Package: autoclasswrapper
AutoClassWrapper: a Python wrapper for AutoClass C classificationAutoClass is an unsupervised Bayesian classification system.AutoClass Cis an implementation of the AutoClass algorithm made by the NASA.AutoClassWrapper is a Python wrapper to ease the use of Autoclass C.Installation and dependenciesAutoClass C installationAutoClass C can be foundhere. The installation process can be achieved with the following commands:$ wget https://ti.arc.nasa.gov/m/project/autoclass/autoclass-c-3-3-6.tar.gz
$ tar zxvf autoclass-c-3-3-6.tar.gz
$ rm -f autoclass-c-3-3-6.tar.gz
$ export PATH=$PATH:$(pwd)/autoclass-cPlease note that is you are running a 64-bit operating system, you will also need to install the standard 32-bit libraries. For instance, on a Debian/Ubuntu-like system:$ sudo apt-get install -y libc6-i386AutoClassWrapper installationDependencies:Python 3.6or abovePython libraries: NumPy, Pandas, Scipy, matplotlib, chardetAutoClassWrapper is available through the Python Package Index (PyPI):$ python3 -m pip install autoclasswrapperDocumentationDocumentation is available onReadTheDocsLicenseAutoClassWrapper is free software made available under the BSD 3-clause license. For more details see theLICENSEfile.ContributingIf you want to report a bug, request a feature, or propose an improvement use theGitHub issue system.Please, see also theCONTRIBUTINGfile.Note that this project is released with aContributor Code of
Conduct. By participating in this project you
agree to abide by its terms. See theCODE_OF_CONDUCTfile.Dev1.5.1Create new release for paper in the Journal of Open Source Software1.5.0Print AutoClass C Version on runUpdate jinja and urllib3 for security issuesRename input.merge_dataframes() to input.prepare_input_data()Increase documentation1.4.1Rename marker files to autoclass-run-success and autoclass-run-failure1.4.0Print columns with missing values one column per lineEmbed column stats in logging output1.3.0Redirect run ouput to log filesUse f-strings1.2.0Handle error while checking for autoclass versionFix missing margin in dendrogram picture1.1.0Rewrite write_dendrogram() methodRename marker files (autoclass_run_*) in snake_case1.0.0Jump to major release0.2.2Remove wrap method for resultsUpdate list of authorized characters in column names0.2.1Move function utilities to tools.pyChange defaut filename to 'autoclass'0.2.0Fix error decorator for Sphinx doc generationUse 'class' (instead of 'cluster') for consistencyMove get_autoclass_version() out of Run() classCreate file marker upon autoclass run success/failure0.1.14update missing dependencies in setup.cfgimprove PEP 8 and PEP 257 complianceadd documentation (Sphinx)0.1.13print Exception content for check_data_type()output class probability for every gene/proteinsimplify the calculation of cluster statsclass/cluster numbering starts at 1 (0-based in autoclass output)add dendrogram of classesadd reproducible run option (test only)add tests for Input() classadd tests for Output() classadd tests for Run() class0.1.12update write_cluster_stats() methods with mean/std columnoutput data+clusters in clust_data.tsv0.1.11add nohup while running autoclass script0.1.10search_autoclass_in_path() returns the PATH0.1.9check autoclass-c executable is in PATHbuilding and running script are in Run() class0.1.8add env in Popen()0.1.7add missing dependencies0.1.6move distribution package to bdist_wheel0.1.5move config options to setup.cfg0.1.4add MANIFEST.in0.1.3remove tests from Python package0.1.2add Markdown support for README descriptionBSD 3-Clause LicenseCopyright (c) 2018, Pierre Poulain
All rights reserved.Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.