diff ratio2circos.py @ 0:e46944a59b31 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ratio2circos.py	Thu Aug 13 09:50:35 2020 -0400
@@ -0,0 +1,20 @@
+import argparse
+import math
+import os
+
+parser = argparse.ArgumentParser()
+parser.add_argument('-i', '--input', required=True, default='./output/sample.bam_ratio.BedGraph', type=str)
+parser.add_argument('-o', '--output', required=True, default='./output/sample.bam_ratio_log2_circos.txt', type=str)
+parser.add_argument('-p', '--ploidy', required=True, default=2, type=int)
+args = parser.parse_args()
+
+path = os.path.dirname(args.input)
+output = os.path.join(path, args.output)
+
+with open(args.input) as file:
+    for line in file.readlines():
+        ls = line.split()
+        if ls[0] != "track" and float(ls[3]) > 0:
+            log2_ratio = math.log2(float(ls[3]) / args.ploidy)
+            with open(output, "a") as out:
+                out.write("{}\t{}\t{}\t{}\n".format(ls[0], ls[1], ls[2], log2_ratio))