Simplify the code
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@ -8,14 +8,6 @@ cdef class FastaFormat:
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self.headerFormater = HeaderFormat(True,
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self.headerFormater = HeaderFormat(True,
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tags,
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tags,
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printNAKeys)
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printNAKeys)
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# def __cinit(self):
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# self.sequenceBufferLength=1000
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# self.sequenceBuffer = malloc(self.sequenceBufferLength)
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#
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# def __dealloc__(self)
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# free(self.sequenceBuffer)
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@cython.boundscheck(False)
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@cython.boundscheck(False)
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def __call__(self, dict data):
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def __call__(self, dict data):
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@ -30,28 +22,7 @@ cdef class FastaFormat:
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brawseq = b'\n'.join(lines)
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brawseq = b'\n'.join(lines)
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return "%s\n%s" % (self.headerFormater(data),bytes2str(brawseq))
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return "%s\n%s" % (self.headerFormater(data),bytes2str(brawseq))
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# cdef char* crowseq = <char*> brawseq
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# cdef size_t needed_size = lseq + 1
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#
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# needed_size += needed_size/ 50
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#
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# if needed_size > self.sequenceBufferLength:
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# self.sequenceBufferLength=needed_size
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# self.sequenceBuffer = realloc(self.sequenceBuffer,
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# self.sequenceBufferLength
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# )
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#
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#
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# for i in range(0,lseq,60):
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# if i+60 <= lseq:
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# fasta[k:(k+60)]=seq[i:(i+60)]
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# fasta[k+60]='\n'
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# k+=61
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# else:
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# fasta[k:(k+lseq-i)]=seq[i:lseq]
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# k+=lseq-i
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