def format_our_single(db_cursor, output):
header = ["our_name",
"ecocyc_id",
"type",
"our_start",
"our_end",
"result",
"their_name",
"their_start",
"their_end",
"their_strand",
"distance",
"interactions",
"odds_ratio"]
fl = open(output, "wb")
fl.write("%s\n" % "\t".join(header))
# keep going over the results until done
row = db_cursor.fetchone()
if row is not None:
print row.keys()
names_to_data = {}
while row is not None:
values_list = []
if row["match_first"]:
values = [row["rna1_name"],
row["rna1_ecocyc_id"],
row["first_type"],
row["our.start_1"],
row["our.end_1"],
"true",
row["name"],
row["start_1"],
row["end_1"],
row["strand_1"],
row["distance_1"],
row["interactions"],
row["odds_ratio"]]
values_list.append(values)
if row["match_second"]:
values = [row["rna2_name"],
row["rna2_ecocyc_id"],
row["second_type"],
row["start_2"],
row["end_2"],
"true",
row["name"],
row["start_1"],
row["end_1"],
row["strand_2"],
row["distance_2"],
row["interactions"],
row["odds_ratio"]]
values_list.append(values)
if not row["match_first"] and not row["match_second"]:
if row["closest_1"] < row["closest_2"]:
values = [row["rna1_name"],
row["rna1_ecocyc_id"],
row["first_type"],
row["our.start_1"],
row["our.end_1"],
"false",
row["name"],
row["start_1"],
row["end_1"],
row["strand_1"],
row["closest_1"],
row["interactions"],
row["odds_ratio"]]
else:
values = [row["rna2_name"],
row["rna2_ecocyc_id"],
row["second_type"],
row["start_2"],
row["end_2"],
"false",
row["name"],
row["start_1"],
row["end_1"],
row["strand_2"],
row["closest_2"],
row["interactions"],
row["odds_ratio"]]
values_list.append(values)
for curr_values in values_list:
TableFormatter._add_names_to_data(names_to_data, curr_values)
fl.write("%s\n" % "\t".join(str(val) for val in curr_values))
# print values
row = db_cursor.fetchone()
fl.close()
TableFormatter._sort_names_to_data(names_to_data)
fl = open("%s.sorted" % output, "wb")
fl.write("%s\n" % "\t".join(header))
for curr in TableFormatter._sort_names_to_data(names_to_data):
fl.write("%s\n" % "\t".join(str(val) for val in curr))
fl.close()
def format_our_single(db_cursor, output):
header = [
"our_name", "ecocyc_id", "type", "our_start", "our_end", "result",
"their_name", "their_start", "their_end", "their_strand", "distance",
"interactions", "odds_ratio"
]
fl = open(output, "wb")
fl.write("%s\n" % "\t".join(header))
# keep going over the results until done
row = db_cursor.fetchone()
if row is not None:
print row.keys()
names_to_data = {}
while row is not None:
values_list = []
if row["match_first"]:
values = [
row["rna1_name"], row["rna1_ecocyc_id"], row["first_type"],
row["our.start_1"], row["our.end_1"], "true", row["name"],
row["start_1"], row["end_1"], row["strand_1"],
row["distance_1"], row["interactions"], row["odds_ratio"]
]
values_list.append(values)
if row["match_second"]:
values = [
row["rna2_name"], row["rna2_ecocyc_id"], row["second_type"],
row["start_2"], row["end_2"], "true", row["name"],
row["start_1"], row["end_1"], row["strand_2"],
row["distance_2"], row["interactions"], row["odds_ratio"]
]
values_list.append(values)
if not row["match_first"] and not row["match_second"]:
if row["closest_1"] < row["closest_2"]:
values = [
row["rna1_name"], row["rna1_ecocyc_id"], row["first_type"],
row["our.start_1"], row["our.end_1"], "false", row["name"],
row["start_1"], row["end_1"], row["strand_1"],
row["closest_1"], row["interactions"], row["odds_ratio"]
]
else:
values = [
row["rna2_name"], row["rna2_ecocyc_id"],
row["second_type"], row["start_2"], row["end_2"], "false",
row["name"], row["start_1"], row["end_1"], row["strand_2"],
row["closest_2"], row["interactions"], row["odds_ratio"]
]
values_list.append(values)
for curr_values in values_list:
TableFormatter._add_names_to_data(names_to_data, curr_values)
fl.write("%s\n" % "\t".join(str(val) for val in curr_values))
# print values
row = db_cursor.fetchone()
fl.close()
TableFormatter._sort_names_to_data(names_to_data)
fl = open("%s.sorted" % output, "wb")
fl.write("%s\n" % "\t".join(header))
for curr in TableFormatter._sort_names_to_data(names_to_data):
fl.write("%s\n" % "\t".join(str(val) for val in curr))
fl.close()
