Metadata-Version: 1.0
Name: pyseqlib
Version: 0.3.1
Summary: pySeqLib: A small python library to process sequencing data.
Home-page: https://github.com/huangyh09/pyseqlib
Author: Yuanhua Huang
Author-email: yuanhua@ebi.ac.uk
License: Apache-2.0
Description: pySeqLib
        ========
        
        A small python library to process sequencing data. It is under active development.
        
        
        What's inside?
        ---------------
        
        * ``intronX``: a program to fetch sequence related features for introns: 
          1) length, 2) splice site motif strength, 3) second structure energy 
          4) frequecy of k-mers. See manual_ and example_.
        
        * ``pymfold``: a python wrap of mfold for calculate energy of RNA secondary 
          structure. We got installation issue from mfold, similar as this_. Therefore,
          we recommend using `pyRNAfold` instead.
        
        * ``pyRNAfold``: a python wrap of for another predictor, RNAfold, of RNA 
          secondary structure energy. It is from the ViennaRNA_ package, which can be 
          installed from the `source code`_, or from BioConda_.
        
        * ``motif-score``: a motif score calculate
        
        * a sequence mapper to find lariat in RNA-seq reads (under test)
        
        * a sam file resampling method
        
        .. _this: http://unafold.rna.albany.edu/?q=node/927
        .. _ViennaRNA: https://www.tbi.univie.ac.at/RNA/index.html
        .. _manual: https://github.com/huangyh09/pyseqlib/blob/master/doc/intronX_manual.rst
        .. _example: https://sourceforge.net/projects/pyseqlib/files/intronX-example/
        .. _source code: https://www.tbi.univie.ac.at/RNA/
        .. _BioConda: https://anaconda.org/bioconda/viennarna
        
        How to install?
        ---------------
        
        Pyseqlib was initially developed in Python 2 environment, hence best to be used 
        in Py2 environment. By using Anaconda platform, no matter Py2 or Py 3, it is 
        easy to set up a conda environment with Py2, for example by following commond:
        
        .. code-block:: bash
        
           conda create -n Py2 python=2.7 numpy==1.15.4 pysam==0.15.2 Cython==0.29.3 matplotlib==2.2.3
           source activate Py2
        
        Once you are in a Python 2 environment, you can download the codes from this 
        github repository and then run the following command line:
        
        ::
        
            python setup.py install
        
        Or 
        
        ::
        
            pip install -U git+https://github.com/huangyh09/pyseqlib
        
        If you don't have the root permission, add ``--user``.
        
        Rquired libraries: ``pysam``,  ``numpy``, ``Cython``.
        
        
Keywords: sequencing data processing
Platform: UNKNOWN
