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        "author": "Loris Mularoni",
        "author_email": "loris.mularoni@gmail.com",
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        "description": "Microsatellites Finder\n======================\nThis program searches for microsatellites in fasta sequences.  \nThe available options are the following:  \n\n- ``-i, --input-fasta``: path of the fasta file containing the sequence(s) to analyze. The file can be either a plain text file or a gzip compressed file.  \n- ``-o, --output-file``: path of the file to save with the results of the analysis. The coordinates of the microsatellites will be 0-based.    \n- ``-l, --seed-length``: length of the seed of the microsatellites, i.e. the number of nucleotides that will be repeated. For instance `-l 2` will find microsatellites like ``ACACACAC`` where the seed ``AC`` is repeated 4 times.  \n- ``-r, --minimum_repetitions``: minimum number of repetitions of the seed. For instance ``-r 3`` will find microsatellites like ``CTACTACTA`` or ``CTACTACTACTA`` where the seed ``CTA`` is repeated at least 3 times. The minimum allowed value is 2 and the default value is 3.  \n- ``-im, --imperfect``: include imperfect microsatellites. With this option microsatellites repeated at least ``-r -1`` times that share the same seed and have a distance up to the \"--imperfect\" value will be merged together and will be considered as a single microsatellite. By default this option is disabled and microsatellites are kept separated.  \n- ``-s, --strict``: when ``--imperfect`` is a positive integer, this option allows to search for imperfect microsatellites only by using nucleotides that are present in the seed. For instance, if the seed is ``AT`` only the nucleotides ``A`` and ``T`` will be considered. By default this option is disabled and all the nucleotides ``ACGT`` are considered.\n- ``-a, --alphabet``: alphabet to use for the microsatellites search. The alphabet can be either **dna** for DNA or **aa** for PROTEINS. Default is \"dna\".\n- ``-f, --flanking``: length of the sequences flanking the microsatellites. The sequences will be written in the output file. Sequences that overstep the boundaries of a chromosome will be truncated. By default this option is disabled.\n- ``-c, --cores``: number of CPUs to use in the computation. By default it will use all the available CPUs.  \n- ``-p, --progress``: track the progress of the computation with a progress bar.  \n\n\nHow to execute the program\n--------------------------\nThe program can be executed by writing of your terminal:\n        \n    find_micro\n\nRequirements:\n-------------\n- Python 3.4+\n\n\nInstallation:\n-------------\n\n    pip install macrosatellites_finder",
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