0][1], db_id2chr_pos)
pdata = QC_250k.read_call_matrix(call_data.call_info_id2fname, self.min_probability, snps_name_set, \
db_id2chr_pos=db_id2chr_pos, db_id2index=db_id2index) #2008-05-20 read_call_matrix returns PassingData object
strain_acc_list, category_list = pdata.ecotype_id_ls, pdata.array_id_ls
write_data_matrix(pdata.data_matrix, self.outputFname,
pdata.header, strain_acc_list, category_list)
def run(self):
db = AtDB(drivername=self.drivername, username=self.db_user,
password=self.db_passwd, hostname=self.hostname, database=self.dbname, schema=self.schema)
passingdata = self.getAlignmentMatrix(self.alignment_id)
self.pickPolymorphicColumns(passingdata)
header = ['id', 'name']
for snp_pos in passingdata.snp_pos_ls:
header.append('%s_%s_%s'%snp_pos)
if self.strain_id_type==1:
ecotype_id_ls = []
for accession_id in passingdata.accession_id_ls:
rows = db.metadata.bind.execute("select * from %s where accession_id=%s"%('accession2tg_ecotypeid', accession_id))
row = rows.fetchone()
ecotype_id_ls.append(row.ecotype_id)
strain_acc_list = ecotype_id_ls
elif self.strain_id_type==2:
strain_acc_list = passingdata.accession_id_ls
else:
sys.stderr.write("strain_id_type %s not supported.\n"%(self.strain_id_type))
sys.exit(2)
write_data_matrix(passingdata.data_matrix, self.output_fname, header, \
strain_acc_list, passingdata.name_ls)
def output_data(self, data_to_output_label_ls, data_to_output_ls, min_distance, output_fname):
"""
2008-11-11
data_to_output_ls is a list of (score_cutoff_ls, data_ls). each score_cutoff_ls might be a bit different from each other.
1. get score_cutoff2index out of all score_cutoffs in descending order
2. each row is same score_cutoff. column is data_ls of one result from analysis_method on phenotype.
3. first column is score cutoffs.
4. 2nd column is min_distance. 3rd and so forth columns are data.
"""
sys.stderr.write("Outputting data matrix ...")
score_cutoff_ls, score_cutoff2index = self.get_score_cutoff2index(data_to_output_ls)
header = ['score_cutoff', 'min_distance'] + data_to_output_label_ls
no_of_cols = len(data_to_output_label_ls)
data_matrix = numpy.zeros([len(score_cutoff2index), no_of_cols], numpy.float)
data_matrix[:] = -1
for j in range(no_of_cols):
sub_score_cutoff_ls, data_ls = data_to_output_ls[j]
for i in range(len(sub_score_cutoff_ls)):
score_cutoff = sub_score_cutoff_ls[i]
data = data_ls[i]
row_index = score_cutoff2index[score_cutoff]
data_matrix[row_index][j] = data
category_list = [min_distance]*len(score_cutoff2index)
write_data_matrix(data_matrix, output_fname, header, score_cutoff_ls, category_list)
sys.stderr.write("Done.\n")
def run(self):
if self.debug:
import pdb
pdb.set_trace()
db = Stock_250kDB(drivername=self.drivername, username=self.db_user,
password=self.db_passwd, hostname=self.hostname, database=self.dbname, schema=self.schema)
db.setup()
session = db.session
results_method_id_info = self.getResultsMethodIDInfo(db, self.call_method_id_ls, self.min_distance, self.get_closest, self.min_MAF)
results_method_id2gene_set = self.getResultsMethodID2GeneSet(db, results_method_id_info, self.results_directory, self.max_rank)
rdata = self.getDataMatrix(results_method_id2gene_set, results_method_id_info)
header = ['', ''] + results_method_id_info.results_method_id_label_ls
strain_acc_list = results_method_id_info.results_method_id_label_ls
category_list = results_method_id_info.results_method_id_ls
if SNPData.isDataMatrixEmpty(rdata.data_matrix):
sys.stderr.write("Nothing fetched from database.\n")
sys.exit(3)
if self.output_fname:
write_data_matrix(rdata.data_matrix, self.output_fname, header, strain_acc_list, category_list)
if self.fig_fname:
font = get_font(self.font_path, font_size=self.font_size) #2008-08-01
value2color_func = lambda x: Value2Color.value2HSLcolor(x, rdata.min_value, rdata.max_value)
im_legend = drawContinousLegend(rdata.min_value, rdata.max_value, self.no_of_ticks, value2color_func, font)
#im.save('%s_legend.png'%self.fig_fname_prefix)
im = drawMatrix(rdata.data_matrix, value2color_func, strain_acc_list,\
strain_acc_list, with_grid=1, font=font)
im = combineTwoImages(im, im_legend, font=font)
im.save(self.fig_fname)
def output_data(self, data_to_output_label_ls, data_to_output_ls,
min_distance, output_fname):
"""
2008-11-11
data_to_output_ls is a list of (score_cutoff_ls, data_ls). each score_cutoff_ls might be a bit different from each other.
1. get score_cutoff2index out of all score_cutoffs in descending order
2. each row is same score_cutoff. column is data_ls of one result from analysis_method on phenotype.
3. first column is score cutoffs.
4. 2nd column is min_distance. 3rd and so forth columns are data.
"""
sys.stderr.write("Outputting data matrix ...")
score_cutoff_ls, score_cutoff2index = self.get_score_cutoff2index(
data_to_output_ls)
header = ['score_cutoff', 'min_distance'] + data_to_output_label_ls
no_of_cols = len(data_to_output_label_ls)
data_matrix = numpy.zeros([len(score_cutoff2index), no_of_cols],
numpy.float)
data_matrix[:] = -1
for j in range(no_of_cols):
sub_score_cutoff_ls, data_ls = data_to_output_ls[j]
for i in range(len(sub_score_cutoff_ls)):
score_cutoff = sub_score_cutoff_ls[i]
data = data_ls[i]
row_index = score_cutoff2index[score_cutoff]
data_matrix[row_index][j] = data
category_list = [min_distance] * len(score_cutoff2index)
write_data_matrix(data_matrix, output_fname, header, score_cutoff_ls,
category_list)
sys.stderr.write("Done.\n")
def run(self): if self.debug: import pdb pdb.set_trace() import MySQLdb conn = MySQLdb.connect(db=self.dbname,host=self.hostname, user=self.user, passwd = self.passwd) curs = conn.cursor() if self.ecotype_duplicate2tg_ecotypeid_table: ecotype_duplicate2tg_ecotypeid = self.get_ecotype_duplicate2tg_ecotypeid(curs, self.ecotype_duplicate2tg_ecotypeid_table) else: ecotype_duplicate2tg_ecotypeid = None from pymodule import figureOutDelimiter delimiter = figureOutDelimiter(self.input_fname) header, strain_acc_list, category_list, data_matrix = read_data(self.input_fname, delimiter=delimiter) tg_ecotypeid2ecotypeid_duplicate_index_ls = self.get_tg_ecotypeid2ecotypeid_duplicate_index_ls(strain_acc_list, category_list, ecotype_duplicate2tg_ecotypeid) ecotypeid2nativename = get_ecotypeid2nativename(curs, ecotype_table=self.ecotype_table) tg_ecotypeid_ls, merge_matrix = self.get_merged_matrix(tg_ecotypeid2ecotypeid_duplicate_index_ls, data_matrix, \ ecotypeid2nativename, self.stat_output_fname) tg_nativename_ls = [] for ecotypeid in tg_ecotypeid_ls: tg_nativename_ls.append(ecotypeid2nativename[ecotypeid]) header[1] = 'nativename' write_data_matrix(merge_matrix, self.output_fname, header, tg_ecotypeid_ls, tg_nativename_ls, delimiter=delimiter)
def run(self):
db = AtDB(drivername=self.drivername,
username=self.db_user,
password=self.db_passwd,
hostname=self.hostname,
database=self.dbname,
schema=self.schema)
passingdata = self.getAlignmentMatrix(self.alignment_id)
self.pickPolymorphicColumns(passingdata)
header = ['id', 'name']
for snp_pos in passingdata.snp_pos_ls:
header.append('%s_%s_%s' % snp_pos)
if self.strain_id_type == 1:
ecotype_id_ls = []
for accession_id in passingdata.accession_id_ls:
rows = db.metadata.bind.execute(
"select * from %s where accession_id=%s" %
('accession2tg_ecotypeid', accession_id))
row = rows.fetchone()
ecotype_id_ls.append(row.ecotype_id)
strain_acc_list = ecotype_id_ls
elif self.strain_id_type == 2:
strain_acc_list = passingdata.accession_id_ls
else:
sys.stderr.write("strain_id_type %s not supported.\n" %
(self.strain_id_type))
sys.exit(2)
write_data_matrix(passingdata.data_matrix, self.output_fname, header, \
strain_acc_list, passingdata.name_ls)
def run(self):
"""
2007-02-27
2007-09-14
filtering_bits
-read_data()
-remove_rows_with_too_many_NAs()
-remove_cols_with_too_many_NAs()
-remove_identity_strains()
-write_data_matrix()
"""
if self.debug:
import pdb
pdb.set_trace()
delimiter = figureOutDelimiter(self.input_fname, report=self.report)
header, strain_acc_list, category_list, data_matrix = read_data(
self.input_fname, int(self.nt_alphabet_bits[0]), delimiter=delimiter
)
data_matrix = num.array(data_matrix)
if self.filtering_bits[0] == "1":
remove_rows_data = self.remove_rows_with_too_many_NAs(data_matrix, self.row_cutoff)
rows_with_too_many_NAs_set = remove_rows_data.rows_with_too_many_NAs_set
strain_index2no_of_NAs = remove_rows_data.row_index2no_of_NAs
else:
rows_with_too_many_NAs_set = Set()
if self.filtering_bits[1] == "1":
remove_cols_data = self.remove_cols_with_too_many_NAs(data_matrix, col_cutoff, rows_with_too_many_NAs_set)
cols_with_too_many_NAs_set = remove_cols_data.cols_with_too_many_NAs_set
else:
cols_with_too_many_NAs_set = Set()
if self.filtering_bits[2] == "1":
no_of_rows, no_of_cols = data_matrix.shape
total_rows_set = Set(range(no_of_rows))
rows_to_be_checked = total_rows_set - rows_with_too_many_NAs_set
total_cols_set = Set(range(no_of_cols))
cols_to_be_checked = total_cols_set - cols_with_too_many_NAs_set
identity_strains_to_be_removed = self.remove_identity_strains(
data_matrix, rows_to_be_checked, cols_to_be_checked
)
else:
identity_strains_to_be_removed = Set()
rows_to_be_tossed_out = rows_with_too_many_NAs_set | identity_strains_to_be_removed
# self.write_data_matrix(data_matrix, self.output_fname, header, strain_acc_list, category_list, rows_to_be_tossed_out, cols_with_too_many_NAs_set, int(self.nt_alphabet_bits[1]))
write_data_matrix(
data_matrix,
self.output_fname,
header,
strain_acc_list,
category_list,
rows_to_be_tossed_out,
cols_with_too_many_NAs_set,
nt_alphabet=int(self.nt_alphabet_bits[1]),
delimiter=delimiter,
)
def run(self): if self.debug==1: import pdb pdb.set_trace() import MySQLdb conn = MySQLdb.connect(db=self.dbname, host=self.hostname, user = self.db_user, passwd = self.db_passwd) curs = conn.cursor() pheno_data = self.getPhenotypeData(curs, self.phenotype_avg_table, self.phenotype_method_table, \ self.ecotype_table, get_raw_data=self.get_raw_data) header = ['ecotype id', 'nativename'] + pheno_data.col_label_ls write_data_matrix(pheno_data.data_matrix, self.output_fname, header, pheno_data.row_id_ls, pheno_data.row_label_ls, \ transform_to_numpy=False)
def run(self):
if self.debug == 1:
import pdb
pdb.set_trace()
#import MySQLdb
#conn = MySQLdb.connect(db=self.dbname, host=self.hostname, user = self.db_user, passwd = self.db_passwd)
#curs = conn.cursor()
pheno_data = self.getPhenotypeData(self.db_250k.metadata.bind, self.phenotype_avg_table, self.phenotype_method_table, \
self.ecotype_table, get_raw_data=self.get_raw_data,\
getPublicPhenotype=self.getPublicPhenotype)
header = ['ecotype id', 'nativename'] + pheno_data.col_label_ls
write_data_matrix(pheno_data.data_matrix, self.outputFname, header, pheno_data.row_id_ls, pheno_data.row_label_ls, \
transform_to_numpy=False)
def run(self):
if self.debug:
import pdb
pdb.set_trace()
import MySQLdb
conn = MySQLdb.connect(db=self.dbname,
host=self.hostname,
user=self.user,
passwd=self.passwd)
curs = conn.cursor()
if self.ecotype_duplicate2tg_ecotypeid_table:
ecotype_duplicate2tg_ecotypeid = self.get_ecotype_duplicate2tg_ecotypeid(
curs, self.ecotype_duplicate2tg_ecotypeid_table)
else:
ecotype_duplicate2tg_ecotypeid = None
from pymodule import figureOutDelimiter
delimiter = figureOutDelimiter(self.input_fname)
header, strain_acc_list, category_list, data_matrix = read_data(
self.input_fname, delimiter=delimiter)
tg_ecotypeid2ecotypeid_duplicate_index_ls = self.get_tg_ecotypeid2ecotypeid_duplicate_index_ls(
strain_acc_list, category_list, ecotype_duplicate2tg_ecotypeid)
ecotypeid2nativename = get_ecotypeid2nativename(
curs, ecotype_table=self.ecotype_table)
tg_ecotypeid_ls, merge_matrix = self.get_merged_matrix(tg_ecotypeid2ecotypeid_duplicate_index_ls, data_matrix, \
ecotypeid2nativename, self.stat_output_fname)
tg_nativename_ls = []
for ecotypeid in tg_ecotypeid_ls:
tg_nativename_ls.append(ecotypeid2nativename[ecotypeid])
header[1] = 'nativename'
write_data_matrix(merge_matrix,
self.output_fname,
header,
tg_ecotypeid_ls,
tg_nativename_ls,
delimiter=delimiter)
def run(self): """ 2007-02-27 2007-09-14 filtering_bits -read_data() -remove_rows_with_too_many_NAs() -remove_cols_with_too_many_NAs() -remove_identity_strains() -write_data_matrix() """ if self.debug: import pdb pdb.set_trace() delimiter = figureOutDelimiter(self.input_fname, report=self.report) header, strain_acc_list, category_list, data_matrix = read_data(self.input_fname, int(self.nt_alphabet_bits[0]), delimiter=delimiter) data_matrix = numpy.array(data_matrix) if self.filtering_bits[0]=='1': remove_rows_data = self.remove_rows_with_too_many_NAs(data_matrix, self.row_cutoff) rows_with_too_many_NAs_set = remove_rows_data.rows_with_too_many_NAs_set strain_index2no_of_NAs = remove_rows_data.row_index2no_of_NAs else: rows_with_too_many_NAs_set = set() if self.filtering_bits[1]=='1': remove_cols_data = self.remove_cols_with_too_many_NAs(data_matrix, col_cutoff, rows_with_too_many_NAs_set) cols_with_too_many_NAs_set = remove_cols_data.cols_with_too_many_NAs_set else: cols_with_too_many_NAs_set = set() if self.filtering_bits[2]=='1': no_of_rows, no_of_cols = data_matrix.shape total_rows_set = set(range(no_of_rows)) rows_to_be_checked = total_rows_set - rows_with_too_many_NAs_set total_cols_set = set(range(no_of_cols)) cols_to_be_checked = total_cols_set - cols_with_too_many_NAs_set identity_strains_to_be_removed = self.remove_identity_strains(data_matrix, rows_to_be_checked, cols_to_be_checked) else: identity_strains_to_be_removed = set() rows_to_be_tossed_out = rows_with_too_many_NAs_set | identity_strains_to_be_removed #self.write_data_matrix(data_matrix, self.output_fname, header, strain_acc_list, category_list, rows_to_be_tossed_out, cols_with_too_many_NAs_set, int(self.nt_alphabet_bits[1])) write_data_matrix(data_matrix, self.output_fname, header, strain_acc_list, category_list, rows_to_be_tossed_out, cols_with_too_many_NAs_set, nt_alphabet=int(self.nt_alphabet_bits[1]), delimiter=delimiter)
def run(self):
"""
2007-04-30
2007-05-14
add nt_alphabet_bits
"""
header, strain_acc_list, category_list, data_matrix = read_data(self.input_fname, int(self.nt_alphabet_bits[0]))
data_matrix = num.array(data_matrix)
strain_homo_perc_vector = self.cal_strain_homo_perc_vector(data_matrix)
snp_locus_log_prob = self.cal_snp_locus_log_prob(data_matrix, strain_homo_perc_vector)
from sets import Set
cols_to_be_tossed_out_set = Set()
for i in range(len(snp_locus_log_prob)):
if snp_locus_log_prob[i]<=min_log_prob:
cols_to_be_tossed_out_set.add(i)
print "%sSNPs removed:"%(len(cols_to_be_tossed_out_set))
for col_index in cols_to_be_tossed_out_set:
print '\t%s\t%s'%(col_index, header[2+col_index])
write_data_matrix(data_matrix, self.output_fname, header, strain_acc_list, category_list, cols_to_be_tossed_out=cols_to_be_tossed_out_set, nt_alphabet=int(self.nt_alphabet_bits[1]))
import pylab
pylab.title("histogram of snp locus log probability")
pylab.hist(snp_locus_log_prob, 20)
pylab.show()
def run(self): """ 2008-05-20 read_call_matrix returns PassingData object """ if self.debug: import pdb pdb.set_trace() db = Stock_250kDB.Stock_250kDB(drivername=self.drivername, username=self.user, password=self.passwd, hostname=self.hostname, database=self.dbname) db.setup(create_tables=False) session = db.session QC_method_id = 0 #just for QC_250k.get_call_info_id2fname() call_data = QC_250k.get_call_info_id2fname(db, QC_method_id, self.call_method_id, filter_calls_QCed=0, \ max_call_info_mismatch_rate=self.max_call_info_mismatch_rate, input_dir=self.input_dir,\ take_unique_ecotype=self.take_unique_ecotype) #snps_with_best_QC_ls = self.get_snps_with_best_QC_ls(db, self.call_method_id) if self.max_snp_mismatch_rate<1 or self.max_snp_NA_rate<1: #2008-05-18 only do this when it's necessary snps_name_set = self.get_snps_name_set_given_criteria(db, self.call_method_id, self.max_snp_mismatch_rate, self.max_snp_NA_rate) else: snps_name_set = None pdata = QC_250k.read_call_matrix(call_data.call_info_id2fname, self.min_probability, snps_name_set) #2008-05-20 read_call_matrix returns PassingData object strain_acc_list, category_list = pdata.ecotype_id_ls, pdata.array_id_ls write_data_matrix(pdata.data_matrix, self.output_fname, pdata.header, strain_acc_list, category_list)
def run(self):
if self.debug:
import pdb
pdb.set_trace()
db = Stock_250kDB.Stock_250kDB(drivername=self.drivername,
username=self.db_user,
password=self.db_passwd,
hostname=self.hostname,
database=self.dbname,
schema=self.schema)
db.setup()
session = db.session
if self.test_result_type == 1:
test_result_class_table = CandidateGeneRankSumTestResult.table.name
test_result_class_table = 'candidate_gene_rank_sum_test_result_2008_09_15'
elif self.test_result_type == 2:
test_result_class_table = CandidateGeneTopSNPTest.table.name
elif self.test_result_type == 3:
test_result_class_table = Stock_250kDB.CandidateGeneRankSumTestResultMethod.table.name
else:
sys.stderr.write(" test_result_type %s not supported.\n" %
(self.test_result_type))
sys.exit(2)
#the condition for min_MAF is tricky because of the floating precision.
if self.test_result_type == 1:
where_condition = "%s r, %s c, %s g where g.id=c.list_type_id and r.analysis_method_id is not null \
and c.results_id=r.id and c.get_closest=%s and c.min_distance=%s and abs(c.min_MAF-%s)<0.00001" \
%(ResultsMethod.table.name, test_result_class_table, GeneListType.table.name, self.get_closest, self.min_distance, self.min_MAF)
elif self.test_result_type == 2:
where_condition = "%s r, %s rg, %s c, %s g where g.id=c.list_type_id and r.analysis_method_id is not null and r.id=rg.results_method_id \
and c.results_id=rg.id and c.get_closest=%s and c.min_distance=%s and abs(c.min_MAF-%s)<0.00001" \
%(ResultsMethod.table.name, ResultsByGene.table.name, test_result_class_table, GeneListType.table.name, self.get_closest, self.min_distance, self.min_MAF)
elif self.test_result_type == 3:
where_condition = "%s r, %s c, %s g where g.id=c.list_type_id and r.analysis_method_id is not null \
and c.results_id=r.id and c.get_closest=%s and c.min_distance=%s and abs(c.min_MAF-%s)<0.00001" \
%(ResultsMethod.table.name, test_result_class_table, GeneListType.table.name, self.get_closest, self.min_distance, self.min_MAF)
if self.call_method_id_ls:
where_condition += " and r.call_method_id in (%s)" % self.call_method_id_ls
if self.analysis_method_id_ls:
where_condition += " and r.analysis_method_id in (%s)" % self.analysis_method_id_ls
if self.super_type_id:
where_condition += " and g.super_type_id=%s" % self.super_type_id
if self.test_type:
where_condition += " and c.test_type=%s" % self.test_type
if self.test_result_type == 1:
pass
where_condition += " and c.max_pvalue_per_gene=%s" % (
self.max_pvalue_per_gene)
elif self.test_result_type == 2:
where_condition += " and c.no_of_top_snps=%s" % (
self.no_of_top_snps)
list_type_id_ls = self.getListTypeInfo(db, where_condition)
analysis_method_id_ls = self.getAnalysisMethodInfo(db, where_condition)
list_type_analysis_method_info = self.orderListTypeAnalysisMethodID(
list_type_id_ls, analysis_method_id_ls)
phenotype_info = self.getPhenotypeInfo(db, where_condition)
rdata = self.get_data_matrix(db, phenotype_info,
list_type_analysis_method_info,
where_condition)
rdata.data_matrix = self.markDataMatrixBoundary(
rdata.data_matrix, phenotype_info, list_type_analysis_method_info)
header = ['list_type_analysis_method', ''
] + phenotype_info.phenotype_method_label_ls
strain_acc_list = list_type_analysis_method_info.list_type_analysis_method_label_ls
category_list = list_type_analysis_method_info.list_type_id_analysis_method_id_ls
if SNPData.isDataMatrixEmpty(rdata.data_matrix):
sys.stderr.write("Nothing fetched from database.\n")
sys.exit(3)
if self.output_fname:
write_data_matrix(rdata.data_matrix, self.output_fname, header,
strain_acc_list, category_list)
if self.fig_fname:
font = get_font(self.font_path,
font_size=self.font_size) #2008-08-01
value2color_func = lambda x: Value2Color.value2HSLcolor(
x, rdata.min_value, rdata.max_value)
im_legend = drawContinousLegend(rdata.min_value, rdata.max_value,
self.no_of_ticks, value2color_func,
font)
#im.save('%s_legend.png'%self.fig_fname_prefix)
im = drawMatrix(rdata.data_matrix, value2color_func, list_type_analysis_method_info.list_type_analysis_method_label_ls,\
phenotype_info.phenotype_method_label_ls, with_grid=1, font=font)
im = combineTwoImages(im, im_legend, font=font)
im.save(self.fig_fname)
def run(self):
if self.debug:
import pdb
pdb.set_trace()
db = Stock_250kDB.Stock_250kDB(drivername=self.drivername, username=self.db_user,
password=self.db_passwd, hostname=self.hostname, database=self.dbname, schema=self.schema)
db.setup()
session = db.session
if self.test_result_type==1:
test_result_class_table = CandidateGeneRankSumTestResult.table.name
test_result_class_table = 'candidate_gene_rank_sum_test_result_2008_09_15'
elif self.test_result_type==2:
test_result_class_table = CandidateGeneTopSNPTest.table.name
elif self.test_result_type==3:
test_result_class_table = Stock_250kDB.CandidateGeneRankSumTestResultMethod.table.name
else:
sys.stderr.write(" test_result_type %s not supported.\n"%(self.test_result_type))
sys.exit(2)
#the condition for min_MAF is tricky because of the floating precision.
if self.test_result_type==1:
where_condition = "%s r, %s c, %s g where g.id=c.list_type_id and r.analysis_method_id is not null \
and c.results_id=r.id and c.get_closest=%s and c.min_distance=%s and abs(c.min_MAF-%s)<0.00001"\
%(ResultsMethod.table.name, test_result_class_table, GeneListType.table.name, self.get_closest, self.min_distance, self.min_MAF)
elif self.test_result_type==2:
where_condition = "%s r, %s rg, %s c, %s g where g.id=c.list_type_id and r.analysis_method_id is not null and r.id=rg.results_method_id \
and c.results_id=rg.id and c.get_closest=%s and c.min_distance=%s and abs(c.min_MAF-%s)<0.00001"\
%(ResultsMethod.table.name, ResultsByGene.table.name, test_result_class_table, GeneListType.table.name, self.get_closest, self.min_distance, self.min_MAF)
elif self.test_result_type==3:
where_condition = "%s r, %s c, %s g where g.id=c.list_type_id and r.analysis_method_id is not null \
and c.results_id=r.id and c.get_closest=%s and c.min_distance=%s and abs(c.min_MAF-%s)<0.00001"\
%(ResultsMethod.table.name, test_result_class_table, GeneListType.table.name, self.get_closest, self.min_distance, self.min_MAF)
if self.call_method_id_ls:
where_condition += " and r.call_method_id in (%s)"%self.call_method_id_ls
if self.analysis_method_id_ls:
where_condition += " and r.analysis_method_id in (%s)"%self.analysis_method_id_ls
if self.super_type_id:
where_condition += " and g.super_type_id=%s"%self.super_type_id
if self.test_type:
where_condition += " and c.test_type=%s"%self.test_type
if self.test_result_type==1:
pass
where_condition += " and c.max_pvalue_per_gene=%s"%(self.max_pvalue_per_gene)
elif self.test_result_type==2:
where_condition += " and c.no_of_top_snps=%s"%(self.no_of_top_snps)
list_type_id_ls = self.getListTypeInfo(db, where_condition)
analysis_method_id_ls = self.getAnalysisMethodInfo(db, where_condition)
list_type_analysis_method_info = self.orderListTypeAnalysisMethodID(list_type_id_ls, analysis_method_id_ls)
phenotype_info = self.getPhenotypeInfo(db, where_condition)
rdata = self.get_data_matrix(db, phenotype_info, list_type_analysis_method_info, where_condition)
rdata.data_matrix = self.markDataMatrixBoundary(rdata.data_matrix, phenotype_info, list_type_analysis_method_info)
header = ['list_type_analysis_method', ''] + phenotype_info.phenotype_method_label_ls
strain_acc_list = list_type_analysis_method_info.list_type_analysis_method_label_ls
category_list = list_type_analysis_method_info.list_type_id_analysis_method_id_ls
if SNPData.isDataMatrixEmpty(rdata.data_matrix):
sys.stderr.write("Nothing fetched from database.\n")
sys.exit(3)
if self.output_fname:
write_data_matrix(rdata.data_matrix, self.output_fname, header, strain_acc_list, category_list)
if self.fig_fname:
font = get_font(self.font_path, font_size=self.font_size) #2008-08-01
value2color_func = lambda x: Value2Color.value2HSLcolor(x, rdata.min_value, rdata.max_value)
im_legend = drawContinousLegend(rdata.min_value, rdata.max_value, self.no_of_ticks, value2color_func, font)
#im.save('%s_legend.png'%self.fig_fname_prefix)
im = drawMatrix(rdata.data_matrix, value2color_func, list_type_analysis_method_info.list_type_analysis_method_label_ls,\
phenotype_info.phenotype_method_label_ls, with_grid=1, font=font)
im = combineTwoImages(im, im_legend, font=font)
im.save(self.fig_fname)
def run(self):
if self.debug:
import pdb
pdb.set_trace()
db = StockDB.StockDB(drivername=self.drivername,
username=self.db_user,
password=self.db_passwd,
hostname=self.hostname,
database=self.dbname,
schema=self.schema)
db.setup(create_tables=False)
session = db.session
order_by_sentence = " order by c.longitude, c.latitude, e.longitude, e.latitude, e.nativename " #how to order strains.
if self.QC_method_id == 4:
sql_table_str = "from %s e, %s s, %s a, %s c"%(StockDB.Ecotype.table.name, StockDB.Site.table.name, StockDB.Address.table.name,\
StockDB.Country.table.name)
common_where_condition = "where e.siteid=s.id and s.addressid=a.id and a.countryid=c.id %s " + order_by_sentence
strain_where_condition = common_where_condition % (
" and e.id=st.ecotypeid")
strain_id_info_query = "select distinct st.id as strainid, e.id as ecotypeid, e.nativename, s.name as sitename, c.abbr %s, %s st %s" % (
sql_table_str, StockDB.Strain.table.name,
strain_where_condition)
else:
sql_table_str = "from %s q, %s e, %s s, %s a, %s c"%(StockDB.QCCrossMatch.table.name, StockDB.Ecotype.table.name, StockDB.Site.table.name, StockDB.Address.table.name,\
StockDB.Country.table.name)
common_where_condition = "where e.siteid=s.id and s.addressid=a.id and a.countryid=c.id %s"+ " and q.qc_method_id=%s and q.no_of_non_NA_pairs>=%s and q.mismatch_rate<=%s "%\
(self.QC_method_id, self.min_no_of_non_NAs, self.max_mismatch_rate) + order_by_sentence
strain_where_condition = common_where_condition % (
" and e.id=st.ecotypeid and st.id=q.strainid")
strain_id_info_query = "select distinct q.strainid, e.id as ecotypeid, e.nativename, s.name as sitename, c.abbr %s, %s st %s" % (
sql_table_str, StockDB.Strain.table.name,
strain_where_condition)
if self.how_to_group_strains == 2 or self.how_to_group_strains == 3:
plate_info = self.alignStrainsAccordingToSeqPlate(db)
id_set_data = PassingData()
id_set_data.strain_id_set = None
id_set_data.target_id_set = None
elif self.input_fname:
id_set_data = self.getStrainidTargetidFromFile(
db, self.QC_method_id, self.input_fname,
self.max_mismatch_rate, self.min_no_of_non_NAs)
else:
id_set_data = PassingData()
id_set_data.strain_id_set = None
id_set_data.target_id_set = None
if self.how_to_group_strains == 2 or self.how_to_group_strains == 3:
strain_id_info = self.getStrainInfoGivenPlateInfo(
db, plate_info, strain_id_info_query, strain_id_set=None)
else:
strain_id_info = self.getStrainIDInfo(db, strain_id_info_query,
id_set_data.strain_id_set)
if self.QC_method_id == 4:
if self.how_to_group_strains == 3:
#2008-09-15 column strain id is in country, strain-longitude order
target_id_info = self.getStrainIDInfo(
db, strain_id_info_query, id_set_data.strain_id_set)
else:
target_id_info = strain_id_info
else:
target_where_condition = common_where_condition % (
" and e.id=q.target_id")
target_id_info_query = "select distinct e.id as strainid, e.id as ecotypeid, e.nativename, s.name as sitename, c.abbr %s %s" % (
sql_table_str, target_where_condition)
target_id_info = self.getStrainIDInfo(db, target_id_info_query)
if self.input_fname:
rdata = self.get_data_matrixFromFile(db, strain_id_info,
target_id_info,
self.QC_method_id,
self.input_fname,
self.max_mismatch_rate,
self.min_no_of_non_NAs)
else:
rdata = self.get_data_matrix(db, strain_id_info, target_id_info,
self.QC_method_id,
self.max_mismatch_rate,
self.min_no_of_non_NAs)
rdata.data_matrix = self.markDataMatrixBoundary(
rdata.data_matrix, strain_id_info, target_id_info)
header = ['strain info', ''] + target_id_info.strain_label_ls
strain_acc_list = strain_id_info.strain_label_ls
category_list = [1] * len(strain_acc_list)
if SNPData.isDataMatrixEmpty(rdata.data_matrix):
sys.stderr.write("Nothing fetched from database.\n")
sys.exit(3)
if self.output_fname:
write_data_matrix(rdata.data_matrix, self.output_fname, header,
strain_acc_list, category_list)
if self.fig_fname:
font = get_font(self.font_path,
font_size=self.font_size) #2008-08-01
value2color_func = lambda x: Value2Color.value2HSLcolor(
x, rdata.min_value, rdata.max_value)
im_legend = drawContinousLegend(rdata.min_value, rdata.max_value,
self.no_of_ticks, value2color_func,
font)
#im.save('%s_legend.png'%self.fig_fname_prefix)
im = drawMatrix(rdata.data_matrix, value2color_func, strain_id_info.strain_label_ls,\
target_id_info.strain_label_ls, with_grid=1, font=font)
im = combineTwoImages(im, im_legend, font=font)
im.save(self.fig_fname)
def run(self):
"""
2008-11-08
generate combinations of results_id, list_type_id and generate plots one after another
save the plots into database if commit=1
"""
if self.debug:
import pdb
pdb.set_trace()
db = Stock_250kDB.Stock_250kDB(drivername=self.drivername,
username=self.db_user,
password=self.db_passwd,
hostname=self.hostname,
database=self.dbname,
schema=self.schema)
db.setup()
session = db.session
param_obj = PassingData(call_method_id=self.call_method_id, \
analysis_method_id=getattr(self, 'analysis_method_id', None),\
analysis_method_id_ls=getattr(self, 'analysis_method_id_ls', None),\
phenotype_method_id_ls=getattr(self, 'phenotype_method_id_ls', None),\
list_type_id_ls=self.list_type_id_ls, \
results_type=self.results_type)
params_ls = MpiGeneListRankTest.generate_params(param_obj)
ResultsClass, TestResultClass = db.getResultsAndTestResultsClass(
results_type=self.results_type)
if ResultsClass is None or TestResultClass is None:
sys.stderr.write("Invalid results type : %s.\n" % pd.results_type)
sys.exit(3)
for results_id, list_type_id in params_ls:
rm = ResultsClass.get(results_id)
list_type = Stock_250kDB.GeneListType.get(list_type_id)
title = 'result(%s) of %s on %s with %s(%s) list'%\
(results_id, rm.analysis_method.short_name, rm.phenotype_method.short_name, list_type.short_name, list_type.id)
TopSNPTestType_id_ls = self.getTopSNPTestType_id_ls(self.get_closest, self.min_MAF, self.allow_two_sample_overlapping, self.results_type, \
self.test_type_id, self.null_distribution_type_id)
if self.commit:
rows = Stock_250kDB.CandidateVsNonRatioPlot.query.filter_by(type_id=TopSNPTestType_id_ls[0]).\
filter_by(results_id=results_id).filter_by(list_type_id=list_type_id)
if rows.count() > 0:
row = rows.first()
sys.stderr.write(
'%s already in db (%s of them) with first id=%s.\n' %
(title, rows.count(), row.id))
continue
if not TopSNPTestType_id_ls:
sys.stderr.write(
"No TopSNPTestType matches the input requirements. Exit.\n"
)
sys.exit(3)
TopSNPTestType_id_ls_str = map(str, TopSNPTestType_id_ls)
from_where_clause = "from %s t, %s y where t.type_id=y.id and t.results_id=%s and t.list_type_id=%s and y.id in (%s)"%\
(TestResultClass.table.name, Stock_250kDB.CandidateGeneTopSNPTestRMType.table.name,\
results_id, list_type_id, ','.join(TopSNPTestType_id_ls_str))
no_of_top_snps_info = self.get_no_of_top_snps_info(
db, from_where_clause)
min_distance_info = self.get_min_distance_info(
db, from_where_clause)
rdata = self.get_data_matrix(db, no_of_top_snps_info, min_distance_info, from_where_clause, need_other_values=True, \
null_distribution_type_id=self.null_distribution_type_id)
header = ['no_of_top_snps', ''] + min_distance_info.label_ls
strain_acc_list = no_of_top_snps_info.label_ls
category_list = no_of_top_snps_info.label_ls
if SNPData.isDataMatrixEmpty(rdata.data_matrix):
sys.stderr.write("Nothing fetched from database.\n")
#sys.exit(3)
continue
if self.output_fname:
write_data_matrix(rdata.data_matrix, self.output_fname, header,
strain_acc_list, category_list)
"""
if self.fig_fname:
font = get_font(self.font_path, font_size=self.font_size) #2008-08-01
value2color_func = lambda x: Value2Color.value2HSLcolor(x, rdata.min_value, rdata.max_value)
im_legend = drawContinousLegend(rdata.min_value, rdata.max_value, self.no_of_ticks, value2color_func, font)
#im.save('%s_legend.png'%self.fig_fname_prefix)
im = drawMatrix(rdata.data_matrix, value2color_func, no_of_top_snps_info.label_ls,\
min_distance_info.label_ls, with_grid=1, font=font)
im = combineTwoImages(im, im_legend, font=font)
im.save(self.fig_fname)
"""
if self.commit:
output_fname_prefix = None
else:
title_cp = title
title_cp = title_cp.replace('/', '_')
output_fname_prefix = '%s_%s_type_%s.png' % (os.path.splitext(
self.fig_fname)[0], title_cp, TopSNPTestType_id_ls[0])
if rm.analysis_method_id == 1 or rm.analysis_method_id == 7:
preset_xlim = [0, 8]
preset_xlim = None
else:
preset_xlim = None
return_data = self.plotCurve(rdata,
no_of_top_snps_info,
min_distance_info,
output_fname_prefix,
title=title,
commit=self.commit,
preset_xlim=preset_xlim)
if self.commit and return_data.png_data:
rows = Stock_250kDB.CandidateVsNonRatioPlot.query.filter_by(type_id=TopSNPTestType_id_ls[0]).\
filter_by(results_id=results_id).filter_by(list_type_id=list_type_id)
if rows.count() > 0:
row = rows.first()
sys.stderr.write(
'%s already in db (%s of them) with first id=%s.\n' %
(title, rows.count(), row.id))
continue
plot = Stock_250kDB.CandidateVsNonRatioPlot(
type_id=TopSNPTestType_id_ls[0],
results_id=results_id,
list_type_id=list_type_id)
plot.png_thumbnail = return_data.png_thumbnail.getvalue()
plot.png_data = return_data.png_data.getvalue()
plot.svg_data = return_data.svg_data.getvalue()
db.session.save(plot)
db.session.flush()
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):
"""
2008-11-08
generate combinations of results_id, list_type_id and generate plots one after another
save the plots into database if commit=1
"""
if self.debug:
import pdb
pdb.set_trace()
db = Stock_250kDB.Stock_250kDB(drivername=self.drivername, username=self.db_user,
password=self.db_passwd, hostname=self.hostname, database=self.dbname, schema=self.schema)
db.setup()
session = db.session
param_obj = PassingData(call_method_id=self.call_method_id, \
analysis_method_id=getattr(self, 'analysis_method_id', None),\
analysis_method_id_ls=getattr(self, 'analysis_method_id_ls', None),\
phenotype_method_id_ls=getattr(self, 'phenotype_method_id_ls', None),\
list_type_id_ls=self.list_type_id_ls, \
results_type=self.results_type)
params_ls = MpiGeneListRankTest.generate_params(param_obj)
for results_id, list_type_id in params_ls:
rm = Stock_250kDB.ResultsMethod.get(results_id)
list_type = Stock_250kDB.GeneListType.get(list_type_id)
title = 'result(%s) of %s on %s with %s(%s) list'%\
(results_id, rm.analysis_method.short_name, rm.phenotype_method.short_name, list_type.short_name, list_type.id)
TopSNPTestType_id_ls = self.getTopSNPTestType_id_ls(self.get_closest, self.min_MAF, self.allow_two_sample_overlapping, self.results_type, \
self.test_type_id, self.null_distribution_type_id)
if self.commit:
rows = Stock_250kDB.CandidateVsNonRatioPlot.query.filter_by(type_id=TopSNPTestType_id_ls[0]).\
filter_by(results_id=results_id).filter_by(list_type_id=list_type_id)
if rows.count()>0:
row = rows.first()
sys.stderr.write('%s already in db (%s of them) with first id=%s.\n'%(title, rows.count(), row.id))
continue
if not TopSNPTestType_id_ls:
sys.stderr.write("No TopSNPTestType matches the input requirements. Exit.\n")
sys.exit(3)
TopSNPTestType_id_ls_str = map(str, TopSNPTestType_id_ls)
from_where_clause = "from %s t, %s y where t.type_id=y.id and t.results_id=%s and t.list_type_id=%s and y.id in (%s)"%\
(Stock_250kDB.CandidateGeneTopSNPTestRM.table.name, Stock_250kDB.CandidateGeneTopSNPTestRMType.table.name,\
results_id, list_type_id, ','.join(TopSNPTestType_id_ls_str))
no_of_top_snps_info = self.get_no_of_top_snps_info(db, from_where_clause)
min_distance_info = self.get_min_distance_info(db, from_where_clause)
rdata = self.get_data_matrix(db, no_of_top_snps_info, min_distance_info, from_where_clause, need_other_values=True, \
null_distribution_type_id=self.null_distribution_type_id)
header = ['no_of_top_snps', ''] + min_distance_info.label_ls
strain_acc_list = no_of_top_snps_info.label_ls
category_list = no_of_top_snps_info.label_ls
if SNPData.isDataMatrixEmpty(rdata.data_matrix):
sys.stderr.write("Nothing fetched from database.\n")
#sys.exit(3)
continue
if self.output_fname:
write_data_matrix(rdata.data_matrix, self.output_fname, header, strain_acc_list, category_list)
"""
if self.fig_fname:
font = get_font(self.font_path, font_size=self.font_size) #2008-08-01
value2color_func = lambda x: Value2Color.value2HSLcolor(x, rdata.min_value, rdata.max_value)
im_legend = drawContinousLegend(rdata.min_value, rdata.max_value, self.no_of_ticks, value2color_func, font)
#im.save('%s_legend.png'%self.fig_fname_prefix)
im = drawMatrix(rdata.data_matrix, value2color_func, no_of_top_snps_info.label_ls,\
min_distance_info.label_ls, with_grid=1, font=font)
im = combineTwoImages(im, im_legend, font=font)
im.save(self.fig_fname)
"""
if self.commit:
output_fname_prefix = None
else:
title_cp = title
title_cp = title_cp.replace('/', '_')
output_fname_prefix='%s_%s_type_%s.png'%(os.path.splitext(self.fig_fname)[0], title_cp, TopSNPTestType_id_ls[0])
if rm.analysis_method_id ==1 or rm.analysis_method_id==7:
preset_xlim = [0,8]
else:
preset_xlim = None
return_data = self.plotCurve(rdata, no_of_top_snps_info, min_distance_info, output_fname_prefix, title=title, commit=self.commit, preset_xlim=preset_xlim)
if self.commit and return_data.png_data:
rows = Stock_250kDB.CandidateVsNonRatioPlot.query.filter_by(type_id=TopSNPTestType_id_ls[0]).\
filter_by(results_id=results_id).filter_by(list_type_id=list_type_id)
if rows.count()>0:
row = rows.first()
sys.stderr.write('%s already in db (%s of them) with first id=%s.\n'%(title, rows.count(), row.id))
continue
plot = Stock_250kDB.CandidateVsNonRatioPlot(type_id=TopSNPTestType_id_ls[0], results_id=results_id, list_type_id=list_type_id)
plot.png_thumbnail = return_data.png_thumbnail.getvalue()
plot.png_data = return_data.png_data.getvalue()
plot.svg_data = return_data.svg_data.getvalue()
db.session.save(plot)
db.session.flush()
def run(self):
if self.debug:
import pdb
pdb.set_trace()
db = StockDB.StockDB(drivername=self.drivername, username=self.db_user,
password=self.db_passwd, hostname=self.hostname, database=self.dbname, schema=self.schema)
db.setup(create_tables=False)
session = db.session
order_by_sentence = " order by c.longitude, c.latitude, e.longitude, e.latitude, e.nativename " #how to order strains.
if self.QC_method_id ==4:
sql_table_str = "from %s e, %s s, %s a, %s c"%(StockDB.Ecotype.table.name, StockDB.Site.table.name, StockDB.Address.table.name,\
StockDB.Country.table.name)
common_where_condition = "where e.siteid=s.id and s.addressid=a.id and a.countryid=c.id %s " + order_by_sentence
strain_where_condition = common_where_condition%(" and e.id=st.ecotypeid")
strain_id_info_query = "select distinct st.id as strainid, e.id as ecotypeid, e.nativename, s.name as sitename, c.abbr %s, %s st %s"%(sql_table_str, StockDB.Strain.table.name, strain_where_condition)
else:
sql_table_str = "from %s q, %s e, %s s, %s a, %s c"%(StockDB.QCCrossMatch.table.name, StockDB.Ecotype.table.name, StockDB.Site.table.name, StockDB.Address.table.name,\
StockDB.Country.table.name)
common_where_condition = "where e.siteid=s.id and s.addressid=a.id and a.countryid=c.id %s"+ " and q.qc_method_id=%s and q.no_of_non_NA_pairs>=%s and q.mismatch_rate<=%s "%\
(self.QC_method_id, self.min_no_of_non_NAs, self.max_mismatch_rate) + order_by_sentence
strain_where_condition = common_where_condition%(" and e.id=st.ecotypeid and st.id=q.strainid")
strain_id_info_query = "select distinct q.strainid, e.id as ecotypeid, e.nativename, s.name as sitename, c.abbr %s, %s st %s"%(sql_table_str, StockDB.Strain.table.name, strain_where_condition)
if self.how_to_group_strains==2 or self.how_to_group_strains==3:
plate_info = self.alignStrainsAccordingToSeqPlate(db)
id_set_data = PassingData()
id_set_data.strain_id_set = None
id_set_data.target_id_set = None
elif self.input_fname:
id_set_data = self.getStrainidTargetidFromFile(db, self.QC_method_id, self.input_fname, self.max_mismatch_rate, self.min_no_of_non_NAs)
else:
id_set_data = PassingData()
id_set_data.strain_id_set = None
id_set_data.target_id_set = None
if self.how_to_group_strains==2 or self.how_to_group_strains==3:
strain_id_info = self.getStrainInfoGivenPlateInfo(db, plate_info, strain_id_info_query, strain_id_set=None)
else:
strain_id_info = self.getStrainIDInfo(db, strain_id_info_query, id_set_data.strain_id_set)
if self.QC_method_id==4:
if self.how_to_group_strains==3:
#2008-09-15 column strain id is in country, strain-longitude order
target_id_info = self.getStrainIDInfo(db, strain_id_info_query, id_set_data.strain_id_set)
else:
target_id_info = strain_id_info
else:
target_where_condition = common_where_condition%(" and e.id=q.target_id")
target_id_info_query = "select distinct e.id as strainid, e.id as ecotypeid, e.nativename, s.name as sitename, c.abbr %s %s"%(sql_table_str, target_where_condition)
target_id_info = self.getStrainIDInfo(db, target_id_info_query)
if self.input_fname:
rdata = self.get_data_matrixFromFile(db, strain_id_info, target_id_info, self.QC_method_id, self.input_fname, self.max_mismatch_rate, self.min_no_of_non_NAs)
else:
rdata = self.get_data_matrix(db, strain_id_info, target_id_info, self.QC_method_id, self.max_mismatch_rate, self.min_no_of_non_NAs)
rdata.data_matrix = self.markDataMatrixBoundary(rdata.data_matrix, strain_id_info, target_id_info)
header = ['strain info', ''] + target_id_info.strain_label_ls
strain_acc_list = strain_id_info.strain_label_ls
category_list = [1]*len(strain_acc_list)
if SNPData.isDataMatrixEmpty(rdata.data_matrix):
sys.stderr.write("Nothing fetched from database.\n")
sys.exit(3)
if self.output_fname:
write_data_matrix(rdata.data_matrix, self.output_fname, header, strain_acc_list, category_list)
if self.fig_fname:
font = get_font(self.font_path, font_size=self.font_size) #2008-08-01
value2color_func = lambda x: Value2Color.value2HSLcolor(x, rdata.min_value, rdata.max_value)
im_legend = drawContinousLegend(rdata.min_value, rdata.max_value, self.no_of_ticks, value2color_func, font)
#im.save('%s_legend.png'%self.fig_fname_prefix)
im = drawMatrix(rdata.data_matrix, value2color_func, strain_id_info.strain_label_ls,\
target_id_info.strain_label_ls, with_grid=1, font=font)
im = combineTwoImages(im, im_legend, font=font)
im.save(self.fig_fname)
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)