diff bin/setTableDefaults.py @ 0:3ca58369469c draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/setTableDefaults.py	Wed Dec 06 19:01:53 2017 -0500
@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+
+import sys
+import string
+
+flankDict = {
+    "tss":2000,
+    "tes":2000,
+    "genebody":2000,
+    "exon":500,
+    "cgi":500,
+    "enhancer":1500,
+    "dhs":1000,
+}
+
+pointLabDict = {
+    "tss":"TSS",
+    "tes":"TES",
+    "genebody":"TSS,TES",
+    "exon":"Acceptor,Donor",
+    "cgi":"Left,Right",
+    "enhancer":"Enhancer",
+    "dhs":"Left,Right",
+}
+
+# FItype = {
+#     "tss":"endsite",
+#     "tes":"endsite",
+#     "genebody":"datatype",
+#     "exon":"subregion",
+#     "cgi":"subregion",
+#     "enhancer":"subregion",
+#     "dhs":"subregion"
+# }
+
+in_f = file(sys.argv[1])
+out_f = file(sys.argv[2], "w")
+out_f.write("\t".join(["Genome", "DefaultDB", "Region", "DefaultFI1", \
+                       "DefaultFI2", "DefaultFI3", "PointLab", "Flank"]) + \
+            "\n")
+
+# while(True):
+for line in in_f:
+    # line = in_f.readline()
+    # if len(line) == 0:
+    #     break;
+    # line = string.strip(line)
+
+    lineL = line.rstrip().split("\t")
+    genome = lineL[0]
+    defaultDB = lineL[1]
+    region = lineL[2]
+
+    if region == "cgi":
+        fi_1 = "NA"
+        fi_2 = "ProximalPromoter"
+        fi_3 = "protein_coding"
+    elif region == "dhs":
+        fi_1 = "H1hesc"
+        fi_2 = "ProximalPromoter"
+        fi_3 = "protein_coding"
+    elif region == "exon":
+        fi_1 = "chipseq"
+        fi_2 = "canonical"
+        fi_3 = "protein_coding"
+    elif region == "genebody":
+        fi_1 = "chipseq"
+        fi_2 = "NA"
+        fi_3 = "protein_coding"
+    elif (region == "enhancer") and (genome == "hg19"):
+        fi_1 = "H1hesc"
+        fi_2 = "genebody"
+        fi_3 = "protein_coding"
+    elif (region == "enhancer") and (genome == "mm9"):
+        fi_1 = "mESC"
+        fi_2 = "genebody"
+        fi_3 = "protein_coding"
+    out_f.write("\t".join([genome, defaultDB, region, fi_1, fi_2, fi_3, \
+                pointLabDict[region], str(flankDict[region])]) + "\n")
+    
+    # Extra: TSS and TES if region = genebody.
+    if region == "genebody":
+        region = "tss"
+        out_f.write("\t".join([genome, defaultDB, region, fi_1, fi_2, fi_3, \
+                    pointLabDict[region], str(flankDict[region])]) + "\n")
+        region = "tes"
+        out_f.write("\t".join([genome, defaultDB, region, fi_1, fi_2, fi_3, \
+                    pointLabDict[region], str(flankDict[region])]) + "\n")
+
+in_f.close()
+out_f.close()