diff rename_tracks.py @ 0:dd6d3b009659 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rename_tracks.py	Fri Jun 22 16:25:42 2018 -0400
@@ -0,0 +1,53 @@
+# -*- coding: utf8 -*-
+
+"""
+Rename the custom evidence tracks so that the tracks use the same sequence names as the renamed reference 
+"""
+import sys
+import csv
+import subprocess
+
+def rename_interval(inputFile, nameDict, renamedFile):
+    writer = open(renamedFile, 'w')
+    with open(inputFile, 'r') as f:
+        lines = f.readlines()
+        for l in lines:
+            if not l.startswith("#"):
+                scaffold_name = l.split()[0]
+                if scaffold_name in nameDict:
+                    l = l.replace(scaffold_name, nameDict[scaffold_name])
+            writer.write(l)
+    writer.close()
+
+def rename_bam(inputFile, nameDict, renamedFile):
+    header = subprocess.Popen(['samtools', 'view', '-H', inputFile], stdout=subprocess.PIPE)
+    array_call = ['sed']
+    for k,v in nameDict.items():
+        substitute = "s/%s/%s/" % (str(k), str(v))
+        array_call.append('-e')
+        array_call.append(substitute)
+    reheader = subprocess.Popen(array_call, stdin=header.stdout, stdout=subprocess.PIPE)
+    out = open(renamedFile, 'w')
+    subprocess.Popen(['samtools', 'reheader', '-', inputFile], stdin=reheader.stdout, stdout=out)
+   
+def getNameDict(nameMapping):
+    nameDict = {}
+    with open(nameMapping, 'r') as f:
+        reader = csv.reader(f)
+        for row in reader:
+            nameDict[row[0]] = row[1]
+    return nameDict
+
+def main():
+    inputFile = sys.argv[1]
+    nameMapping = sys.argv[2]
+    inputFormat = sys.argv[3]
+    outputfile = sys.argv[4]
+    nameDict = getNameDict(nameMapping)
+    if inputFormat == "bed" or inputFormat == "gff3" or inputFormat == "gtf":
+        rename_interval(inputFile, nameDict, outputfile)
+    elif inputFormat == "bam":
+        rename_bam(inputFile, nameDict, outputfile)
+
+if __name__ == "__main__":
+    main()
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