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