Merge pull request #7 from DanielFaulkner/SortUtility

New annotation sort utility and changes to trackobj class header line.

annosort.py

@@ -0,0 +1,47 @@
+#!/usr/bin/python3
+# annosort
+#
+# A terminal prompt interface to sort entries within an annotation file.
+#
+# By Daniel R Faulkner
+
+from lib import libAnnoSort
+from lib import libAnnoShared
+import argparse
+
+## Command line options:
+### Parse the command line arguments
+parser = argparse.ArgumentParser(description="Sort annotation file by genomic position")
+# Arguments:
+# Required
+parser.add_argument("input", help="Input filename", type=argparse.FileType('r'))
+# Optional
+parser.add_argument("-o","--output", help="Output filename", type=argparse.FileType('w'))
+parser.add_argument("-s","--status", help="View current sort status", action="store_true")
+
+# Any commands entered without a flag
+args = parser.parse_args()
+
+# Run the command
+print("Indexing reference file")
+trackobj = libAnnoShared.loadTrackFile(args.input)
+if args.status:
+    # Display the current status of the annotation file
+    sortstr = "NO"
+    orderstr = "NO"
+    if trackobj.ordered:
+        orderstr = "YES"
+    if trackobj.sorted:
+        sortstr = "YES"
+    print("Annotation file grouped by chromosome: "+orderstr)
+    print("Annotation file sorted by start position: "+sortstr)
+elif args.output:
+    # Sort the file
+    libAnnoSort.sort(trackobj,args.output)
+else:
+    print("Status [-s] or Output filename [-o] option required")
+
+# Close files
+args.input.close()
+if args.output:
+    args.output.close()

lib/libAnnoShared.py

@@ -204,7 +204,11 @@ def __init__(self, fileobj, filetype="", fixedannotype="", indexlines=0, smallon
             self.type=filetype.upper()
         # Store the first line incase it is a header line needed later
         self.fileobj.seek(0)
-        self.header = self.fileobj.readline()
+        line = self.fileobj.readline()
+        self.header = line              # Store the first line as a header regardless
+        while line[0]=="#":
+            self.header = line          # Replace with the last comment line if multiple lines are present
+            line = self.fileobj.readline()
         self.fileobj.seek(0)
         # Index the file for faster access times later
         self.indexFile()

lib/libAnnoSort.py

@@ -0,0 +1,41 @@
+# libAnnoSort
+# Functions related to the sorting of annotation files.
+#
+# By Daniel R Faulkner
+
+from lib import libAnnoShared
+
+# Groups annotations within a file by chromsome and sorts by start position.
+# Example usage:
+#trackobj = libAnnoShared.loadTrackFile(open("AnnotationFilename"))     # Create track object from file
+#sort(trackobj, open('OutputFilename','w'))                             # Perform sort
+def sort(trackobj, outputfile):
+    """Sort an annotation file by genomic position"""
+    trackobj.fileobj.seek(0)
+    # Copy any preceeding comment lines across unaltered
+    line = trackobj.fileobj.readline()
+    while line[0]=="#":
+        outputfile.write(line)
+        line = trackobj.fileobj.readline()
+    # Sort and store the chromosome list
+    chrlist = sorted(trackobj.chrIndex)
+    for chromsome in chrlist:
+        chrlineindex = []
+        trackobj.fileobj.seek(trackobj.chrIndex.get(chromsome.upper()))
+        # Create a list of alignment start positions and line positions
+        line = trackobj.fileobj.readline()
+        while line:
+            annoentry = libAnnoShared.Annotation(line, trackobj.type, trackobj.header)
+            if annoentry.chrName.upper()==chromsome:
+                chrlineindex.append([annoentry.alignStart,trackobj.fileobj.tell()-len(line)])
+            elif annoentry.chrName.upper()!=chromsome and trackobj.ordered==1:
+                line = None
+            if line:
+                line = trackobj.fileobj.readline()
+        # Sort the start positions
+        sortedlinestarts = sorted(chrlineindex)
+        # Write out the lines in the correct order
+        for item in sortedlinestarts:
+            trackobj.fileobj.seek(item[1])
+            line = trackobj.fileobj.readline()
+            outputfile.write(line)