Metadata-Version: 1.1
Name: microsatellites_finder
Version: 1.2.1
Summary: Python package that searches for microsatellites in fasta sequences
Home-page: https://bitbucket.org/batterio/microsatellites_finder/
Author: Loris Mularoni
Author-email: loris.mularoni@gmail.com
License: The MIT License (MIT)
Download-URL: https://bitbucket.org/batterio/microsatellites_finder/get/1.2.1.tar.gz
Description: 
        Microsatellites Finder
        ======================
        This program searches for microsatellites in fasta sequences.  
        The available options are the following:  
        
        - ``-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.  
        - ``-o, --output-file``: path of the file to save with the results of the analysis. The coordinates of the microsatellites will be 0-based.    
        - ``-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.  
        - ``-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.  
        - ``-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.  
        - ``-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.
        - ``-a, --alphabet``: alphabet to use for the microsatellites search. The alphabet can be either **dna** for DNA or **aa** for PROTEINS. Default is "dna".
        - ``-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.
        - ``-c, --cores``: number of CPUs to use in the computation. By default it will use all the available CPUs.  
        - ``-p, --progress``: track the progress of the computation with a progress bar.  
        
        
        How to execute the program
        --------------------------
        The program can be executed by writing of your terminal:
                
            find_micro
        
        Requirements:
        -------------
        - Python 3.4+
        
        
        Installation:
        -------------
        
            pip install macrosatellites_finder
        
Keywords: repeats,microsatellites
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
