def run(self):
if self.debug:
import pdb
pdb.set_trace()
import MySQLdb
mysql_conn = MySQLdb.connect(db=self.dbname, host="banyan.usc.edu", user=self.db_user, passwd=self.db_passwd)
mysql_curs = mysql_conn.cursor()
from pymodule import get_gene_symbol2gene_id_set
gene_symbol2gene_id_set = get_gene_symbol2gene_id_set(
mysql_curs, 3702, table="genome.gene_symbol2id", upper_case_gene_symbol=1
) # 3702 is At's tax id
from variation.src.DrawSNPRegion import DrawSNPRegion
DrawSNPRegion_ins = DrawSNPRegion(
db_user=self.db_user,
db_passwd=self.db_passwd,
hostname=self.hostname,
database=self.dbname,
input_fname="/tmp/dumb",
output_dir="/tmp",
debug=0,
) # input_fname and output_dir are just random stuff
gene_annotation = DrawSNPRegion_ins.dealWithGeneAnnotation(
self.gene_annotation_picklef, cls_with_db_args=DrawSNPRegion_ins
)
self.improveTAIRGeneGFF(self.input_fname, gene_symbol2gene_id_set, gene_annotation, self.output_fname)
def run(self):
if self.debug==1:
import pdb
pdb.set_trace()
from DrawSNPRegion import DrawSNPRegion
DrawSNPRegion_instance = DrawSNPRegion(db_user=self.db_user, db_passwd=self.db_passwd, hostname=self.hostname, \
database=self.dbname, input_fname='/tmp/dumb', output_dir='/tmp', debug=0)
grand_dataStructure = DrawSNPRegion_instance.loadDataStructure(self.gene_annotation_picklef, self.LD_info_picklef, self.LD_fname, min_MAF=self.min_MAF, min_distance=20000, list_type_id=None)
snp_region_ls = self.get_snp_region_ls(self.input_fname, grand_dataStructure.snp_info, self.min_distance)
value_criteria={(1, 'value'):8., (7, 'value'):6., (5, 'rank'):self.min_margarita_rank,(6, 'rank'):self.min_rf_rank} #minimum threshold for different analysis methods
self.checkRegions(DrawSNPRegion_instance, grand_dataStructure.snp_info, snp_region_ls, self.output_fname, value_criteria)
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(create_tables=False) session = db.session #session.begin() snps_context_wrapper = GeneListRankTest.dealWithSnpsContextWrapper(self.snps_context_picklef, self.min_distance, self.get_closest) gene_annotation = DrawSNPRegion.dealWithGeneAnnotation(self.gene_annotation_picklef) snp_info = DrawSNPRegion.getSNPInfo(db) snp_annotation_short_name2id = self.getSNPAnnotationShortName2id() self._constructSNPAnnotation(session, snp_info, snps_context_wrapper, gene_annotation, snp_annotation_short_name2id) if self.commit: session.flush() session.commit()
def calculateOverlappingStatForOneCombo(self, db, phenotype_method_id, call_method_id, analysis_method_id_ls, \
no_of_top_snps=1000, association_overlapping_type=None, commit=False, \
results_directory=None):
"""
2012.3.23
pass argument db_250k to ResultsMethod2Results.rm2result()
2009-11-2
"""
sys.stderr.write("Calculating overlapping stat for phenotype %s and combo %s ...\n"%(phenotype_method_id, \
repr(analysis_method_id_ls),))
session = db.session
snp_id_set_ls = []
for analysis_method_id in analysis_method_id_ls:
rm = Stock_250kDB.ResultsMethod.query.filter_by(phenotype_method_id=phenotype_method_id).\
filter_by(call_method_id=call_method_id).filter_by(analysis_method_id=analysis_method_id).first()
if rm.id in self.results_id2snp_id_set:
snp_id_set = self.results_id2snp_id_set.get(rm.id)
else:
association_entries = Stock_250kDB.Results.query.filter_by(results_id=rm.id).\
filter(Stock_250kDB.Results.rank<=no_of_top_snps)
no_of_association_entries = association_entries.count()
if no_of_association_entries < no_of_top_snps:
min_rank = no_of_association_entries + 1
max_rank = no_of_top_snps
if self.snp_info is None:
self.snp_info = DrawSNPRegion.getSNPInfo(db)
ResultsMethod2Results.rm2result(session, rm, self.snp_info, min_rank=min_rank, max_rank=max_rank, \
commit=commit, results_directory=results_directory, db_250k=db)
association_entries = Stock_250kDB.Results.query.filter_by(results_id=rm.id).\
filter(Stock_250kDB.Results.rank<=no_of_top_snps)
no_of_association_entries = association_entries.count()
if no_of_association_entries != no_of_top_snps:
sys.stderr.write(
"Error: The number of SNPs %s from Result %s (analysis_method_id %s) doesn't match the no_of_top_snps %s.\n"
% (no_of_association_entries, rm.id,
rm.analysis_method_id, no_of_top_snps))
return
snp_id_set = set()
for entry in association_entries:
snp_id_set.add(entry.snps_id)
self.results_id2snp_id_set[rm.id] = snp_id_set
snp_id_set_ls.append(snp_id_set)
overlapping_snp_id_set = snp_id_set_ls[0]
for i in range(1, len(snp_id_set_ls)):
snp_id_set = snp_id_set_ls[i]
overlapping_snp_id_set = overlapping_snp_id_set & snp_id_set
no_of_overlapping_snps = len(overlapping_snp_id_set)
entry = Stock_250kDB.AssociationOverlappingStat(phenotype_method_id=phenotype_method_id, call_method_id=call_method_id, \
no_of_top_snps=no_of_top_snps, no_of_overlapping_snps=no_of_overlapping_snps)
entry.overlapping_type = association_overlapping_type
session.save(entry)
session.flush()
sys.stderr.write("%s overlapping SNPs out of %s results. Done.\n" %
(no_of_overlapping_snps, len(snp_id_set_ls)))
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(create_tables=False) session = db.session #session.begin() snps_context_wrapper = GeneListRankTest.dealWithSnpsContextWrapper(self.snps_context_picklef, self.min_distance, \ self.get_closest) gene_annotation = DrawSNPRegion.dealWithGeneAnnotation(self.gene_annotation_picklef, tax_id=self.tax_id, \ cls_with_db_args=self) snp_info = DrawSNPRegion.getSNPInfo(db) snp_annotation_short_name2id = self.getSNPAnnotationShortName2id() self._constructSNPAnnotation(session, snp_info, snps_context_wrapper, gene_annotation, snp_annotation_short_name2id) if self.commit: session.flush() session.commit()
def calculateOverlappingStatForOneCombo(self, db, phenotype_method_id, call_method_id, analysis_method_id_ls, \
no_of_top_snps=1000, association_overlapping_type=None, commit=False, \
results_directory=None):
"""
2009-11-2
"""
sys.stderr.write("Calculating overlapping stat for phenotype %s and combo %s ...\n"%(phenotype_method_id, \
repr(analysis_method_id_ls),))
session = db.session
snp_id_set_ls = []
for analysis_method_id in analysis_method_id_ls:
rm = Stock_250kDB.ResultsMethod.query.filter_by(phenotype_method_id=phenotype_method_id).\
filter_by(call_method_id=call_method_id).filter_by(analysis_method_id=analysis_method_id).first()
if rm.id in self.results_id2snp_id_set:
snp_id_set = self.results_id2snp_id_set.get(rm.id)
else:
association_entries = Stock_250kDB.Results.query.filter_by(results_id=rm.id).\
filter(Stock_250kDB.Results.rank<=no_of_top_snps)
no_of_association_entries = association_entries.count()
if no_of_association_entries<no_of_top_snps:
min_rank = no_of_association_entries+1
max_rank = no_of_top_snps
if self.snp_info is None:
self.snp_info = DrawSNPRegion.getSNPInfo(db)
ResultsMethod2Results.rm2result(session, rm, self.snp_info, min_rank=min_rank, max_rank=max_rank, \
commit=commit, results_directory=results_directory)
association_entries = Stock_250kDB.Results.query.filter_by(results_id=rm.id).\
filter(Stock_250kDB.Results.rank<=no_of_top_snps)
no_of_association_entries = association_entries.count()
if no_of_association_entries!=no_of_top_snps:
sys.stderr.write("Error: The number of SNPs %s from Result %s (analysis_method_id %s) doesn't match the no_of_top_snps %s.\n"%(no_of_association_entries, rm.id, rm.analysis_method_id, no_of_top_snps))
return
snp_id_set = set()
for entry in association_entries:
snp_id_set.add(entry.snps_id)
self.results_id2snp_id_set[rm.id] = snp_id_set
snp_id_set_ls.append(snp_id_set)
overlapping_snp_id_set = snp_id_set_ls[0]
for i in range(1, len(snp_id_set_ls)):
snp_id_set = snp_id_set_ls[i]
overlapping_snp_id_set = overlapping_snp_id_set&snp_id_set
no_of_overlapping_snps = len(overlapping_snp_id_set)
entry = Stock_250kDB.AssociationOverlappingStat(phenotype_method_id=phenotype_method_id, call_method_id=call_method_id, \
no_of_top_snps=no_of_top_snps, no_of_overlapping_snps=no_of_overlapping_snps)
entry.overlapping_type = association_overlapping_type
session.save(entry)
session.flush()
sys.stderr.write("%s overlapping SNPs out of %s results. Done.\n"%(no_of_overlapping_snps, len(snp_id_set_ls)))
def on_button_draw_annotation_clicked(self, widget, data=None):
"""
2008-12-16
use DrawSNPRegion.drawGeneModel() to draw gene models
2008-02-02
"""
if not self.chr_id2size:
sys.stderr.write("No genome-wide pvalue plot has been drawn yet. Do it first!\n")
return
#if not self.gene_id2model:
# self.gene_id2model, self.chr_id2gene_id_ls = self.get_gene_id2model(self.postgres_curs, tax_id=3702)
if not self.gene_annotation:
self.db_connect()
xlim = self.axe_gene_model.get_xlim()
left_chr, left_pos = get_chr_pos_from_x_axis_pos(xlim[0], self.chr_gap, self.chr_id2cumu_size, self.chr_id_ls)
right_chr, right_pos = get_chr_pos_from_x_axis_pos(xlim[1], self.chr_gap, self.chr_id2cumu_size, self.chr_id_ls)
#fake a snps_within_this_region for drawGeneModel()
snps_within_this_region = PassingData(chr_pos_ls=[[left_chr, left_pos],[right_chr, right_pos]])
base_y_value = 1
gene_width = 0.8
gene_position_cycle = 5
return_data = DrawSNPRegion.drawGeneModel(self.axe_gene_model, snps_within_this_region, self.gene_annotation, candidate_gene_set=None,\
gene_width=gene_width, gene_position_cycle=gene_position_cycle, base_y_value=base_y_value, \
gene_box_text_gap=20, label_gene=0, rotate_xy=False,\
chr_id2cumu_size=self.chr_id2cumu_size, chr_id2size=self.chr_id2size, chr_gap=self.chr_gap,\
artist_obj_id2artist_gene_id_ls=self.artist_obj_id2artist_gene_id_ls, \
gene_id2artist_object_id=self.gene_id2artist_object_id, drawGeneOnTheBoundary=False)
#set drawGeneOnTheBoundary to False because later adding text to these genes would corrupt the running program.
self.axe_gene_model.set_ylim([base_y_value-gene_width, gene_position_cycle+gene_width*2])
"""
for gene_id in self.chr_id2gene_id_ls[left_chr]:
gene_model = self.gene_id2model[gene_id]
if gene_model.start!=None and gene_model.stop!=None and gene_model.stop>left_pos and gene_id not in self.gene_id2artist_object_id:
if left_chr==right_chr: #same chromosome
if gene_model.start>right_pos: #totally out of range, skip it
continue
y_value = len(self.gene_id2artist_object_id)%4 #cycling through the y position to avoid clogging
self.plot_one_gene(self.ax, gene_id, self.gene_id2model, self.chr_id2cumu_size, self.chr_id2size, self.chr_gap, y_value=-1-y_value, gene_width=self.gene_width)
if left_chr!=right_chr:
for gene_id in self.chr_id2gene_id_ls[right_chr]:
gene_model = self.gene_id2model[gene_id]
if gene_model.start!=None and gene_model.stop!=None and gene_model.start<right_pos and gene_id not in self.gene_id2artist_object_id:
y_value = len(self.gene_id2artist_object_id)%4 #cycling through the y position to avoid clogging
self.plot_one_gene(self.ax, gene_id, self.gene_id2model, self.chr_id2cumu_size, self.chr_id2size, self.chr_gap, y_value=-1-y_value, gene_width=self.gene_width)
"""
self.canvas_matplotlib.draw()
def run(self):
if self.debug:
import pdb
pdb.set_trace()
import MySQLdb
mysql_conn = MySQLdb.connect(db=self.dbname,
host='banyan.usc.edu',
user=self.db_user,
passwd=self.db_passwd)
mysql_curs = mysql_conn.cursor()
from pymodule import get_gene_symbol2gene_id_set
gene_symbol2gene_id_set = get_gene_symbol2gene_id_set(
mysql_curs,
3702,
table='genome.gene_symbol2id',
upper_case_gene_symbol=1) #3702 is At's tax id
from variation.src.DrawSNPRegion import DrawSNPRegion
DrawSNPRegion_ins = DrawSNPRegion(db_user=self.db_user, db_passwd=self.db_passwd, hostname=self.hostname, database=self.dbname,\
input_fname='/tmp/dumb', output_dir='/tmp', debug=0) #input_fname and output_dir are just random stuff
gene_annotation = DrawSNPRegion_ins.dealWithGeneAnnotation(
self.gene_annotation_picklef, cls_with_db_args=DrawSNPRegion_ins)
self.improveTAIRGeneGFF(self.input_fname, gene_symbol2gene_id_set,
gene_annotation, self.output_fname)
def db_connect(self):
"""
2010-1-15
pass "cls_with_db_args=self" to DrawSNPRegion.dealWithGeneAnnotation()
2009-12-09
add db_user, db_passwd to MySQLdb.connect()
2008-12-16
add gene_annotation_picklef
2008-02-01
read the data in dialog_db_connect and establish the connections to two databases
"""
sys.stderr.write("Database Connecting ...")
self.drivername = 'mysql'
self.hostname = self.entry_mysql_hostname.get_text()
self.dbname = self.entry_mysql_dbname.get_text()
self.db_user = self.xml.get_widget("entry_db_user").get_text()
self.db_passwd = self.xml.get_widget("entry_db_passwd").get_text()
import MySQLdb
try:
self.mysql_conn = MySQLdb.connect(db=self.dbname, host=self.hostname, user=self.db_user, passwd=self.db_passwd)
self.mysql_curs = self.mysql_conn.cursor()
self.db = Stock_250kDB.Stock_250kDB(drivername=self.drivername, username=self.db_user,
password=self.db_passwd, hostname=self.hostname, database=self.dbname)
self.db.setup(create_tables=False)
self.session = self.db.session
except:
sys.stderr.write('DB connection error: %s\n'%repr(sys.exc_info()))
traceback.print_exc()
if not self.gene_annotation:
gene_annotation_picklef = self.entry_gene_annotation_picklef.get_text()
self.gene_annotation = DrawSNPRegion.dealWithGeneAnnotation(gene_annotation_picklef, cls_with_db_args=self)
#2010-1-13 for postgresql. commented out
#hostname = self.entry_postgres_hostname.get_text()
#dbname = self.entry_postgres_dbname.get_text()
#schema = self.entry_postgres_schema.get_text()
#from annot.bin.codense.common import db_connect #2008-12-16 don't need postgres conn anymore
#self.postgres_conn, self.postgres_curs = db_connect(hostname, dbname, schema)
sys.stderr.write("Done.\n")
def run(self): """ 2009-6-10 set Results.beta = getattr(data_obj, 'beta1', None) """ 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(create_tables=False) session = db.session session.begin() snp_info = DrawSNPRegion.getSNPInfo(db) query = Stock_250kDB.ResultsMethod.query.filter_by(call_method_id=self.call_method_id).\ filter(Stock_250kDB.ResultsMethod.analysis_method_id.in_(self.analysis_method_id_ls)) for rm in query: self.rm2result(session, rm, snp_info, max_rank=self.max_rank, commit=self.commit, results_directory=self.results_directory) if self.commit: session.commit()
def improveTAIRGeneGFF(self, input_fname, gene_symbol2gene_id_set, gene_annotation, output_fname):
"""
2009-2-5
apply the improvement to any non-chromosome lines with 'ID' entry
escape ';' by '%3B', which is regarded as a separator for every "name=value"
escape ',' by '%2C', which is regarded as a separator for every "value"
esacpe gene_symbol/Alias whose value matches individual chromosome (like gene 'CHR5' = 'Gene CHR5')
2009-2-4
if the last column has 'ID' in it, find corresponding gene id using its value and add gene_symbol and description
"""
sys.stderr.write("Improving TAIR Gene GFF with symbols and descriptions ...\n")
import re
p_ID_acc_ver = re.compile(r"ID=(\w+)\.(\d+);")
p_ID_acc = re.compile(r"ID=(\w+);")
p_ID_protein_acc = re.compile(r"ID=(\w+)\.(\d+)-Protein;")
p_chr_name = re.compile(r"CHR\d+$") # to esacpe gene_symbol/Alias whose value matches individual chromosome
delimiter = figureOutDelimiter(input_fname)
reader = csv.reader(open(input_fname), delimiter=delimiter)
writer = csv.writer(
open(output_fname, "w"), delimiter=delimiter, lineterminator="\n"
) # lineterminator is important. GFF3Loader would break down if it's dos terminator('\r\n').
counter = 0
success_counter = 0
for row in reader:
last_col = row[-1]
tair_id = None
if p_ID_acc_ver.search(last_col):
tair_id, version = p_ID_acc_ver.search(last_col).groups()
if p_ID_acc.search(last_col):
tair_id, = p_ID_acc.search(last_col).groups()
if p_ID_protein_acc.search(last_col):
tair_id, version = p_ID_protein_acc.search(last_col).groups()
counter += 1
if tair_id is not None and row[2] != "chromosome":
gene_id_set = getGeneIDSetGivenAccVer(tair_id, gene_symbol2gene_id_set)
gene_id = None
if gene_id_set == None:
sys.stderr.write(
"Linking to gene id failed for %s. No such gene_symbol, %s, in gene_symbol2gene_id_set.\n"
% (last_col, tair_id)
)
elif len(gene_id_set) == 1:
gene_id = list(gene_id_set)[0]
success_counter += 1
elif len(gene_id_set) > 1:
sys.stderr.write("Too many gene_ids: %s, %s.\n" % (tair_id, gene_id_set))
elif len(gene_id_set) == 0:
sys.stderr.write(
"Linking to gene id failed for %s. There is gene_symbol, %s, in gene_symbol2gene_id_set but it's empty.\n"
% (last_col, tair_id)
)
else:
sys.stderr.write(
"not supposed to happen: original_name=%s, gene_symbol=%s, gene_id_set=%s\n."
% (last_col, tair_id, gene_id_set)
)
if gene_id is not None:
gene_model = gene_annotation.gene_id2model.get(gene_id)
if gene_model is not None:
gene_commentary = gene_model.gene_commentaries[0]
gene_desc_ls = DrawSNPRegion.returnGeneDescLs(
self.gene_desc_names,
gene_model,
gene_commentary,
cutoff_length=600,
replaceNoneElemWithEmptyStr=1,
)
local_gene_desc_names = map(string.upper, self.gene_desc_names)
description = ", ".join(
[": ".join(entry) for entry in zip(local_gene_desc_names, gene_desc_ls)]
)
description = description.replace(
";", "%3B"
) # escape ';', which is regarded as a separator for every "name=value"
description = description.replace(
",", "%2C"
) # escape ',', which is regarded as a separator for every "value"
if last_col[-1] != ";": # no ; delimiter at the end, append one
last_col += ";"
gene_symbol = gene_model.gene_symbol
gene_symbol = gene_symbol.replace(";", "%3B")
gene_symbol = gene_symbol.replace(",", "%2C")
if p_chr_name.match(gene_symbol): # match the chromosome name, change
gene_symbol = "Gene %s" % gene_symbol
last_col += "Alias=%s;" % gene_symbol
last_col += "description=%s" % description
row[-1] = last_col
if last_col[-1] == ";":
last_col = last_col[:-1]
row[-1] = last_col
if counter % 5000 == 0:
sys.stderr.write("%s%s\t%s" % ("\x08" * 80, success_counter, counter))
writer.writerow(row)
sys.stderr.write("%s/%s Done.\n" % (success_counter, counter))
def run(self):
"""
2008-12-08 if the plot under configuration is already in db, abort only if the program is gonna commit the database transaction.
2008-10-19
save figures in database if commit
"""
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(create_tables=False)
session = db.session
#session.begin()
if self.results_type==1:
ResultsClass = Stock_250kDB.ResultsMethod
snps_context_wrapper = self.dealWithSnpsContextWrapper(self.snps_context_picklef, self.min_distance, self.get_closest)
elif self.results_type==2:
ResultsClass = Stock_250kDB.ResultsByGene
else:
sys.stderr.write("Invalid results type : %s.\n"%self.results_type)
return None
hist_type = self.getHistType(self.call_method_id, self.min_distance, self.get_closest, self.min_MAF, \
self.allow_two_sample_overlapping, self.results_type, self.null_distribution_type_id)
candidate_gene_list = self.getGeneList(self.list_type_id)
if len(candidate_gene_list)<self.min_sample_size:
sys.stderr.write("Candidate gene list of %s too small: %s.\n"%(self.list_type_id, len(candidate_gene_list)))
sys.exit(4)
#candidate_gene_list = [] #2009-01-12 just to plot the histogram of pvalue
candidate_gene_set = Set(candidate_gene_list)
list_type = Stock_250kDB.GeneListType.get(self.list_type_id)
if list_type is None:
sys.exit(3)
phenotype_id2results_id_ls = self.getResultsIDLs(db, ResultsClass, self.results_type, self.phenotype_id_ls, \
self.min_distance, self.get_closest, self.min_MAF, self.call_method_id)
param_data = PassingData(results_directory=self.results_directory, candidate_gene_list=candidate_gene_list, \
min_MAF=self.min_MAF, allow_two_sample_overlapping=self.allow_two_sample_overlapping, need_the_value=1, \
do_log10_transformation=False)
#need_the_value means to get the pvalue/score
#force no log10 transformation. otherwise, transformation based on analysis_method
if self.null_distribution_type_id==2 or self.null_distribution_type_id==3: #gw-looping or random gene list
snp_info = DrawSNPRegion.getSNPInfo(db)
candidate_gene_snp_index_ls = self.get_candidate_gene_snp_index_ls(candidate_gene_set, snp_info.chr_pos_ls, snps_context_wrapper)
no_of_snps = len(snp_info.chr_pos_ls)
no_of_permutations = no_of_snps/len(candidate_gene_snp_index_ls) + 1
param_data.chr_pos2index = snp_info.chr_pos2index #pass to getGenomeWideResultFromFile
if self.null_distribution_type_id==2:
non_candidate_gene_snp_index_ls = self.get_non_candidate_gene_snp_index_ls_by_permutation(candidate_gene_snp_index_ls, no_of_snps, no_of_permutations)
elif self.null_distribution_type_id == 3:
gene_id_ls = get_total_gene_ls(db.metadata.bind)
no_of_candidate_genes = len(candidate_gene_set)
non_candidate_gene_snp_index_ls = numpy.zeros(0, numpy.int)
while len(non_candidate_gene_snp_index_ls)<no_of_snps:
non_candidate_gene_set = Set(random.sample(gene_id_ls, no_of_candidate_genes))
_non_candidate_gene_snp_index_ls = self.get_candidate_gene_snp_index_ls(non_candidate_gene_set, snp_info.chr_pos_ls, snps_context_wrapper)
non_candidate_gene_snp_index_ls = numpy.hstack((non_candidate_gene_snp_index_ls, _non_candidate_gene_snp_index_ls))
for phenotype_id, results_id_ls in phenotype_id2results_id_ls.iteritems():
if hist_type.id: #hist_type already in database
rows = Stock_250kDB.ScoreRankHistogram.query.filter_by(phenotype_method_id=phenotype_id).\
filter_by(list_type_id=self.list_type_id).filter_by(hist_type_id=hist_type.id)
if rows.count()>0 and self.commit: #2008-12-08 only skip if the database transaction is gonna commit.
row = rows.first()
sys.stderr.write("Histogram already in database. id=%s, phenotype_id=%s, list_type_id=%s, hist_type_id=%s.\n"%\
(row.id, row.phenotype_method_id, row.list_type_id, row.hist_type_id))
continue
phenotype_method = Stock_250kDB.PhenotypeMethod.get(phenotype_id)
if not phenotype_method:
continue
score_rank_data_ls = []
sys.stderr.write("Checking phenotype %s (%s) on list_type %s (%s) ...\n"%\
(phenotype_method.id, phenotype_method.short_name, list_type.id, list_type.short_name))
for results_id in results_id_ls:
try:
rm = ResultsClass.get(results_id)
score_rank_data = None
if self.null_distribution_type_id==1:
if self.results_type==1:
permData = self.prepareDataForPermutationRankTest(rm, snps_context_wrapper, param_data)
if not permData:
continue
score_rank_data = PassingData(candidate_score_ls=permData.candidate_gene_snp_value_ls, \
candidate_rank_ls=permData.candidate_gene_snp_rank_ls,\
non_candidate_score_ls=permData.non_candidate_gene_snp_value_ls, non_candidate_rank_ls=permData.non_candidate_gene_snp_rank_ls,\
analysis_method=rm.analysis_method)
del permData
elif self.results_type==2:
score_rank_data = self.getScoreRankFromRBG(rm, candidate_gene_set, self.results_directory)
elif self.null_distribution_type_id==2 or self.null_distribution_type_id==3:
genome_wide_result = self.getResultMethodContent(rm, param_data.results_directory, param_data.min_MAF, pdata=param_data)
if not genome_wide_result:
continue
score_rank_data = self.getScoreRankFromPermIndexLs(genome_wide_result, candidate_gene_snp_index_ls, non_candidate_gene_snp_index_ls)
if score_rank_data:
score_rank_data.analysis_method = rm.analysis_method
if score_rank_data:
score_rank_data_ls.append(score_rank_data)
except:
sys.stderr.write("Exception happened for results_id=%s, phenotype_id=%s.\n"%(results_id, phenotype_id))
traceback.print_exc()
sys.stderr.write('%s.\n'%repr(sys.exc_info()))
continue
if score_rank_data_ls:
score_png_data, score_svg_data = self.plotHistForOnePhenotype(phenotype_method, list_type, score_rank_data_ls, self.output_dir, data_type='score', commit=self.commit)
rank_png_data, rank_svg_data = self.plotHistForOnePhenotype(phenotype_method, list_type, score_rank_data_ls, self.output_dir, data_type='rank', commit=self.commit)
if self.commit:
score_rank_hist = Stock_250kDB.ScoreRankHistogram(phenotype_method_id=phenotype_id, list_type_id=list_type.id)
score_rank_hist.hist_type = hist_type
score_rank_hist.score_hist = score_png_data.getvalue()
score_rank_hist.score_hist_svg = score_svg_data.getvalue()
score_rank_hist.rank_hist = rank_png_data.getvalue()
score_rank_hist.rank_hist_svg = rank_svg_data.getvalue()
session.save(score_rank_hist)
session.flush()
del score_png_data, score_svg_data, rank_png_data, rank_svg_data
"""
def improveTAIRGeneGFF(self, input_fname, gene_symbol2gene_id_set,
gene_annotation, output_fname):
"""
2009-2-5
apply the improvement to any non-chromosome lines with 'ID' entry
escape ';' by '%3B', which is regarded as a separator for every "name=value"
escape ',' by '%2C', which is regarded as a separator for every "value"
esacpe gene_symbol/Alias whose value matches individual chromosome (like gene 'CHR5' = 'Gene CHR5')
2009-2-4
if the last column has 'ID' in it, find corresponding gene id using its value and add gene_symbol and description
"""
sys.stderr.write(
"Improving TAIR Gene GFF with symbols and descriptions ...\n")
import re
p_ID_acc_ver = re.compile(r'ID=(\w+)\.(\d+);')
p_ID_acc = re.compile(r'ID=(\w+);')
p_ID_protein_acc = re.compile(r'ID=(\w+)\.(\d+)-Protein;')
p_chr_name = re.compile(
r'CHR\d+$'
) #to esacpe gene_symbol/Alias whose value matches individual chromosome
delimiter = figureOutDelimiter(input_fname)
reader = csv.reader(open(input_fname), delimiter=delimiter)
writer = csv.writer(
open(output_fname, 'w'), delimiter=delimiter, lineterminator='\n'
) #lineterminator is important. GFF3Loader would break down if it's dos terminator('\r\n').
counter = 0
success_counter = 0
for row in reader:
last_col = row[-1]
tair_id = None
if p_ID_acc_ver.search(last_col):
tair_id, version = p_ID_acc_ver.search(last_col).groups()
if p_ID_acc.search(last_col):
tair_id, = p_ID_acc.search(last_col).groups()
if p_ID_protein_acc.search(last_col):
tair_id, version = p_ID_protein_acc.search(last_col).groups()
counter += 1
if tair_id is not None and row[2] != 'chromosome':
gene_id_set = getGeneIDSetGivenAccVer(tair_id,
gene_symbol2gene_id_set)
gene_id = None
if gene_id_set == None:
sys.stderr.write(
"Linking to gene id failed for %s. No such gene_symbol, %s, in gene_symbol2gene_id_set.\n"
% (last_col, tair_id))
elif len(gene_id_set) == 1:
gene_id = list(gene_id_set)[0]
success_counter += 1
elif len(gene_id_set) > 1:
sys.stderr.write("Too many gene_ids: %s, %s.\n" %
(tair_id, gene_id_set))
elif len(gene_id_set) == 0:
sys.stderr.write(
"Linking to gene id failed for %s. There is gene_symbol, %s, in gene_symbol2gene_id_set but it's empty.\n"
% (last_col, tair_id))
else:
sys.stderr.write(
"not supposed to happen: original_name=%s, gene_symbol=%s, gene_id_set=%s\n."
% (last_col, tair_id, gene_id_set))
if gene_id is not None:
gene_model = gene_annotation.gene_id2model.get(gene_id)
if gene_model is not None:
gene_commentary = gene_model.gene_commentaries[0]
gene_desc_ls = DrawSNPRegion.returnGeneDescLs(self.gene_desc_names, gene_model, gene_commentary, cutoff_length=600,\
replaceNoneElemWithEmptyStr=1)
local_gene_desc_names = map(string.upper,
self.gene_desc_names)
description = ', '.join([
': '.join(entry) for entry in zip(
local_gene_desc_names, gene_desc_ls)
])
description = description.replace(
';', '%3B'
) #escape ';', which is regarded as a separator for every "name=value"
description = description.replace(
',', '%2C'
) #escape ',', which is regarded as a separator for every "value"
if last_col[
-1] != ';': #no ; delimiter at the end, append one
last_col += ';'
gene_symbol = gene_model.gene_symbol
gene_symbol = gene_symbol.replace(';', '%3B')
gene_symbol = gene_symbol.replace(',', '%2C')
if p_chr_name.match(
gene_symbol
): #match the chromosome name, change
gene_symbol = 'Gene %s' % gene_symbol
last_col += 'Alias=%s;' % gene_symbol
last_col += 'description=%s' % description
row[-1] = last_col
if last_col[-1] == ';':
last_col = last_col[:-1]
row[-1] = last_col
if counter % 5000 == 0:
sys.stderr.write("%s%s\t%s" %
('\x08' * 80, success_counter, counter))
writer.writerow(row)
sys.stderr.write("%s/%s Done.\n" % (success_counter, counter))
