Saravanan666/pypi-org huggingface dataset:
Package: phylomito
phylomitoA python script for mitochondrial supermatrix phylogenomics.usage: phylomito.py [-h] -i [INPATH] [-o [OUTPATH]]
                    [-e [EXTENSION [EXTENSION ...]]] [-b [BOOTSTRAP]]
                    [-p [PROTEIN]] [-g [GENE_TREE]] [-d [DLOOP]]This program is licensed under GPLv3.Quick start:Save your genebank files in a folder (for example, ./genebank/) and create a folder for the output (./output/).Make sure your genebank files have the extension '.gbk' or '.gb'.Run the command:python phylomito.py -i ./genebank/ -o ./outpath/Your results will be in the ./outpath/ folder. The final tree file will be namedall_nuc.phy_phyml_tree.txtby default.Requisites:You need to installPhyML,Clustal Omega,python 3and theBiopython libraryto run this program.This program was tested on a Linux machine.How does it work:This program finds all genebank files (mitogenomes) in a folder and saves, in a multifasta file, each gene that is present in all mitogenomes.
These files are aligned with CLUSTALW and the alignment is concatenated in a single file (all_nuc.aln, by default) that contains all aligned genes from all mitogenomes.
Phyml uses this file to generate a Maximum Likelihood tree.Advanced features:You can generate an amino acid alignment and phylogeny using the -p (or --protein) flag. The default is nucleotidic alignment and phylogeny.Running the program with the -g (or --gene_tree) flag will generate a tree for every gene.Using -g along with -d (or --dloop) will generate a tree of the DLOOP region.
The supermatrix tree will also include this region. Do not use the -d flag with the -p flag, as it will translate the DLOOP region, generating gibberish.Default number of bootstrap resamples is 100. You can change this with the -b (or --bootstrap) flag.
Changing this will affect how long it takes to run the phylogeny.Common errors:The most common problem is bad formatted genebank files. The error will look like this:mitochondria1.gb
mitochondria2.gb
mitochondria3.gb
COX_1 is not a known gene. Replace the CDS gene id with one of the following:
ND1  ND2  COX1  COX2  ATP8  ATP6  ND3  ND4L  ND4  ND5  CYTB  ND6  COX3
Traceback (most recent call last):
  File "/path/phylomito/phylomito.py", line 315, in <module>
    main(args)
  File "/path/phylomito/phylomito.py", line 70, in main
    split_seqs(inpath, outpath, protein, extension, dloop)
  File "/path/phylomito/phylomito.py", line 140, in split_seqs
    gene_key = gene_dict[header]
KeyError: 'COX_1'Wheremitochondria3.gbis the file where the error was found.
In this case the solution is to edit your file and replace all occurrences ofCOX_1withCOX1.
Package: phylopandas
Bringing thePandasDataFrameto phylogenetics.PhyloPandas provides a Pandas-like interface for reading sequence and phylogenetic tree data into pandas DataFrames. This enables easy manipulation of phylogenetic data using familiar Python/Pandas functions. Finally, phylogenetics for humans!How does it work?Don't worry, we didn't reinvent the wheel.PhyloPandasis simply aDataFrame(great for human-accessible data storage) interface on top ofBiopython(great for parsing/writing sequence data) andDendroPy(great for reading tree data).PhyloPandas does two things:It offers newreadfunctions to read sequence/tree data directly into a DataFrame.It attaches a newphyloaccessorto the Pandas DataFrame. This accessor provides writing methods for sequencing/tree data (powered by Biopython and dendropy).Basic UsageSequence data:Read in a sequence file.importphylopandasasphdf1=ph.read_fasta('sequences.fasta')df2=ph.read_phylip('sequences.phy')Write to various sequence file formats.df1.phylo.to_clustal('sequences.clustal')Convert between formats.# Read a format.df=ph.read_fasta('sequences.fasta')# Write to a different format.df.phylo.to_phylip('sequences.phy')Tree data:Read newick tree datadf=ph.read_newick('tree.newick')Visualize the phylogenetic data (powered byphylovega).df.phylo.display(height=500,)ContributingIf you have ideas for the project, please share them on the project'sGitter chat.It'seasyto create new read/write functions and methods for PhyloPandas. If you
have a format you'd like to add, please submit PRs! There are many more formats
in Biopython that I haven't had the time to add myself, so please don't be afraid
to add them! I thank you ahead of time!TestingPhyloPandas includes a smallpytestsuite. Run these tests from base directory.$ cd phylopandas
$ pytestInstallInstall from PyPI:pip install phylopandasInstall from source:git clone https://github.com/Zsailer/phylopandas
cd phylopandas
pip install -e .DependenciesBioPython: Library for managing and manipulating biological data.DendroPy: Library for phylogenetic scripting, simulation, data processing and manipulationPandas: Flexible and powerful data analysis / manipulation library for Pythonpandas_flavor: Flavor pandas objects with new accessors using pandas' new register API (with backwards compatibility).
Package: phylopypruner
AboutOrthologsare genes that are related through a speciation event, whileparalogsare genes that are related through a gene duplication event.
Accurate identification of orthologs is a prerequisite for phylogenomics, since
including genes that diverged because of a gene duplication event for species
tree inference can cause an erroneous inference of speciation nodes, due to
disparencies between individual gene trees and the species tree. Unfortunately,
contaminants present in even a single taxon can cause a tree-based orthology
inference method to erroneuosly infer paralogy and unnecessarily exclude
sequences.PhyloPyPruner is a Python package for phylogenetic tree-based orthology
inference, using the species overlap method. It uses trees and alignments
inferred from the output of a graph-based orthology inference approach, such
asOrthoMCL,OrthoFinderorHaMStR, in order to obtain sets
of sequences that are 1:1 orthologous. In addition to algorithms seen in
pre-existing tree-based tools (for example,PhyloTreePruner,UPhO,AgalmaorPhylogenomic Dataset
Reconstruction), this package
provides new methods for reducing potential contamination.Figure 1.A rough overview of a tree-based orthology inference approach.Quick installationThe easiest way to install PhyloPyPruner is by using the package manager for
Python,pip:pipinstallphylopypruner# install for all userspipinstall--userphylopypruner# install for the current user onlyOnce installed, the program is located within$HOME/.local/bin. Depending on
your OS, you might have to add the directory to your$PATHto avoid typing
the entire path. Once in your path, you run the program like this:phylopyprunerDocumentationAbout PhyloPyPrunerTutorialInstallationInput dataOutput filesMethodsOptionsCiteOur manuscript is still in preparation, it will be posted here once a preprint
of the article is available.©Kocot Lab2019
Package: phylotoast
The PhyloToAST project is a collection of python code and scripts that
modify the QIIME [1] pipeline by adding/changing several
steps including: support for cluster-computing, multiple primer support
(eliminate primer bias) [2], enhanced support for species-specific
analysis, and additional visualization tools.InstallationTo install PhyloToAST from PyPI:$pipinstallphylotoastFrom source:$pythonsetup.pyinstallDocumentationFull documentation for the scripts and code is available atdocs.phylotoast.org(hosted byRead the Docs)RequirementsThe list of required modules will vary depending on which executable scripts and/or
parts of the API you may use. For this reason there are no required dependencies
that will be automatically installed along with PhyloToAST. Each executable script will
check that the required libraries are installed and will print a message if any are not
found.If you would like to install everything up front, the following is a complete list of libraries
that are used in PhyloToAST:numpyscipymatplotlib>= 1.5.0biopython>= 1.60scikit-bioscikit-learnpandasstatsmodelspalettablebiom-format>= 2.1.5h5py(for parsing BIOM v2.x format files)SourceThePhyloToAST sourceis hosted on github.CitingDabdoub, S. M.et al.PhyloToAST: Bioinformatics tools for species-level analysis and
visualization of complex microbial datasets.Sci. Rep.6, 29123; doi: 10.1038/srep29123 (2016).Publications using PhyloToASTTsigarida and Dabdoub et al.,The Influence of Smoking on the Peri-Implant
Microbiome. Journal of Dental Research, 2015;doi: 10.1177/0022034515590581Mason et al.,The subgingival microbiome of clinically healthy current
and never smokers. The ISME Journal, 2014;doi:10.1038/ismej.2014.114Dabdoub et al.,Patient-specific Analysis of Periodontal and Peri-implant Microbiomes.
Journal of Dental Research, 2013;doi: 10.1177/0022034513504950References[1] J Gregory Caporaso, et al.,QIIME allows analysis of
high-throughput community sequencing data. Nature Methods, 2010;doi:10.1038/nmeth.f.303[2] Kumar PS, et al.,Target Region Selection Is a Critical Determinant
of Community Fingerprints Generated by 16S Pyrosequencing. PLoS ONE
(2011) 6(6): e20956.doi:10.1371/journal.pone.0020956
Package: phylotypes
PhylotypesGroup features (e.g. 16s rRNA gene variable region sequence variants) placed on a common phylogenetic tree by phylogenetic distance.This is particularly useful when attempting a metanalysis of 16s rRNA gene variable region amplicons, in which the amplicons were made with different primers, etc.Input:--jplace <file>A jplace file (deduplicated) as made bypplacerorepa-ng.Output:--out <file>Path where the output should be placed inCSVformat. This will be a header-containing CSV file in long-format with two columns: phylogroup and feature-id.Parameters:--lwr-overlap <0.0 - 1.0>Minimum like-weight-ratio overlap for two placed features (e.g. sequence variants) to be pre-grouped. Default of 0.1 should be fine for most use cases.--threshold_pd <float>Phylogenetic distance at which to cluster features. Default of 1.0 corresponds roughly to somewhere between species-level and genus-level grouping for 16s rRNA V4 region amplicons.
Package: phylovega
PhyloVegaVisualize phylogenetic trees in Vega from Python.Declarative tree visualizations in Python powered by Vega.Declarative GrammarfromphylovegaimportTreeChart# Construct Vega Specificationchart=TreeChart.read_newick('tree.newick',height_scale=200,# Node attributesnode_size=200,node_color="#ccc",# Leaf attributesleaf_labels="id",# Edge attributesedge_width=2,edge_color="#000",)chart.display()Interactive treesUse Vega grammarHow does it work?PhyloVega defines a Vega grammar (specifically, a set of transforms) to draw phylogenetic trees.Why?Python is due for a simple, interactive phylogenetic tree viewer. Vega has done
most of the heavy lifting here. PhyloVega simply leverages Vega transform specifications for building interactive visualizations.In the worksHere is a list of features that will eventually make it into PhyloVega.More InteractivityCollapible Clades.Circular trees... (feel free to add to this list).InstallGet the latest release withpip:pip install phylovegaInstall the development version by cloning this repo and calling:pip install -e .DependenciesPhyloVega uses the Vega4 specification. It works out-of-the-box with JupyterLab.JupyterLab: The next generation Jupyter notebook.PhyloPandas: Pandas DataFrame for Phylogenetics
Package: phylox
PhyloXPhyloX is a python package with tools for constructing, manipulating, and analyzing phylogenetic networks.Installation as pypi package phylox is simple via pip or conda:pip install phyloxYou can load the package methods withimport phyloxin python.For more information, see thedocumentation.Citing PhyloXFor now, simply refer to the github page to cite PhyloX. Registering the software for a DOI is still on the to do list.Use of NetworkXThe implementation of PhyloX is based on NetworkX (NetworkX is distributed with the3-clause BSD license):Aric A. Hagberg, Daniel A. Schult and Pieter J. Swart, “Exploring network structure, dynamics, and function using NetworkX”, in Proceedings of the 7th Python in Science Conference (SciPy2008), Gäel Varoquaux, Travis Vaught, and Jarrod Millman (Eds), (Pasadena, CA USA), pp. 11–15, Aug 2008Citing specific functionsWhen citing PhyloX, you are most likely also using specific methods, which can be traced back to their original papers. Please take care to cite the original papers as well. A reference to the original paper should be found in the documentation of the method, or of the module containing the method.DevelopmentFor a development version, simply pull the project and in the home of the project do:pip install -e .This installs the phylox package from the source. When you change things in the source, the package gets updated as well.Releaseset new version number in master branchCHANGELOG.mdpyproject.tomlrelease current versiongit checkout release
git merge main
git tag [version number]
git push --atomic origin release [version number]Lintingprecommit is yet to be configured, for now, simply run black and isort.DocumentationDocumentation is in the docs folder, and is created uses sphinx.
to build the documentation, go to the docs folder and do:make htmlthe docs will be indocs/build/html.
Package: phylum-ci
phylum-ciPython package for handling CI and other integrationsLocal DevelopmentHere's how to set upphylum-cifor local development.Clone thephylum-cirepo locallygitclonegit@github.com:phylum-dev/phylum-ci.gitEnsurepoetryis installedInstall dependencies withpoetry, which will automatically create a virtual environment:cdphylum-ci
poetryinstallCreate a branch for local development:gitcheckout-b<name-of-your-branch>Now you can make your changes locally.When you're done making changes, check that your changes pass the tests:poetryrunpytestCommit your changes and push your branch to GitHub:gitadd.
gitcommit-m"Description of the changes goes here"gitpush--set-upstreamorigin<name-of-your-branch>Submit a pull request through the GitHub website
Package: phyper
A Python toolbox for hYPERspectral data. This toolbox includes methods for reading hyperspectral images and provides an interface for basic machine learning algorithms like decomposition and clustering.InstallationNOTEBefore being able to clone the code from this repository (either editable or non-editable), you will have to set a GitLab password (Preferences>Password) to authenticate yourself and your device.Non-editable installation(Optional) create virtual environmentconda create -n my_env python=3.8conda activate my_env1.a Directly install from PyPi directory where pyper is saved as 'phyper' (WITH h!)pip install phyperOR1.b Directly intall from gitlab repostiorypip install git+https://gitlab.kuleuven.be/u0123403/pyper.gitEditable installationUse this installation if you want to make changes to the code yourself.(Optional) create virtual environmentconda create -n my_env python=3.8conda activate my_envClone the repository to your local machinegit clone https://gitlab.kuleuven.be/u0123403/pyper.gitcd pyperUse pip to install the package in editable formatpip install -e .AcknowledgementsWritten by Remi Van Belleghem. Based on Matlab toolbox from Niels Wouters.
Package: phyplot
# <img alt=”Phyplot” src=”/docs/logo/phylograph_logo.png”># Phyplothttp://www.sciphy.org/Phyplot is a plotting library for use with Sci-Phy (statistical analysis and modelling of evolved data using phylogenetic trees).## Authors
By Chris Organ & Andrew Meade## Requirements
Python 3.8+
Sci-Phy
Package: phyprops
ContentsThe Simple Python Interface of CoolPropThe Simple Python Interface of CoolPropphyprops useASHRAEas  the reference state of enthalpy and entropytc(refrigerant)   Critical point temperaturepc(refrigerant)   Critical point pressuretx_p(t, x, refrigerant)   tx_h(t, x, refrigerant)  tx_s(t, x, refrigerant)px_t(p, x, refrigerant)   px_h(p, x, refrigerant)  px_s(p, x, refrigerant)pt_h(p, t, refrigerant)   pt_s(p, t, refrigerant)ps_h(p, s, refrigerant)   ps_t(p, s, refrigerant)   ps_x(p, s, refrigerant)ph_s(p, h, refrigerant)   ph_t(p, h, refrigerant)   ph_x(p, h, refrigerant)PropertiesUnitsymbolPressureMPapTemperature°CtSpecific enthalpykJ/kghSpecific entropykJ/(kg·K)sSteam qualityx
Package: phypy
PhyPyLibrary of tools for wireless, physical layer research, simulations, and testing.Free software: MIT licenseDocumentation:https://phypy.readthedocs.io.FeaturesTODOCreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History0.2.8 (2019-09-26)Critical fix for LS estimation regarding conjugate transposeUpdated cookiecutter template to get new versions of thingsStarted (but unfinished MIMO module)0.2.7 (2019-03-22)Fix OFDM modulation and Demodulation dropping the middle subcarrierFix EVM calculation0.2.6 (2019-03-21)Added Demodulation to OFDMAdded EVM calculation to demodulation0.2.5 (2019-03-10)Make it so the MemoryPolynomial is a superclass for PAs and DPDsAdd a memory_stride parameter for memory polynomial modeling0.2.4 (2019-03-10)Fix an issue where the DPD was limited to 7th order with 4 taps.0.2.3 (2019-03-10)Fix an issue where the memory taps in DPD were defaulting to “1” instead of 0.Change to plain LS since I didn’t trust the regularization0.2.2 (2019-03-01)Includes what is probably a working DPD0.2.1 (2019-02-18)Adds a random number seed to OFDM0.2.0 (2019-02-01)Add a DSP module with a frequency shifter0.1.1 (2019-01-23)Adds a working PA and OFDM modulator.Begins working on basic DPD0.1.0 (2019-01-22)First release on PyPI.
Package: phyra
Phyra CLIpip install phyraIntroducingPhyra is the next generation ofElder-CLIwhich has been discontinued. Now Phyra is an interactive CLI for programmers and everyone.FeaturesCreate and Delete Github Repository (Need Github personal credentials)Weather informationYoutube DownloaderAnd many more (Coming soon)RequirementsPython -https://www.python.org/Pip -https://bootstrap.pypa.io/get-pip.pyExample CommandsGithubphyra github create <repo name>phyra github delete <repo name>Weatherphyra weather -l <country/city> currentphyra weather -l <country/city> forecastYoutube Downloaderpyhra ytdl -v <video link>pyhra ytdl --video <video link>Phyra SearchFor one sentencephyra search -n <query>phyra search --now <query>For two sentences or more use " "phyra search -n "<query>"phyra search --now "<query>"Supported OSWindows :StableLinux :Not supportI'll fix soonMacOS :Uncertain(Need testers. Open issue if you want to be a tester)About PhyraPhyra was born on September 12, 2021. Made in less than 1 month. Created by 1 person. Born exactly with the Developer's birthday. Made with care. Introducing "Phyra"
Package: phys2bids
phys2bidsphys2bidsis a python3 library meant to format physiological files in BIDS.
It was born for AcqKnowledge files (BIOPAC), and at the moment it supports.acqfiles as well as.txtfiles obtained by labchart
(ADInstruments) and GE MRI files.If you usephys2bidsin your work, please support it by citing the zenodo DOI of the version you used. You can find the latest versionhereWe also support gathering all relevant citations viaDueCredit.Read the latest documentationfor more information on phys2bids!Shortcuts:RequirementsInstallationUsageHow to use phys2bidsContributing to phys2bidsDeveloper installationContributor guideCode of ConductDeveloper calls calendarTested OSsWhile all version until2.6.2were tested on Linux and Windows, starting from version2.7onward we had todrop Windows testing. The reason is related to the cost of running such tests: for each Windows test, we can run up to 8 tests on Linux instead. Partial Windows testing might be reintroduced in future releases.Hence, whilewe cannot ensure that phys2bids will run on Windows, however we don't see any reason it shouldn't. Besides, it will run on Linux Subsistems.We apologise for the discomfort.We're looking for code contributors,but any suggestion/bug report is welcome! Feel free to open issues!This project follows theall-contributorsspecification. Contributions of any kind welcome!Contributors ✨Thanks goes to these wonderful people (emoji key):Daniel Alcalá🎨Apoorva Ayyagari🖋🔣📖Katie Bottenhorn💻🧑‍🏫👀Molly Bright🖋🔣🤔Cesar Caballero Gaudes🖋🔣🤔Inés Chavarría💻Vicente Ferrer🐛💻📖👀⚠️Yaroslav Halchenko🚇Soichi Hayashi🐛Vittorio Iacovella💻François Lespinasse💻⚠️Ross Markello🐛💻🖋🤔🚇👀⚠️🧑‍🏫Stefano Moia💻🖋🔣🤔🚇📆👀📖🧑‍🏫Robert Oostenveld🤔👀David Romero-Bascones🐛💻📖Taylor Salo🤔💻👀Rachael Stickland🐛💻🔣📖📓👀Eneko Uruñuela🐛💻🚇👀⚠️🧑‍🏫merelvdthiel💻Kristina Zvolanek🔣🖋📖Marcel Zwiers🔌victox5📖LicenseCopyright 2019-2020, The Phys2BIDS community.Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
Package: phys2denoise
phys2denoiseThe project is currently under development.
Any suggestion/bug report is welcome! Feel free to open an issue.This project follows theall-contributorsspecification. Contributions of any kind welcome!Contributors ✨Thanks goes to these wonderful people (emoji key):Cesar Caballero Gaudes💻🤔Raphaël Fournier💻📓📖Tomas Lenc🐛⚠️rzlim08💻⚠️Ross Markello🚇🧑‍🏫Stefano Moia🔣🚇📆💻🤔📖🧑‍🏫Alice Patin💻Taylor Salo💻🤔👀Inés Chavarría🚇Kristina Zvolanek🚇👀📓LicenseCopyright 2019, The phys2denoise community.Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
Package: physalia
[![Build Status](https://travis-ci.org/TQRG/physalia.svg?branch=master)](https://travis-ci.org/TQRG/physalia)[![PyPI version](https://badge.fury.io/py/physalia.svg)](https://badge.fury.io/py/physalia)[![PyPI downloads](https://img.shields.io/pypi/d/physalia.svg)](https://pypi.python.org/pypi/physalia)[![PyPI status](https://img.shields.io/pypi/status/physalia.svg)](https://pypi.python.org/pypi/physalia)[![Code Health](https://landscape.io/github/TQRG/physalia/master/landscape.svg?style=flat)](https://landscape.io/github/TQRG/physalia/master)# PhysaliaEnergy measurement framework for Mobile Apps.More info and documentation in the [website](https://tqrg.github.io/physalia/).## Install```$ pip install https://github.com/luiscruz/PyMonsoon$ pip install physalia```## ExampleThe simplest way to measure something:```from physalia.power_meters import MonsoonPowerMeterfrom time import sleep# change voltage and serial number accordingly:power_meter = MonsoonPowerMeter(voltage=3.8, serial=12886)power_meter.start()sleep(2) # some workenergy_consumption, duration, error_flag = power_meter.stop()```Several things need to be done to make sure we can measure energy consumption in Android devices (e.g., setup WiFi control and disable USB).Physalia takes care of that already:````from physalia.power_meters import MonsoonPowerMeterfrom physalia.energy_profiler import AndroidUseCasefrom time import sleep# change voltage and serial number accordingly:power_meter = MonsoonPowerMeter(voltage=3.8, serial=12886)def run(usecase):sleep(2) # some workuse_case = AndroidUseCase('login','path/to/apk','com.test.app','0.0',prepare=None,run=run,cleanup=None)measurement = use_case.run(power_meter=power_meter)print(measurement)````## ContributingPlease help us improve this library!If you have ideas for new features or anything behaves unexpectedly please report an issue.If you find an issue you can actually help fixing please make a pull request of your code.### Running testsTo run all tests and checks locally run:`$ detox -e py27,py36`