73 lines
2.3 KiB
Python
Executable File
73 lines
2.3 KiB
Python
Executable File
#!/usr/bin/env python
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import string
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class align_block:
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def __init__(self, indel_count, length, mismatches):
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self.indel_count = int(indel_count)
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self.length = int(length)
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self.mismatches = int(mismatches)
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def __str__(self):
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return string.join( map( str, [self.indel_count, self.length, self.mismatches]), ' ')
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class qltout_record:
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def __init__(self, obj):
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self.fields = []
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self.align_blocks = []
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if type(obj) == str:
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self.setValuesFromString( obj );
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else:
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raise TypeError("qltout_record did not recognize type: "+str(type(obj)))
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def setValuesFromString( self, line ):
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formats = [str, int, int, int, int, int, int, int, int, int, int]
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split_line = line.split()
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self.fields = map( lambda f, v: f(v), formats, split_line[:11] )
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next_align_block = 11
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while next_align_block < len(split_line):
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self.align_blocks.append( align_block(*split_line[next_align_block:next_align_block+3]) )
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next_align_block += 3
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#print self.__str__()
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def indelled_bases(self):
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return sum([ab.indel_count for ab in self.align_blocks])
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def __str__(self):
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return string.join( map( str, self.fields ), ' ')+' '+string.join( map( str, self.align_blocks ), ' ')
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def id(self): return self.fields[1]
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def contig(self): return self.fields[6]
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def offset(self): return self.fields[7]
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def pos(self): return self.fields[7]+1
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def offset_end(self): return self.fields[8]
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def pos_end(self): return self.fields[8]+1
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def linear_start(self): return self.fields[9]
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def map_qual(self): return 100 # This only exists in maq files
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# for ILT and Merlin, we assume the same confidence for all mappings
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class qltout_file:
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def __init__(self, filename):
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self.filename = filename
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self.fqlt = open(self.filename)
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def RecordGenerator(self):
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for line in self.fqlt:
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#fields = line.rstrip("\n").split("\t")
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if not line.startswith("QUERY"):
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continue
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yield qltout_record(line) #fields)
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raise StopIteration
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def __iter__(self):
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return self.RecordGenerator()
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