GEOparse 2.0.4

Python library to access Gene Expression Omnibus Database (GEO)

Python library to access Gene Expression Omnibus Database (GEO).

GEOparse is python package that can be used to query and retrieve data from Gene Expression Omnibus database (GEO). The inspiration and the base for it is great R library GEOquery.

• Free software: BSD license

• Documentation: https://GEOparse.readthedocs.org.

Features

• Download GEO series, datasets etc. as SOFT files

• Download supplementary files for GEO series to use them locally

• Load GEO SOFT as easy to use and manipulate objects

• Prepare your data for GEO upload

Installation

At the command line:

$ pip install GEOparse

TODO

There is still work to do so any contribution is welcome. Any bug/error that you report will improve the library.

The main issues are:

• add checking for compatibility with SOFT files

• expand GEOTypes objects with useful functions for differential expression analysis

• share your idea

• add more tests - that’s always good idea :)

History

2.0.3 (2021-02-03)

• BUGFIX: shutil.move can lead to “operation not permitted” error

• Allow to download small GSE object by using how parameter

2.0.2 (2020-08-26)

• Allow to pass kwargs to open function to controll eg. encoding

2.0.1 (2020-02-20)

• prevent installation on old python versions

2.0.0 (2020-02-20)

• Drop support for python 2

• Fix issue with SRR entiries not being available through FTP server

• Better error message if entry is not available

• Better code formatting

• Some small improvements

1.2.0 (2019-08-21)

• Remove BioPython dependency - use requests instead

• Replace wget with custom file downloader

• Allow to parse GSE file partially

• Support for parallel-fastq-dump

• Allow to use proxy server (FTP)

• Fix Travis-CI issues with FTP download

• Various bugfixes

1.1.0 (2018-09-10)

• Allow parallel download of supplementary files

• Add timeout to urlopen callsq

• Bugfix: Keep logger as a module name and rename logger object to geoparse_logger. This is a breaking change.

• Bugfix: Some samples do not have table data error in python 3

• Bugfix: broken download when supplementary_files is empty or contains invalid URLs

• Some small bugfixes

1.0.5 (2018-01-12)

• Bugfix: Some samples do not have table data error in python 3

1.0.4 (2018-01-08)

• Bugfix: Empty line in the SOFT file caused an error in python 3

1.0.3 (2017-11-01)

• Bugfix: Fixed the FTP link

1.0.2 (2017-11-01)

• Bugfix: type name was depended on the order of entries

1.0.1 (2017-08-10)

• Hotfix: wrong path split in Windows

1.0.0 (2017-07-21)

• Many small bug fixes: * unknown subset types added to columns * silent=True is really silent * correct treatment of duplicated columns * illegal file names and no filtering of user input from GEO to create the file names * platform was not imported but used * fixed issues of python 2 and 3 compatibility

• Logging replaced stdout and stderr + ability to set verbosity and log file

• Return downloaded paths from download functions

• Updated documentation according to Google docstring style guide

• Tests update

• Code refactored to be more PEP-8 friendly

0.1.10 (2017-03-27)

• Important fix for SRA download

• Fix duplicated columns issue

• Python 2 and 3 open compatibility

0.1.9 (2017-03-10)

• Added property phenotype_data to access phenotype data of GSE

• Fixed windows issue with file names

• replaced default download function with wgetter

• Update documentation

• Various bugfixes

0.1.8 (2016-11-02)

Thanks to Tycho Bismeijer:

• Python 3 Compatibility

• Bio.Entrez dependency optional

0.1.7 (2016-05-30)

Thanks to Simon van Heeringen:

• bugfix in datasets with multiple associated relations

• –split-files to fastq-dump to support paired-end experiments by default

• parse a GPL that also contains series and sample information

• gsm2fastq command to make download easier

• initial Aspera download support

0.1.6 (2016-04-12)

• Bugfixes

• SRA function of GSE can now filter GSMs

0.1.5 (2016-02-03)

• Added functions to download supplementary files including raw files from SRA

0.1.4 (2015-09-27)

• Updated documentation including example

• Updated tests: they now cover 80% of library with all important functions

• Added pivot_and_annotate method to GSE object

• Bugfixes

0.1.3 (2015-08-30)

• Updated documentation

• Added pivot_samples to GSE object

• Code of GEOTypes was refactored

• All objects now have to_soft function

• Various bugfixes

0.1.2 (2015-08-23)

• Added GDS support

• Added to_soft methods to GSE, GSM and GPL

• Added DATABASE entry support to GSE and GDS

0.1.1 (2015-08-16)

• Brown-Bag release

0.1.0 (2015-08-16)

• First release on PyPI.