88 lines
2.6 KiB
Python
88 lines
2.6 KiB
Python
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#!/usr/bin/env python
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import string, sys
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class aln_record:
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"Stores one record of data from a MAQ .aln.txt file"
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field_names = (
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"read name",
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"chromosome",
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"position",
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"strand",
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"insert size from the outer coorniates of a pair",
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"paired flag",
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"mapping quality",
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"single-end mapping quality",
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"alternative mapping quality",
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"number of mismatches of the best hit",
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"sum of qualities of mismatched bases of the best hit",
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"number of 0-mismatch hits of the first 24bp",
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"number of 1-mismatch hits of the first 24bp on the reference",
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"length of the read",
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"read sequence",
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"sequence quality"
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)
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max_field_name_len = max(map(len, field_names))
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def __init__(self, obj, parse = True):
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self.fields = []
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if type(obj) == str:
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self.setValuesFromString( obj, parse );
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else:
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raise TypeError("aln_record did not recognize type: "+str(type(obj)))
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def setValuesFromString( self, line, parse = True ):
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if parse:
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formats = [str, str, int, str, int, int, int, int, int, int, int, int, int, int, str, str]
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self.fields = map( lambda f, v: f(v), formats, line.split() )
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else:
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self.fields = line.split()
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def __str__(self):
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s = ""
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for n,v in zip(aln_record.field_names, self.fields):
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s += ("%"+str(aln_record.max_field_name_len)+"s : %s\n") % (n, str(v))
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return s
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#return string.join( map( str, self.fields ), ' ')
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def id(self): return self.fields[0]
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def contig(self): return self.fields[1]
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def offset(self): return self.fields[2]-1
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def pos(self): return self.fields[2]
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# Quality of read mapping (only maq gives this field)
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def map_qual(self): return self.fields[6]
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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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class aln_file:
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def __init__(self, filename, parse=True):
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self.filename = filename
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self.parse = parse
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self.faln = open(self.filename)
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def RecordGenerator(self):
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for line in self.faln:
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yield aln_record(line, self.parse)
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raise StopIteration
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def __iter__(self):
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return self.RecordGenerator()
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if __name__ == "__main__":
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if len(sys.argv) != 2:
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print "To test aln_file class:\naln_file.py ALN_FILE"
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else:
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count = 0
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for aln in aln_file(sys.argv[1]):
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print aln
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count += 1
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#if count > 5:
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# break
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