Module transdecode :: Class TranssysDNADecoder
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Class TranssysDNADecoder

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Decodes genome sequences into transsys programs. The overall gene structure is:

 ...|----activator area-----|----repressor area ----|-geneStart-|--structural area--|-geneEnd...
    |<-activatorAreaLength->|<-repressorAreaLength->|

The structural area length is variable. Gene start and end can also be variable, as enabled by regular expressions.

This decoder uses the following constants:

Notice that strength of activation / repression does not depend on binding strength in this decoder.

Instance Methods [hide private]
 
__init__(self) source code
 
__str__(self) source code
 
write(self, f) source code
 
parse(self, f) source code
 
setGeneStartRE(self, r) source code
 
setGeneEndRE(self, r) source code
 
rawDNAGenes(self, genome)
separate a genome into raw genes.
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decode_transsys(self, transsys_name, genome)
construct a transsys program by decoding a genome sequence.
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Class Variables [hide private]
  savefile_magic = 'TranssysDNADecoderParameters-1.3'
Method Details [hide private]

decode_transsys(self, transsys_name, genome)

source code 

construct a transsys program by decoding a genome sequence. The process is: (1) split the genome into sequence portions that represent genes, based on the gene start and end regular expressions. (2) For each Gene, translate the structural parts of a gene into a DNABinder; the set of all DNABinders constitutes the proteome. (3) For each gene, determine the multiset of DNABinders that bind in the activating and the repressing regions, respectively. (4) Construct a transsys program of the genes and the proteome found, with promoters constructed based on (3).