Saravanan666/pypi-org huggingface dataset:
Package: mbexcelexport2csv
mbExcelExport2csvThis simple command line tool can be used to take an.xlsfile (that is actually formatted in xml), and output it as a csv. The main use case in mind here is to convert excel files downloaded from ManageBac and upload them to Google Sheets, without having to open Excel.This tool provides the exact same output if the xls file was opened in Excel, copied, and then pasted into Google Sheets, but without requiring Excel.Getting StartedRequires Python 3.6.1 or above. Install Python 3 at python.org. Installing Python also installs a package manager (called pip) that can install the command mbExcelExport2csv into your command line environment.pip3 install mbExcelExport2csvThen, open the mini app using this command:mbExcelExport2csv guiFor those who want the command line, use:mbExcelExport2csv cmdSee "Command Line" below for more infoUpgradeShould you need to update to the latest version, you can do:pip install --upgrade mbExcelExport2csvCommand LineAfter pip install worked, it is now installed on your path, and the command mbExcelExport2csv is now available:mbExcelExport2csv cmd ~/path/to/xml.xls ~/path/to/output.csvYou can then import the csv file into Google Sheets. The delimiter used is a comma.Alternatively, on Mac, you can skip the step of saving the csv file, and just run the following fancy command line, and it'll be on your clipboard.mbExcelExport2csv cmd ~/path/to/xml.xls - | pbcopyJust paste into "A1" cell of your Google Sheet, Data -> Split Text into Columns.
Package: mb-excelexport-2csv
mb-excelexport-2csvThis simple command line tool can be used to take an.xlsfile (that is actually formatted in xml), and output it as a csv. The main use case in mind here is to convert excel files downloaded from ManageBac and upload them to Google Sheets, without having to open Excel.This tool provides the exact same output if the xls file was opened in Excel, copied, and then pasted into Google Sheets, but without requiring Excel.Getting StartedRequires Python 3.6.1 or above. Install Python 3 at python.org. Installing Python also installs a package manager (called pip) that can install the commandmb_excelexport_2csvinto your command line environment.pip3 install mb_excelexport_2csvThen, open the mini app using this command:mb_excelexport_2csv guiFor those who want the command line, use:mb_excelexport_2csv cmdSee "Command Line" below for more infoUpgradeShould you need to update to the latest version, you can do:pip install --upgrade mb_excelexport_2csvCommand LineAfter pip install worked, it is now installed on your path, and the command mb_excelexport_2csv is now available:mb_excelexport_2csv cmd ~/path/to/xml.xls ~/path/to/output.csvYou can then import the csv file into Google Sheets. The delimiter used is a comma.Alternatively, on Mac, you can skip the step of saving the csv file, and just run the following fancy command line, and it'll be on your clipboard.mb_excelexport_2csv cmd ~/path/to/xml.xls - | pbcopyJust paste into "A1" cell of your Google Sheet, Data -> Split Text into Columns.
Package: mbf-anysnake
mbf_anysnakeDocumentationhttps://mbf_anysnake.readthedocs.io/en/latest/Version controlled, per project Python, Python packages, R, Bioconductor and CRAN,
all inside a Docker container.Python:any version of Pythonversioned package installation from pypieditable installation of libraries under development (git/mercurial)two virtual environments at once, a local one and a global one for development toolsR (optional):any version of Rany bioconductor version (R version matched to bioconductor)bioconductor version oriented CRAN version controlall of CRANRpy2always matching the Python and R version usedAll this from simple,tomlbased configuration file.This solves the problem of providing a reproducible yet flexible
environment for bioinformatic and data science projects.Motivations in brief:any python -> independent of os packaging -> quick updates
solved via python-build (pyenv)Bioconductor -> R version -> screen scrapping -> matching rpy2 to python versions
-> docker volume mounts instead of inside-docker installrelocatable projects -> docker volume mounts abstract paths, allow relocatable
venvsdual venv - install development tools system wide, so you have always the latest jupyter
without having to rebuild docker containers (fragile)bioconductor dependes on CRAN packages of undefined version -> use microsoft
cran snapshot mirror and packages as of release date of bioconductor
(that's an approximation that may not always hold up in practice. Sometimes
bioconductor uses package verisons that were not released when the
bioconductor release happen. But it's a useful approximation for automatisation)some bioconductor packages require annotation/experimental data:
filter these packages by default, but allow user to request them
(this is a space saving measure. Full bioconductor software + full cran: 50 gb,
Bioconductor minus annotation: 21 GB, Bioconductor minus and minimal cran: 5GB),cran package annotation is somewhat messy (duplicate entries, non existing
versions, missing dependencies) -> hotfix.install as much of cran/bioconductor as possible: Don't fight with the stuff
in your daily workflow -> ton of apt-packages in the docker, see_inside_dockfill_bioconductor.pyfor list of things that are filtedR install.packages (and derivates) suffers from neglect:
it can't cache the downloaded files, it ignores the dependencies when installing from files and whenever multi-cores
are used.
It is 2019, installing on a single core is unacceptable.
We use apypipegraphto work around this.mbf_anysnake followssemver
Package: mbf-bam
mbf_bamFast, multi-core read counters and the like based on the BAM fileformat and rust-htslib.Part of the mbf_* suite fromhttps://github.com/IMTMarburgbuild wheels using
'docker run --rm -v $(pwd):/io ghcr.io/pyo3/maturin build --release -f'
then 'twine upload target/wheels/*'To use in nix, a flake that provides a function taking
nixpkgs, mach-nix and the version to report to nix is
provided.
Package: mbf-gtf
mbf_gtfPossibly the fastes Ensembl-GTF parser around
(reads the 1GB human GTF in about 10s on my system).Usage: mbf_gtf.parse_ensembl_gtf("filename.gtf", []) -> A dict of DataFramesThe file may be compressed with gzip - it must then end with ".gz".The second parameter may be a list of 'features' to retrieve - getting
just a subset can greatly improve performance.Note that this is very ensembl specific, it does not deal with any other GTF
format, and that it throws away attributes that are repeated on the sub elements -
ie. exons have only gene_id, not gene_name, gene_version, gene_....The resulting coordinates are pythonic - ie. starting at 0 (ie. shifted -1 from
the values in the GTF).This is part of the mbf_* family of bioinformatic libraries.
Package: mbf-heatmap
mbf_heatmapHeatmaps for ChIPseq lanes and delayed DataFrames.This is the swiss army knife of ChIPseq heatmaps.Example usage:frompathlibimportPathimportmbf_alignimportmbf_genomesimportmbf_genomicsimportmbf_heatmap.chipseqashcimportpypipegraphasppgppg.new_pipegraph()genome=mbf_genomes.EnsemblGenome('Homo_sapiens',100)lane1=mbf_align.lanes.AlignedSample("one","chipseq_one.bam",genome,False,None)lane2=mbf_align.lanes.AlignedSample("two","chipseq_two.bam",genome,False,None)input_regions=mbf_genomics.regions.Regions_FromBed("My_regions","input.bed",genome)hm=hc.Heatmap(input_ergions,[lane1,lane2],region_strategy=hc.regions.RegionsFromCenter(2000)# +- 1000bp,smoothing_strategy=hc.Smooth.SmoothExtendedReads(200)# extend reeads *by* 200bp)Path('results').mkdir(exists_ok=True)hm.plot("results/my_first_heatmap.png",norm=hc.norm.AsIs(),order=hc.order.AsIs(),)Part of the mbf_* suite fromhttps://github.com/IMTMarburg
Package: mbforbes-python-utils
python-utilsSo maybe I stop writing the same things over and over.Installation# Python 3.9+ only (due to PEP 585 type annotations)pipinstallmbforbes-python-utilsUsagefrommbforbes_python_utilsimportread,write,flatten# read() removes leading/trailing whitespace.contents=read("foo.txt")# write() creates intermediate directories if needed.# Pass `info_print = False` to disable printing.write("bar/baz.txt",contents)# flatten() flattens lists.flatten([[1,[2,[3]]]])# -> [1, 2, 3]Testspythontest_mbforbes_python_utils.pyReleasingI don't do this enough to remember how to do it# Increment version in setup.py. Then,pipinstalltwinewheel
pythonsetup.pysdistbdist_wheel
twinecheckdist/*# If the above failed, `rm -rf build/ dist/ *.egg-info` before retryingtwineuploaddist/*
Package: mbf-pandas-msgpack
pandas-msgpackis a package providing an interface to msgpack from pandasIn 2019, pandas deprecated the msgpack io interface,
suggesting people use pyarrow instead.Unfortunatly, pyarrow doesn’t do columns-containing-tuples,
and we do have older msgpacked DataFrames that we still need to unpack.Somebody had already forked the msgpack code earlier,
but it had bitrotted away from the current pandas internal.This fork restores it to mostly-working order - notably,
all datetime and sparse array handling have been removed.
Datetime, because the numpy dtype no longer stores timezones,
and it wasn’t important to our particular mission,
and sparse arrays because they have been deprecated anyway
(and were not important to our mission).InstallationInstall latest development version$pipinstallmbf_pandasUsageSee thepandas-msgpack documentationfor more details,
just replace allimport pandas_msgpackwithimport mbf_pandas_msgpack
Package: mbfxml2ex
This program converts MBF XML to Ex format suitable for CMLibs-Zinc.Installpip install mbfxml2exUsagembfxml2exconverter /path/to/input.xmlFor more information use the help:mbfxml2exconverter --helpDevelopingWhen developing install the required packages for running the tests with:pip install .[test]Then run the tests with:nosetestsfrom the repository root directory.To see the coverage statistics for the package run:nosetests --with-coverage --cover-package=mbfxml2exFor a nice HTML rendering of the coverage statistics run:nosetests --with-coverage --cover-package=mbfxml2ex --cover-htmlTo view the HTML coverage output:cd cover
python -m http.server 9432Then, in a web browser navigate tohttp://localhost:9432
Package: mbgui
Maildir GUI based onmblazeRequirementspython3mblazeInstall$ pip install mbguiRun$ mbgui path/to/maildir ...All command line arguments are passed tomdirscommand (with additional-aargument).By double clicking on single message in messages list, selected message is
printed to standard output. This can be used for pipingmbguiwith
other mblase commands.Licensembgui - Maildir GUI based on mblazeCopyright (C) 2022 Bozo KopicThis program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.
Package: mbh-s3tool
S3cmd lets you copy files from/to Amazon S3
(Simple Storage Service) using a simple to use
command line client. Supports rsync-like backup,
GPG encryption, and more. Also supports management
of Amazon’s CloudFront content delivery network.Authors:Florent Viard <florent@sodria.com>Michal Ludvig  <michal@logix.cz>Matt Domsch (github.com/mdomsch)
Package: mbin
mBin overviewmBin: a methylation-based binning framework for metagenomic SMRT sequencing readsThe mBin pipeline is designed to discover the unique signals of DNA methylation in metagenomic SMRT sequencing reads and leverage them for organism binning of assembled contigs or unassembled reads. Becauseallcellular DNA is modified by the same set of methyltransferases encoded in the genome, DNA methylation signals can be used for binning not just chromosomal sequences, but also extrachromosomal mobile genetic elements like plasmids.The pipeline consists of four routines:buildcontrols: Gets unmethylated IPD values for motifs from whole-genome amplified (WGA) sequencingfiltermotifs: Identifies methylated motifs in native metagenomic sequencingmethylprofiles: Creates methylation profiles for sequences using specified motifsmapfeatures: Visualizes landscape of methylation features across all sequencesDocumentationFor a comprehensive guide on how to install and run mBin, please see the fulldocumentation.CitationsBeaulaurier J, Zhu S, Deikus G, Mogno I, Zhang XS, Davis-Richardson A, Canepa R, Triplett E, Faith J, Sebra R, Schadt EE, Fang G. Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.Nature Biotechnology36, 61-69 (2018). doi:10.1038/nbt.4037.CreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History1.0.0 (2017-06-13)First release on PyPI.
Package: mbinobs
Mix binary obfuscation toolObfuscate -> Binary code into ipv4 / ipv6 / mac / uuid adresses <-Instalation:pip3 install mbinobsor clone repo and runpip3 install .Command line usage :python3 -m mbinobs binary.bin ipv4/ipv6/mac/uuidExemple :3m@ss:~/mbin-obs$ echo 'qwertyuiopasdfghjkl123456789' > test.bin

Binary encoded as ipv4:
['113.119.101.114', '116.121.117.105', '111.112.97.115', '100.102.103.104', '106.107.108.49',
'50.51.52.53', '54.55.56.57', '10.0.0.0']

Binary encoded as ipv6:
['7177:6572:7479:7569:6f70:6173:6466:6768', '6a6b:6c31:3233:3435:3637:3839:0a00:0000']

Binary encoded as mac:
['71:77:65:72:74:79', '75:69:6f:70:61:73', '64:66:67:68:6a:6b', '6c:31:32:33:34:35', '36:37:38:39:0a:00']

Binary encoded as uuid:
['71776572-7479-7569-6f70-617364666768', '6a6b6c31-3233-3435-3637-38390a000000']You can also import the encoding functions:frommbinobsimport*bfile=open('path_to_file','rb')# Use read bytes option ('rb')uuid_list=uuid._encode(bfile)ipv6_list=ipv6._encode(bfile)ipv4_list=ipv6._encode(bfile)mac_list=mac._encode(bfile)You could useRtlIpv6StringToAddressAorRtlIpv4StringToAddressAand similar apis calls to convert those ASCII text to binary code.Used byHive ransomware gangto encode shellcode payloads.
Package: mbio
# mbio----## What is **`mbio`**?This is a biology python package I used in my working. I will translate some algorithms from other language into python. I will try to make the program fast and easy to use. I mainly working on protein sequence analysis.Now we have v1.1.2, welcome to download and tell me your feeling.The package is dependent on numpy and prody.Now, I have* MI* MIp* OMES* SCA* DI* PSICOV* DICOV* APC* BND* PPV (for PSICOV)* Sequence shuffleWe also have some functions for different file formats.* PDB (which could support the .tar.gz bundle PDB parser and writer.)* Fasta* Numpy Matrix* MRC (support .mrc.gz parser and writer.)----## UsageI probably will post some examples in the furture.----## Work togetherIf you are interested in developing, please e-mail me and I will be happy to work together with you.If you think some algorithms should be added into this package, you could also e-mail me.----## Thanks* [wzmao](https://github.com/wzmao) (Only me now)----## LicenseSee the [LICENSE](LICENSE.rst) file for license rights and limitations (MIT).
Package: mbitutils
mbitutils (micro:bit Utilities)A Python module for the 4tronix Bit:bot XL and stubs for the BBC micro:bit.The intention is to use this package with the Visual Studio Code extension found athttps://github.com/oivron/microbit-extension-vscode. This extension is also available fromVisual Studio Code Marketplace.The stubs for micro:bit complements the following:https://github.com/PhonicCanine/microbit.Installationpip install mbitutilsUsageSeemicro:bit Micropython APIfor a complete documentation/API on how to use the micro:bit.Importfrom bitbot import *
from music import *
from speech import *Bit:bot XL APIbias(direction, percent)
# Set left/right bias to match motors.
# Direction: LEFT or RIGHT.
# Bias in %.go(direction, speed)
# Move robot forwards or backwards at speed.
# Direction: FORWARD or REVERSE.
# Speed in %.goms(direction, speed, duration)
# Move robot forwards or backwards at speed for milliseconds.
# Direction: FORWARD or REVERSE.
# Speed in %.
# Duration in milliseconds.spin(direction, speed)
# Rotate robot in direction at speed.
# Direction: LEFT or RIGHT.
# Speed in %.spinms(direction, speed, duration)
# Rotate robot in direction at speed for milliseconds.
# Direction: LEFT or RIGHT.
# Speed in %.
# Duration in milliseconds.buzz(duration)
# Sound a buzz for milliseconds.
# Duration in milliseconds.linesensor(direction)
# Read line sensor.
# Directon: LEFT or RIGHT.stop()
# Stops the Bit:bot.
Package: mblibs
mblibsFast tools for programminginstallation$pipinstallmblibsUsage for settings# Using settingsfrommblibs.fastimportFastSettingssettings=FastSettings("/path/to/yaml_or_json")value=settings.get("/path/to/key","default_value")integer=settings.getInt("/path/to/keyInt",12)# => 18/07/2018date=settings.getWithDateFormat("/path/to/current_date","{dd}/{mm}/{yyyy}")# => 19/07/2018date=settings.getWithDateFormat("/path/to/tomorrow_date""{tomorrow_dd}/{tomorrow_mm}/{tomorrow_yyyy}")# => 17/07/2018date=settings.getWithDateFormat("/path/to/yesterday_date","{yesterday_dd}/{yesterday_mm}/{yesterday_yyyy}")# sample{'data':[{'ident':'name1','rows':[{'key':1},{'key':2}]},{'ident':'name2','rows':[{'key':3},{'key':4}]}]}settings.get("/data[1]/rows[0]/key")=>3settings.get("/data[0]/rows")=>[{'key':1},{'key':2}]Usage for email# Using email objectfrommblibs.fastimportFastEmail# email bodybody="""<p>Lorem <em><strong>ipsum</strong></em> dolor !</p><p>Ceci est un message de test de l&#39;application</p><img class="picture" src="cid:graphic1" alt="Graphique en pi&egrave;ce jointe" /><p>Merci pour le graphique&nbsp;<br />Mick</p><img class="picture" src="cid:graphic2" alt="Graphique en pi&egrave;ce jointe" />"""# init email objectmailer=FastEmail()mailer.mail_from=settings.get("/smtp/mail_from")mailer.mail_subject="A subject for the mail."mailer.mail_text='Merci de lire le message depuis un lecteur acceptant le HTML.'mailer.mail_html=bodymailer.smtp_host="localhost"mailer.smtp_port=25mailer.smtp_tls=Falsemailer.smtp_login=""mailer.smtp_password=""# send emailTo=["mail1@mail.mx","mail2@mail.mx"]Cc=["mail3@mail.mx"]Bcc=["mail4@mail.mx","mail5@mail.mx"]filename="./ridev.png"ret=mailer.send_mail(to=To,cc=Cc,bcc=Bcc,attachfiles=[filename],embeddedimages_tag="graphic",embeddedimages=["./python.png",filename])
Package: mblog
mblog: A minimal markdown blogA simple Markdown based blog that you can use every day.Main FeaturesVery usableCustomizableSimple to runInstallationThis should be fairly easy to install, if you havePythoninstalled.$pipinstallmblogUsageYou should be generally able to start it with:$mblogand in case that does not work, as:$python-mmblogIn some cases, yourpythoncould be namedpython3, so try:$python3-mmblogIt launches as a web server running on port5000and tries to bind on all IP addresses (0.0.0.0).You can override this behavior by manually specifying thePORTandHOSTvariables.In a typical install, you should be able to openhttp://localhost:5000in your browser. Use theLoginlink to sign in. The default password isPassword. You should change it by following the directions
below.DatabaseTypically, when you want to run this onHerokuor a cloud provider, you may
want to use a MySQL database than the SQLite provider. Set theDATABASEenvironment
variable tomysql://user:password@host/database.StorageBy default, this software relies on the local file system. If you wish to use Cloud Hosting,
useS3,MinIOor some other service to host your files and images. Then use those
links directly when composing your blogs.Admin CredentialsYou typically authenticate via theADMIN_PASSWORD_HASHvariable. Hashed Passwords
are obtained by hashing withSHA-256encoded toBase64:For the default password which isPassword, you would get its hash
as588+9PF8OZmpTyxvYS6KiI5bECaHjk4ZOYsjvTjsIho=$echo-nPassword|openssldgst-binary-sha256|base64588+9PF8OZmpTyxvYS6KiI5bECaHjk4ZOYsjvTjsIho=AcknowledgmentsThe original version of this can be foundhere.This was taken and customized for adding File Uploads, Password Hashing, Better
Error Handling, Custom Branding with Python2 and Python3 Portability.Questions?Reach out to me for any feedback.Now Enjoy!Author: Karthik Kumar ViswanathanWeb   :https://karthikkumar.orgEmail :karthikkumar@gmail.com
Package: mbmutils
mbmutilsSimpmle common utilities.Installationpip install mbmutilsf-FunctionsThef-functions are simple string utilities of common actions. They have the
standard pattern of:return string after|before|between the keysThese all use the "first found" index. Meaning if there are more than one
instance of the key found, they use the first. Because of this there are functions
that look from the front (f_left | f_right) and functions that look from the
back (f_left_back | f_right_back).functionDescriptionf_rightreturn everything to therightof the keyf_leftreturn everything to theleftof the keyf_right_backreturn everything to therightof the key, starting from the backf_left_backreturn everything to theleftof the key, starting from the backf_betweenreturn everything between the keysYou will also find anot_foundparameter to these functions. This
allows you to define what is returned if the key is not found in the string.Examplesfrommbmutilsimportmumy_string="hello there fancy world!"print({mu.f_right(my_string,' fancy ')})# -> world!print({mu.f_left(my_string,' fancy ')})# -> hello thereprint({mu.f_left(my_string,'will not find')})# -> Noneprint({mu.f_left(my_string,'will not find',not_found="not here")})# -> not herePath functionsThere are also a fewpath-findingfunctions that search for a path
containing thepartial_pathprovided. These will search the current path
and then begin looking upward from there.There are 2 functions: 1 for files and the other for directories.frommbmutilsimportmu# assuming current folder is# /path/to/python/codemu.find_folder_path('data')# will return the first valid:#   -> path/to/python/code/data#   -> path/to/python/data#   -> path/to/data#   -> path/data# again, assuming current folder is# /path/to/python/codemu.find_folder_path('my_file.json')# will return the first valid:#   -> path/to/python/code/my_file.json#   -> path/to/python/my_file.json#   -> path/to/my_file.json#   -> path/my_file.json
Package: mbnk
MbnkSync/Async Python3 Monobank APIIntroductionmbnk- python lib for:• Monobank Open APIofficial docs:https://api.monobank.ua/docs/lib docs:https://github.com/yeghorkikhai/mbnk/blob/master/docs/monobank_open_api.md• Monobank Open API for providersofficial docs:https://api.monobank.ua/docs/corporate.htmllib docs:https://github.com/yeghorkikhai/mbnk/blob/master/docs/monobank_corp_open_api.md• MonoPay - Monobank Acquiringofficial docs:https://api.monobank.ua/docs/acquiring.htmllib docs:https://github.com/yeghorkikhai/mbnk/blob/master/docs/monopay_api.mdGithubhttps://github.com/yeghorkikhai/mbnkInstallationpipinstallmbnkGet Started with Monobank Open APIAsync example:importosimportasynciofrommbnk.asyncioimportAsyncMonobankOpenAPIasyncdefmain():async_mono=AsyncMonobankOpenAPI(api_token=os.getenv("MONOBANK_API_TOKEN"))currency_list=awaitasync_mono.public.currency()if__name__=="__main__":asyncio.run(main())Sync example:importosfrommbnkimportMonobankOpenAPImono=MonobankOpenAPI(api_token=os.getenv("MONOBANK_API_TOKEN"))# Get currencies rates listcurrency_list=mono.public.currency()