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comparison bedClass.py @ 0:b001b50f2009 draft default tip

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:28:06 -0500
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-1:000000000000 0:b001b50f2009
1 #!/usr/bin/python
2
3 import os.path
4 import sys
5
6 class bed:
7 def __init__(self):
8 self.numberTargets = 0
9 self.referenceSequences = {}
10 self.referenceSequenceList = []
11
12 def openBed(self, filename):
13 if filename == "stdin": self.filehandle = sys.stdin
14 else:
15 try: self.filehandle = open(filename,"r")
16 except IOError:
17 print >> sys.stderr, "Failed to find file: ",filename
18 exit(1)
19
20 # Get a bed record.
21 def getRecord(self):
22 self.record = self.filehandle.readline()
23 if not self.record: return False
24
25 self.numberTargets = self.numberTargets + 1
26 self.ref = ""
27 self.start = 0
28 self.end = 0
29
30 # bed file should be 0-based, half-open, so the start coordinate
31 # must be that in the bed file plus one.
32 entries = self.record.rstrip("\n").split("\t")
33 self.referenceSequence = entries[0]
34
35 # Add the reference sequence to the dictionary. If it didn't previously
36 # exist append the reference sequence to the end of the list as well.
37 # This ensures that the order in which the reference sequences appeared
38 # in the header can be preserved.
39 if self.referenceSequence not in self.referenceSequences:
40 self.referenceSequences[self.referenceSequence] = True
41 self.referenceSequenceList.append(self.referenceSequence)
42
43 try: self.start = int(entries[1]) + 1
44 except:
45 text = "start position need is not an integer"
46 self.generalError(text, "start", entries[1])
47
48 try: self.end = int(entries[2])
49 except:
50 text = "end position need is not an integer"
51 self.generalError(text, "end", entries[2])
52
53 # Check that the record is a valid interval.
54 if self.end - self.start < 0:
55 print >> sys.stderr, "Invalid target interval:\n\t", self.record
56 exit(1)
57
58 return True
59
60 # Parse through the bed file until the correct reference sequence is
61 # encountered and the end position is greater than or equal to that requested.
62 def parseBed(self, referenceSequence, position):
63 success = True
64 if self.referenceSequence != referenceSequence:
65 while self.referenceSequence != referenceSequence and success: success = self.getRecord()
66
67 while self.referenceSequence == referenceSequence and self.end < position and success: success = self.getRecord()
68
69 return success
70
71 # Close the bed file.
72 def closeBed(self, filename):
73 self.filehandle.close()
74
75 # Define error messages for different handled errors.
76 def generalError(self, text, field, fieldValue):
77 print >> sys.stderr, "\nError encountered when attempting to read:"
78 if field != "": print >> sys.stderr, "\t", field, ": ", fieldValue
79 print >> sys.stderr, "\n", text
80 exit(1)