Metadata-Version: 1.1
Name: geoDL
Version: 1.0b20
Summary: Dowload FASTQ files from GEO-NCBI with ease.
Home-page: https://gitlab.com/jduc/geoDL
Author: Julien Duc
Author-email: jduc@protonmail.ch
License: GPL
Description: **************************************************
        geoDL
        **************************************************
        
        **Please note that geoDL is in beta version, therefore expect bugs**
        
        .. image:: geoDL/logo.png
            :height: 100px
            :width: 200px
            :align: center
        
        geoDL is a python program to download FASTQ files from `GEO-NCBI <http://www.ncbi.nlm.nih.gov/geo/>`_. The program inputs a #GEO access number and perform a search on the `EMBL-EBI/ENA <http://www.ebi.ac.uk/ena/data/warehouse/search>`_ website to gather metadata and download FASTQ files. The metadata are used to rename the samples with the experiment sample names (rather than the SRR numbers).
        
        Dependencies
        ------------
        - geoDL should work with both **Python3** and **Python2** but test have to be run still
        - **Beautifulsoup4**, **colorama** and **six** python package are required
        - **wget** is used internally and thus is a dependency of geoDL
        
        Install
        -------
        On linux and MacOSx
        
        .. code-block:: bash
        
            $ pip install --user geoDL
        
        
        Note it is possible that the flag `--pre` is needed for installing the beta version.
        
        Usage
        -------
        
        .. code-block:: bash
        
            usage: geoDL.py [-h] [--dry] [--samples [SAMPLES [SAMPLES ...]]] [--colname COLNAME]
                            {geo,meta,ena} GSE|metadata|ENA
        
          {geo,meta,ena}        Specify which type of input
          GSE|metadata|ENA      geo:  GSE accession number, eg: GSE13373
                                      Map the GSE accession to the ENA study accession and fetch the metadata
        
                                meta: Use metadata file instead of fetching it on ENA website (bypass GEO)
                                      Meta data should include at minima the following columns: ['Fastq files
                                      (ftp)', 'Submitter's sample name']
        
                                ena:  ENA study accession number, eg: PRJEB13373
                                      Fetch the metadata directely on the ENA website
        
            optional arguments:
              -h, --help            show this help message and exit
              --dry                 Don't actually download anything, just print the wget
                                    cmds
              --samples [SAMPLES [SAMPLES ...]]
                                    Space separated list of GSM samples to download. For
                                    ENA mode, subset the metadata
              --colname COLNAME     Name of the column to use in the metadata file to name
                                    the samples
        
        
        Example
        -------
        Download metadata and all the samples of the serie GSE13373 and rename them to their sample names:
        
        .. code-block:: bash
        
            $ geoDL geo GSE13373
        
        Download only some samples:
        
        .. code-block:: bash
        
            $ geoDL GSE13373 -s GSM00001 GSM00003
        
        Download use a pre downloaded metadata and use column run_alias as name for the samples: 
        
        .. code-block:: bash
        
            $ geoDL meta my_metadata.txt --column run_alias
        
        
        Use a ENA code instead of a GSE code:
        
        .. code-block:: bash
        
            $ geoDL ena PRJEB13373
        
        Beta test
        ---------
        - Test python2 support
        - Test handling of wget
        
        Changelog
        ---------
        
        `changelog <changelog.md>`_
        
        
Keywords: geo ncbi fastq bioinformatic genomic sra
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
