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"author": "Julien Duc",
"author_email": "jduc@protonmail.ch",
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"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License (GPL)",
"Programming Language :: Python :: 2.7",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering"
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"description": "**************************************************\ngeoDL\n**************************************************\n\n**Please note that geoDL is in beta version, therefore expect bugs**\n\n.. image:: geoDL/logo.png\n :height: 100px\n :width: 200px\n :align: center\n\ngeoDL is a python program to download FASTQ files from `GEO-NCBI `_. The program inputs a #GEO access number and perform a search on the `EMBL-EBI/ENA `_ 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).\n\nDependencies\n------------\n- geoDL should work with both **Python3** and **Python2** but test have to be run still\n- **Beautifulsoup4**, **colorama** and **six** python package are required\n- **wget** is used internally and thus is a dependency of geoDL\n\nInstall\n-------\nOn linux and MacOSx\n\n.. code-block:: bash\n\n $ pip install --user geoDL\n\n\nNote it is possible that the flag `--pre` is needed for installing the beta version.\n\nUsage\n-------\n\n.. code-block:: bash\n\n usage: geoDL.py [-h] [--dry] [--samples [SAMPLES [SAMPLES ...]]] [--colname COLNAME]\n {geo,meta,ena} GSE|metadata|ENA\n\n {geo,meta,ena} Specify which type of input\n GSE|metadata|ENA geo: GSE accession number, eg: GSE13373\n Map the GSE accession to the ENA study accession and fetch the metadata\n\n meta: Use metadata file instead of fetching it on ENA website (bypass GEO)\n Meta data should include at minima the following columns: ['Fastq files\n (ftp)', 'Submitter's sample name']\n\n ena: ENA study accession number, eg: PRJEB13373\n Fetch the metadata directely on the ENA website\n\n optional arguments:\n -h, --help show this help message and exit\n --dry Don't actually download anything, just print the wget\n cmds\n --samples [SAMPLES [SAMPLES ...]]\n Space separated list of GSM samples to download. For\n ENA mode, subset the metadata\n --colname COLNAME Name of the column to use in the metadata file to name\n the samples\n\n\nExample\n-------\nDownload metadata and all the samples of the serie GSE13373 and rename them to their sample names:\n\n.. code-block:: bash\n\n $ geoDL geo GSE13373\n\nDownload only some samples:\n\n.. code-block:: bash\n\n $ geoDL GSE13373 -s GSM00001 GSM00003\n\nDownload use a pre downloaded metadata and use column run_alias as name for the samples: \n\n.. code-block:: bash\n\n $ geoDL meta my_metadata.txt --column run_alias\n\n\nUse a ENA code instead of a GSE code:\n\n.. code-block:: bash\n\n $ geoDL ena PRJEB13373\n\nBeta test\n---------\n- Test python2 support\n- Test handling of wget\n\nChangelog\n---------\n\n`changelog `_",
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"keywords": "geo ncbi fastq bioinformatic genomic sra",
"license": "GPL",
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