Mercurial > repos > devteam > vcf_filter
diff bedClass.py @ 0:4502baf7ac42 draft default tip
Imported from capsule None
author | devteam |
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date | Thu, 23 Jan 2014 12:32:12 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bedClass.py Thu Jan 23 12:32:12 2014 -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)