Metadata-Version: 1.1
Name: GTsegments
Version: 0.21
Summary: UNKNOWN
Home-page: UNKNOWN
Author: Philippe Bordron
Author-email: philippe.bordron+GTsegments@gmail.com
License: LGPL
Description: Genomic & Transcriptomic segments (GTsegments)
        ==========================================
        
        This program is design to work with
        ``python 2.7``, ``python 3.2+`` and ``pypy``. It needs the following libraries:
        
        - `Biopython <https://pypi.python.org/pypi/biopython/>`_
        - `NetworkX <https://pypi.python.org/pypi/networkx/>`_
        - `numpy <https://pypi.python.org/pypi/numpy>`_ (please follow the `numpypy install process <http://pypy.org/download.html#installing-numpy>`_ for ``pypy``)
        - `progressbar2 <https://pypi.python.org/pypi/progressbar2>`_
        - `UFx <https://pypi.python.org/pypi/UFx>`_
        
        
        Parameters
        ----------
        .. code-block::
        
            gts.py [-h] [--genome_type {gbk,tsv,seq}] [--graph_type {gexf,list}]
                          [-min INT] [-max INT] [-d THRESHOLD] [--no_filter] [-o FILE]
                          [-no_dom] [-m | --no_gene_list] [-q]
                          COEXP_GRAPH [GENOME [GENOME ...]]
        
            Compute the list of GTsegments from a genome and a coexpression network.
        
            example:
            gts.py -min 2 -max 50 -d 0.6 coexp_graph.gexf genome.gbk
        
            positional arguments:
              COEXP_GRAPH           Coexpression graph
              GENOME                genome file(s) containing genomic organization of
                                    chromosomes
        
            optional arguments:
              -h, --help            show this help message and exit
              -q, --quiet           Quiet mode: display only critical errors
        
            File type:
              --genome_type {gbk,tsv,seq}
                                    Type of the genome file(s) (default: gbk)
              --graph_type {gexf,list}
                                    Type of the coexpression graph file (default: gexf)
        
            GTsegments size:
              -min INT, --min_size INT
                                    Minimum length of a GTsegment (default: 2)
              -max INT, --max_size INT
                                    Maximum length of a GTsegment (default: maximum
                                    possible)
        
            Density option:
              -d THRESHOLD, --density THRESHOLD
                                    Select GTsegments with a genomic density ≥ THRESHOLD
                                    in ]0,1] (default: 0.6)
              --no_filter           Do not apply density filtering
        
            Output options:
              -o FILE, --output FILE
                                    Output file name
              -no_dom, --no_domination
                                    Keep all the GTsegments instead of the dominant ones
              -m, --matrix          Output the density matrix instead of the listing of
                                    GTsegments
              --no_gene_list        Do not add the gene list column in the listing of
                                    GTsegments
        
        Example
        -------
        
        seq.txt
        
        .. code-block::
        
            1
            2
            3
            4
            5
            6
            7
            8
            9
            10
            11
            12
            13
            14
            15
            16
            17
            18
            19
            20
            21
            22
            23
            24
            25
            #26
        
        
        graph.txt
        
        .. code-block::
        
            2       4
            4       5
            7       8
            6       9
            6       10
            9       10
            12      16
            14      15
            14      16
            14      18
            11      17
            17      23
            25      1
            # The node 26 does not exist in the genome (commented) and will ignored
            25      26
        
        The following command ...
        
        .. code-block::
        
            gts.py graph.txt seq.txt --graph_type list --genome_type seq
        
        will produce the following output:
        
        .. code-block::
        
            chromosome	start	end	length	active_genes	density	list_of_active_genes
            seq.txt	2	5	4	3	0.75	2 4 5
            seq.txt	4	5	2	2	1.0	4 5
            seq.txt	6	10	5	3	0.6	6 9 10
            seq.txt	7	8	2	2	1.0	7 8
            seq.txt	9	10	2	2	1.0	9 10
            seq.txt	12	16	5	4	0.8	12 14 15 16
            seq.txt	12	18	7	5	0.714285714286	12 14 15 16 18
            seq.txt	14	16	3	3	1.0	14 15 16
            seq.txt	14	18	5	4	0.8	14 15 16 18
            seq.txt	25	1	2	2	1.0	25 1
        
Keywords: bioinformatics Genome Genomic Transcriptome Trancriptomic GTsegments
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Operating System :: OS Independent
