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Merge pull request #100 from Darcy220606/dev
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Update to 2.0.0
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@Darcy220606
Darcy220606 authored Nov 15, 2024
2 parents 83b4ffc + f5112ca commit a21c7ad
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12 changes: 11 additions & 1 deletion .gitignore
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Expand Up @@ -7,9 +7,19 @@ sample_2/
AMPcombi_summary.tsv
Ampcombi.log

test_faa/
test_files/
test_gbk/
test_optional_files/

app_orig.py
modules_orig.py
plots_orig.py

README_original.md

temp
docs/_build/

__pycache__/
ampcombi/__pycache__/
ampcombi/__pycache__/
14 changes: 10 additions & 4 deletions CHANGES.txt
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Expand Up @@ -4,7 +4,7 @@ v<0.1.2>, <date> -- minor changes.
v<0.1.3>, <10.10.2022> -- PyPi package and conda-recipe / biocontainer release.
v<0.1.4>, <18.10.2022>
-- Included a new optional argument "--complete_summary" to concatenate the results from multiple samples in one table
-- Added a universal log file, to append to an existing log file rather than creating multiple new ones every time a sample is run.
-- Added a universal log file, to append to an existing log file rather than creating multiple new ones every time a sample is run
-- The "--path_list" can be called multiple times to include a list of files from individual samples in multiple lists
v<0.1.5>, <27.10.2022> -- Initial release.
-- adapt reading of hmmer_hmmsearch output to deal with varying header lines
Expand Down Expand Up @@ -42,12 +42,18 @@ v<0.2.0>, <09.02.2024>
-- Added the submodule to cluster the AMP hits with the parameters to modify the clustering using [MMSeqs2](https://github.com/soedinglab/MMseqs2) for e.g., '--cluster_cov_mode' '--cluster_mode' '--cluster_coverage' '--cluster_seq_id' '--cluster_sensitivity' '--cluster_remove_singletons' '--cluster_retain_label' '--cluster_min_member'
-- Added the submodule to predict signaling peptide using [SignalP-6.0h](https://services.healthtech.dtu.dk/services/SignalP-6.0/)
-- Removed the HTML output for the complete summary and replaced it with shiny for python app that can be viewed using the commandline
-- Updated AMPcombi to use subcommands for ease of use with standardized and portable piplines
-- Updated AMPcombi to use subcommands for ease of use with standardized and portable pipelines
v<0.2.1>, <14.03.2024>
-- Fixed the package versions in setup
-- Adjusted readme for installation setup
-- Fixed the `./temp` dir removal step at the end of the process
-- Changed the default matrix in diamond blastp to PAM250
v<0.2.2>, <21.03.2024>
-- Added a check if ./temp dir is found before removal. This caused problems with pipeline setups.

-- Added a check if ./temp dir is found before removal. This caused problems with pipeline setups
v<2.0.0>, <XX.11.2024>
-- Added the function to use the output from [InterProScan](https://github.com/ebi-pf-team/interproscan) if supplied with `--use_interproscan` and `--interproscan_output` to remove any AMPs classified as ribosomal proteins
-- Fix DRAMP download script to remove any non aminoacid characters
-- Added APD and UniRef100 databases to identify the AMP classes
-- Removed DIAMOND alignment and replaced it by MMseqs2 search
-- Fixed error 'Nonetype' when no AMP hits are retrieved by teh set thresholds or no AMP hits aligned to the database chosen
-- Created Read the Docs for AMPcombi documentation
43 changes: 43 additions & 0 deletions LICENSE.txt
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Expand Up @@ -19,3 +19,46 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

A list of all licenses of packages installed or used in AMPcombi:

Name Version License URL
AMPcombi 2.0.0.dev0 MIT License http://pypi.python.org/pypi/AMPcombi/
Jinja2 3.1.4 BSD License https://github.com/pallets/jinja/
MarkupSafe 3.0.2 BSD License https://github.com/pallets/markupsafe/
PyYAML 6.0.2 MIT License https://pyyaml.org/
Pygments 2.18.0 BSD License https://pygments.org
Sphinx 8.1.3 BSD License https://www.sphinx-doc.org/
alabaster 1.0.0 BSD License https://alabaster.readthedocs.io/
babel 2.16.0 BSD License https://babel.pocoo.org/
biopython 1.80 Freely Distributable https://biopython.org/
certifi 2024.8.30 Mozilla Public License 2.0 (MPL 2.0) https://github.com/certifi/python-certifi
charset-normalizer 3.4.0 MIT License https://github.com/Ousret/charset_normalizer
colorama 0.4.6 BSD License https://github.com/tartley/colorama
docutils 0.21.2 BSD License; GNU General Public License (GPL); Public Domain; Python Software Foundation License https://docutils.sourceforge.io
idna 3.10 BSD License https://github.com/kjd/idna
imagesize 1.4.1 MIT License https://github.com/shibukawa/imagesize_py
iniconfig 2.0.0 MIT License https://github.com/pytest-dev/iniconfig
joblib 1.4.2 BSD License https://joblib.readthedocs.io
markdown-it-py 3.0.0 MIT License https://github.com/executablebooks/markdown-it-py
mdit-py-plugins 0.4.2 MIT License https://github.com/executablebooks/mdit-py-plugins
mdurl 0.1.2 MIT License https://github.com/executablebooks/mdurl
myst-parser 4.0.0 MIT License https://github.com/executablebooks/MyST-Parser
numpy 1.26.4 BSD License https://numpy.org
packaging 24.2 Apache Software License; BSD License https://github.com/pypa/packaging
pandas 1.5.2 BSD License https://pandas.pydata.org
pluggy 1.5.0 MIT License https://github.com/pytest-dev/pluggy
python-dateutil 2.9.0.post0 Apache Software License; BSD License https://github.com/dateutil/dateutil
pytz 2024.2 MIT License http://pythonhosted.org/pytz
requests 2.32.3 Apache Software License https://requests.readthedocs.io
six 1.16.0 MIT License https://github.com/benjaminp/six
snowballstemmer 2.2.0 BSD License https://github.com/snowballstem/snowball
sphinx-rtd-theme 3.0.2 MIT License https://github.com/readthedocs/sphinx_rtd_theme
sphinxcontrib-applehelp 2.0.0 BSD License https://www.sphinx-doc.org/
sphinxcontrib-devhelp 2.0.0 BSD License https://www.sphinx-doc.org/
sphinxcontrib-htmlhelp 2.1.0 BSD License https://www.sphinx-doc.org/
sphinxcontrib-jquery 4.1 BSD License https://github.com/sphinx-contrib/jquery/
sphinxcontrib-jsmath 1.0.1 BSD License http://sphinx-doc.org/
sphinxcontrib-qthelp 2.0.0 BSD License https://www.sphinx-doc.org/
sphinxcontrib-serializinghtml 2.0.0 BSD License https://www.sphinx-doc.org/
urllib3 2.2.3 MIT License https://github.com/urllib3/urllib3/blob/main/CHANGES.rst
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