def run(self):
"""
--db_connect()
--get_gene_id2gene_symbol()
--get_go_id2name()
--get_mcl_id2pred_go_id2gene_id_set_from_db()
--get_prot_interaction_graph()
--get_gene_id_set()
--get_mt_no2gene_id_set()
--get_go_id2gene_set_from_db()
--get_mcl_id2mt_no_set()
--draw_all_patterns()
--draw_augmented_PI_graph()
--draw_pattern()
2006-11-21
add prot_interaction_graph
2006-12-29
split draw_all_patterns()
add another way to call draw_all_patterns() through pattern_id_list
"""
conn, curs = db_connect(self.hostname, self.dbname, self.schema)
gene_id2gene_symbol = get_gene_id2gene_symbol(curs, self.tax_id)
go_id2name = get_go_id2name(curs)
if not os.path.isdir(self.output_dir):
os.makedirs(self.output_dir)
#mcl_id2pred_go_id2gene_id_set = self.get_mcl_id2pred_go_id2gene_id_set(input_fname)
mcl_id2pred_go_id2gene_id_set = self.get_mcl_id2pred_go_id2gene_id_set_from_db(curs, self.input_fname, self.gene_p_table)
prot_interaction_graph = self.get_prot_interaction_graph(curs, self.prot_interaction_table, self.tax_id)
gene_id_set = self.get_gene_id_set(curs, self.gene_table)
comp_mt_no2gene_id_set = self.get_mt_no2gene_id_set(curs, self.comp_tf_mapping_table, gene_id_set)
expt_mt_no2gene_id_set = self.get_mt_no2gene_id_set(curs, self.expt_tf_mapping_table, gene_id_set)
go_id2gene_set = self.get_go_id2gene_set_from_db(curs, self.go_table)
comp_mcl_id2mt_no_set = self.get_mcl_id2mt_no_set(curs, self.comp_cluster_bs_table)
expt_mcl_id2mt_no_set = self.get_mcl_id2mt_no_set(curs, self.expt_cluster_bs_table)
for pattern_id in self.pattern_id_list:
self.draw_all_patterns(curs, pattern_id, mcl_id2pred_go_id2gene_id_set, comp_mt_no2gene_id_set, \
expt_mt_no2gene_id_set, go_id2gene_set, comp_mcl_id2mt_no_set, expt_mcl_id2mt_no_set,\
self.pattern_table, self.output_dir, gene_id2gene_symbol, go_id2name, prot_interaction_graph)
pattern_id = raw_input("Please input a pattern id:")
while pattern_id:
self.draw_all_patterns(curs, pattern_id, mcl_id2pred_go_id2gene_id_set, comp_mt_no2gene_id_set, \
expt_mt_no2gene_id_set, go_id2gene_set, comp_mcl_id2mt_no_set, expt_mcl_id2mt_no_set,\
self.pattern_table, self.output_dir, gene_id2gene_symbol, go_id2name, prot_interaction_graph)
pattern_id = raw_input("Please input a pattern id:")
def run(self): """ 2006-11-15 """ conn, curs = db_connect(self.hostname, self.dbname, self.schema) if self.running_type==1: go_id2gene_set = self.get_informative_node2gene_set(self.go_fname) elif self.running_type==2: go_id2gene_set = self.get_go_id2gene_set_from_prediction_table(curs, self.p_gene_table, self.gene_p_table) go_id2name = get_go_id2name(curs) self.draw_GO_node_structure_graph(go_id2gene_set, self.fig_output_fname,\ self.sharing_threshold, label_map=go_id2name, is_to_show=0)
def run(self): """ 07-07-05 --db_connect() --get_gene_no2id() --get_go_id2name() --fetch_predicted_function() --gene_no2go_id_set_from_gene_p_table() --output() --p_go_id_set_list_distinct() """ conn, curs = db_connect(hostname, dbname) gene_no2id = get_gene_no2id(curs) go_id2name =get_go_id2name(curs) gene_no2go_id_set_list, go_id_set_list = self.fetch_predicted_function(self.schema_list,self.netmine_fname_list) self.output(curs, gene_no2go_id_set_list,go_id_set_list, support, prefix, gene_no2id, go_id2name, self.schema_list)
def run(self):
"""
10-31-05
2006-09-26
modify it to be compatible with the modified pipeline from haifeng
2006-11-06
add type
2006-12-13
use font_path and font_size
--form_schema_tables()
--db_connect()
--get_char_dimension()
--get_no_of_p_funcs_gene_no_go_no_list()
--get_recurrence_go_no_rec_array_cluster_id_ls()
--get_go_no2name()
--draw_function_map()
--draw_gene_function_map()
--get_recurrence_rec_array_bs_no_list()
--get_mt_no2tf_name()
--draw_tf_map()
"""
schema_instance = form_schema_tables(self.inputfname, self.acc_cutoff, self.lm_bit)
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
font = ImageFont.truetype(self.font_path, self.font_size)
char_dimension = font.getsize('a')
#char_dimension = get_char_dimension()
#go_no2name = get_go_no2name(curs)
go_no2name = get_go_id2name(curs)
if self.type==1:
go_no2go_id = get_go_no2go_id(curs)
given_p_gene_set = p_gene_id_set_from_gene_p_table(curs, schema_instance.gene_p_table)
no_of_p_funcs_gene_no_go_no_list, mcl_id2go_no_set = self.get_no_of_p_funcs_gene_no_go_no_list_from_db(curs, \
schema_instance.p_gene_table, given_p_gene_set, go_no2go_id)
elif self.type==2:
no_of_p_funcs_gene_no_go_no_list, mcl_id2go_no_set = self.get_no_of_p_funcs_gene_no_go_no_list_from_file(self.inputfname)
recurrence_go_no_rec_array_cluster_id_ls, no_of_datasets, mcl_id2enc_recurrence = \
self.get_recurrence_go_no_rec_array_cluster_id_ls(curs, self.pattern_table, mcl_id2go_no_set)
no_of_functions = len(recurrence_go_no_rec_array_cluster_id_ls)
function_map_output_fname = '%s.function_map.png'%self.output_prefix
go_no2index, function_name_region = self.draw_function_map(recurrence_go_no_rec_array_cluster_id_ls, no_of_datasets,\
go_no2name, function_map_output_fname, self.function_name_length, char_dimension, no_of_functions, font)
gene_function_map_output_fname = '%s.gene_function_map.png'%self.output_prefix
self.draw_gene_function_map(no_of_p_funcs_gene_no_go_no_list, go_no2index, function_name_region,\
gene_function_map_output_fname, self.function_name_length, char_dimension, no_of_functions, font)
#tf_map requires mcl_id2enc_recurrence and no_of_datasets from above
recurrence_rec_array_bs_no_list = self.get_recurrence_rec_array_bs_no_list(curs, self.cluster_bs_table, mcl_id2enc_recurrence)
mt_no2tf_name = get_gene_id2gene_symbol(curs, tax_id=9606)
#mt_no2tf_name = get_mt_no2tf_name()
tf_map_output_fname = '%s.tf_map.png'%self.output_prefix
self.draw_tf_map(recurrence_rec_array_bs_no_list, no_of_datasets, mt_no2tf_name, \
tf_map_output_fname, self.function_name_length, char_dimension, font)
