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data_combiner.py
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data_combiner.py
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import os, sys
# combine pval, weight or annotation file and convert the file into the libSVM format
# supported by ipac c++
#
# if weight is empty, default weight is 1.0 for each instance
# if pval is empty, return error
# if annotation is empty, annotation is not used
#
#
class DataCombiner:
def combine(self, data, data_out):
if data.has_key("pval") == False:
sys.stderr.write("pval information is missing\n")
sys.exit(1)
if data.has_key("weight") == False:
sys.stderr.write("weight information is missing\n")
sys.exit(1)
if data.has_key("annotation") == False:
sys.stderr.write("annotation information is missing\n")
sys.exit(1)
# begin to process
weight_data = data["weight"]
weight_len = len(weight_data)
pval_data = data["pval"]
pval_len_m = len(pval_data)
if pval_len_m == 0:
sys.stderr.write("pval data must exist\n")
sys.exit(1)
pval_len_n = len(pval_data[0])
if pval_len_n == 0:
sys.stderr.write("pval data must exist and cannot be empty\n")
sys.exit(1)
annotation_data = data["annotation"]
annotation_len = len(annotation_data)
if weight_len != 0 and weight_len != pval_len_m:
sys.stderr.write("weight len can only be 0 or %d\n" % pval_len_m)
sys.exit(1)
if annotation_len != 0 and annotation_len != pval_len_m:
sys.stderr.write("annotation len can only be 0 or %d\n" % pval_len_m)
sys.exit(1)
os.system("rm -rf %s*" % data_out)
f_writer = open(data_out, "w")
for i in xrange(0, pval_len_m):
o_line = ""
if weight_len > 0:
o_line = "%s" % weight_data[i]
else:
o_line = "1"
v_index = 0
for j in xrange(0, pval_len_n):
o_line = "%s %d:%s" % (o_line, v_index, pval_data[i][j])
v_index += 1
if annotation_len > 0:
for j in xrange(0, len(annotation_data[i])):
o_line = "%s %d:%s" % (o_line, v_index, annotation_data[i][j])
v_index += 1
f_writer.write("%s\n" % o_line)
f_writer.close()