No description, website, or topics provided.
Switch branches/tags
Nothing to show
Clone or download
Latest commit 8bb79aa Aug 10, 2017
Failed to load latest commit information.
scripts clean start, python3 version added Aug 10, 2017
src clean start, python3 version added Aug 10, 2017
.gitignore clean start, python3 version added Aug 10, 2017
README fix typo README Aug 10, 2017



Launch the script /src/, the options are below.
The library MPMATH is highly recommanded for long sequences:

The script /src/ is a python3 version of the IncaRNAtion software.

    -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

    -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')

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