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