transformation to bed implemented

.gitignore

+.idea/
+venv/
+*.bed
+*.txt.gz

generate.py

+import gzip
+import ntpath
+import sys
+
+
+def transform(input_line):
+    chromosome = input_line[2]
+    chromosome_start = input_line[4]
+    chromosome_end = input_line[5]
+    name = input_line[12]
+    score = input_line[11]
+    strand = input_line[3]
+    thick_start = input_line[6]
+    thick_end = input_line[7]
+    item_rgb = "255,0,0"
+    block_count = input_line[8]
+    block_starts = []
+    block_sizes = []
+
+    block_starts_tmp = input_line[9].split(",")
+    block_ends_tmp = input_line[10].split(",")
+    for i in range(0, int(block_count)):
+        block_starts.append(block_starts_tmp[i])
+        block_sizes.append(str(int(block_ends_tmp[i]) - int(block_starts_tmp[i])))
+    output = [chromosome, chromosome_start, chromosome_end, name, score, strand, thick_start, thick_end, item_rgb,
+              block_count, ",".join(block_sizes), ",".join(block_starts)]
+    return output
+
+
+inputFile = sys.argv[1]
+outputFile = ntpath.basename(inputFile).replace(".txt.gz", "") + ".bed"
+
+output = open(outputFile, "w")
+
+with gzip.open(inputFile, 'rt') as hIN:
+    for line in hIN:
+        F = line.rstrip('\n').split('\t')
+        output_line = transform(F)
+        print("\t".join(output_line), file=output)
+output.close()