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README

README

IncaRNAtion

Launch the script /src/IncaRNAtion.py, the options are below.
The library MPMATH is highly recommanded for long sequences:https://github.com/fredrik-johansson/mpmath/

  Required:
    -d <file_path> 
      A file containing the target secondary structure and an optional MSA
    -a <float> 
      The value of alpha, between 0 and 1.
      1 takes only into account the secondary structure, 0 only the MSA

  Optional:
    -m <int> 
      The max penality for an invalid base pair, -1 for infinity
    -b <int> 
      print 'n' stochasticly backtracked sequences
    -no_profile <> 
      Doesn't output a profile
    -s_gc <target_gc> <nb_samples> 
      Sampling sequences with a 0<=target_gc<=1 and a given
      number of samples 
    -gc_sec_struct <>
      Only the nucleotides with an interaction in the secondary structure
      will be considered for the GC content
    -gc_max_err <float>
      Max error from GC target allowed in sample, default 0.1
    -gc_data <file_name>
      Create a file with the given name, will print to it a first line
      the weight of 'C' and on the next the list of sampled GC content
    -t <float>
      The temperature (default 310.5K)
    -c <IUPAC sequence>
      An IUPAC sequence to constrain the outputed sequences
    -p <file_path> 
      A data file with  starting RNA profile (i.e. every lines contains
       nucleotides probability in order: 'ACGU')

  e.g.
    python IncaRNAtion -d data.txt -a 0.5 -m 20
    python IncaRNAtion -d data.txt -a 1 -m 20 -no_profile -s_gc 0.5 100
    python IncaRNAtion -d data.txt -a 0.5 -m 20 -b 5 -no_profile
    """