diff rename_tracks.py @ 0:8b19a698d90e draft

planemo upload commit b615ca3bfed9f2115f62d1af30d4726fe8ba08d8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rename_tracks.py	Mon Jun 25 15:01:41 2018 -0400
@@ -0,0 +1,69 @@
+# -*- 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
+import tempfile
+
+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 rename_bigwig(inputFile, renamedReference, nameDict, renamedFile):
+    bedGraphFile = tempfile.NamedTemporaryFile(bufsize=0)
+    chrom_sizes = tempfile.NamedTemporaryFile(bufsize=0)
+    sorted_bedGraphFile = tempfile.NamedTemporaryFile(bufsize=0)
+    renamed_sorted_bedGraphFile = tempfile.NamedTemporaryFile(bufsize=0)
+
+    subprocess.call(['bigWigToBedGraph', inputFile, bedGraphFile.name])
+    subprocess.call(['faSize', '-detailed', '-tab', renamedReference], stdout=chrom_sizes)
+    subprocess.call(['sort', '-k1,1', '-k2,2n', bedGraphFile.name], stdout=sorted_bedGraphFile)
+    rename_interval(sorted_bedGraphFile.name, nameDict, renamed_sorted_bedGraphFile.name)
+    subprocess.call(['bedGraphToBigWig', renamed_sorted_bedGraphFile.name, chrom_sizes.name, renamedFile])
+   
+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)
+    elif inputFormat == "bigwig":
+        renamedReference = sys.argv[5]
+        rename_bigwig(inputFile, renamedReference, nameDict, outputfile)
+
+if __name__ == "__main__":
+    main()
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