diff tools/vcf_tools/bedClass.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/vcf_tools/bedClass.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,80 @@
+#!/usr/bin/python
+
+import os.path
+import sys
+
+class bed:
+  def __init__(self):
+    self.numberTargets = 0
+    self.referenceSequences = {}
+    self.referenceSequenceList = []
+
+  def openBed(self, filename):
+    if filename == "stdin": self.filehandle = sys.stdin
+    else:
+      try: self.filehandle = open(filename,"r")
+      except IOError:
+        print >> sys.stderr, "Failed to find file: ",filename
+        exit(1)
+
+# Get a bed record.
+  def getRecord(self):
+    self.record = self.filehandle.readline()
+    if not self.record: return False
+
+    self.numberTargets = self.numberTargets + 1
+    self.ref = ""
+    self.start = 0
+    self.end = 0
+
+# bed file should be 0-based, half-open, so the start coordinate
+# must be that in the bed file plus one.
+    entries = self.record.rstrip("\n").split("\t")
+    self.referenceSequence = entries[0]
+
+# Add the reference sequence to the dictionary.  If it didn't previously
+# exist append the reference sequence to the end of the list as well. 
+# This ensures that the order in which the reference sequences appeared
+# in the header can be preserved.
+    if self.referenceSequence not in self.referenceSequences:
+      self.referenceSequences[self.referenceSequence] = True
+      self.referenceSequenceList.append(self.referenceSequence)
+
+    try: self.start = int(entries[1]) + 1
+    except:
+      text = "start position need is not an integer"
+      self.generalError(text, "start", entries[1])
+
+    try: self.end = int(entries[2])
+    except:
+      text = "end position need is not an integer"
+      self.generalError(text, "end", entries[2])
+
+# Check that the record is a valid interval.
+    if self.end - self.start < 0:
+      print >> sys.stderr, "Invalid target interval:\n\t", self.record
+      exit(1)
+
+    return True
+
+# Parse through the bed file until the correct reference sequence is
+# encountered and the end position is greater than or equal to that requested.
+  def parseBed(self, referenceSequence, position):
+    success = True
+    if self.referenceSequence != referenceSequence:
+      while self.referenceSequence != referenceSequence and success: success = self.getRecord()
+
+    while self.referenceSequence == referenceSequence and self.end < position and success: success = self.getRecord()
+
+    return success
+
+# Close the bed file.
+  def closeBed(self, filename):
+    self.filehandle.close()
+
+# Define error messages for different handled errors.
+  def generalError(self, text, field, fieldValue):
+    print >> sys.stderr, "\nError encountered when attempting to read:"
+    if field != "": print >> sys.stderr, "\t", field, ":             ", fieldValue
+    print >> sys.stderr,  "\n", text
+    exit(1)