def ne_matrix_symbols(global_variables, out_path, biotype):
out_file = open(os.path.join(out_path, "data", "ne_matrix_symbols.csv"), "w")
master_gene_table = global_variables["master_gene_table"]
# gets the header
header_list = ["symbol"]
header_list += get_gene_ne_header(global_variables)
out_file.write("\t".join(header_list) + "\n")
# gets the gene expression
for gene_ID in master_gene_table:
gene_dictionary = master_gene_table[gene_ID]
gene_symbol = gene_dictionary["SYMBOL"]
# tests for a valid gene:
valid_gene = False
if gene_dictionary["ne_flag"]:
if global_variables["GENE_BIOTYPE_FLAG"] and (gene_dictionary["BIOTYPE"] == biotype or biotype == "all_genes"):
valid_gene = True
if global_variables["GENE_BIOTYPE_FLAG"] == False:
valid_gene = True
if valid_gene:
gene_out_list = [gene_symbol]
gene_out_list += get_gene_ne(global_variables, gene_dictionary)
out_file.write("\t".join(str(x) for x in gene_out_list) + "\n")
def Mde_any_significant_annotated(global_variables, out_path, biotype, de_IDs):
out_file = open(
os.path.join(out_path, "data",
"genes_significant_in_any_des_annotated.csv"), "w")
master_gene_table = global_variables["master_gene_table"]
# gets the header
header_list = ["ID"]
header_list += get_gene_background_header(global_variables)
header_list += get_gene_mde_header(de_IDs)
header_list += get_gene_ne_header(global_variables)
header_list += get_gene_ne_stats_header(global_variables)
header_list += get_gene_annotations_header(global_variables)
out_file.write("\t".join(header_list) + "\n")
# gets the genes
for gene_ID in master_gene_table:
gene_dictionary = master_gene_table[gene_ID]
# tests for a valid gene:
valid_gene = False
present_in_any_de = False
if gene_dictionary["ne_flag"]:
if (global_variables["GENE_BIOTYPE_FLAG"] and
(gene_dictionary["BIOTYPE"] == biotype
or biotype == "all_genes")
) or global_variables["GENE_BIOTYPE_FLAG"] == False:
valid_gene = True
for de_ID in de_IDs:
if de_ID not in gene_dictionary:
valid_gene = False
else:
de_Dict = gene_dictionary[de_ID]
if not de_Dict["in_gl"]:
valid_gene = False
if de_Dict["sig"]:
present_in_any_de = True
if valid_gene and present_in_any_de:
gene_out_list = [gene_ID]
gene_out_list += get_gene_background(global_variables,
gene_dictionary)
gene_out_list += get_gene_mde(global_variables, gene_dictionary,
de_IDs)
gene_out_list += get_gene_ne(global_variables, gene_dictionary)
gene_out_list += get_gene_ne_stats(global_variables,
gene_dictionary)
gene_out_list += get_gene_annotations(global_variables,
gene_dictionary)
out_file.write("\t".join(str(x) for x in gene_out_list) + "\n")
def de_annotated_significant_downregulated(global_variables, out_path, biotype,
de_ID):
out_file = open(
os.path.join(out_path, "data",
"de_annotated_significant_downregulated.csv"), "w")
master_gene_table = global_variables["master_gene_table"]
# gets the header
header_list = ["ID"]
header_list += get_gene_background_header(global_variables)
header_list += get_gene_de_header(global_variables)
header_list += get_gene_ne_header(global_variables)
header_list += get_gene_ne_stats_header(global_variables)
header_list += get_gene_annotations_header(global_variables)
out_file.write("\t".join(header_list) + "\n")
# gets the genes
for gene_ID in master_gene_table:
gene_dictionary = master_gene_table[gene_ID]
# tests for a valid gene:
valid_gene = False
if gene_dictionary["ne_flag"] and de_ID in gene_dictionary:
de_Dict = gene_dictionary[de_ID]
if de_Dict["in_gl"] and de_Dict["sig"] and de_Dict["log2fold"] < 0:
if global_variables["GENE_BIOTYPE_FLAG"] and (
gene_dictionary["BIOTYPE"] == biotype
or biotype == "all_genes"):
valid_gene = True
if global_variables["GENE_BIOTYPE_FLAG"] == False:
valid_gene = True
if valid_gene:
gene_out_list = [gene_ID]
gene_out_list += get_gene_background(global_variables,
gene_dictionary)
gene_out_list += get_gene_de(global_variables, de_Dict)
gene_out_list += get_gene_ne(global_variables, gene_dictionary)
gene_out_list += get_gene_ne_stats(global_variables,
gene_dictionary)
gene_out_list += get_gene_annotations(global_variables,
gene_dictionary)
out_file.write("\t".join(str(x) for x in gene_out_list) + "\n")