yeastmine | using YeastMine

by fomightez Python Version: Current License: No License

X-Ray Key Features Code Snippets Community Discussions Vulnerabilities Install Support

kandi X-RAY | yeastmine Summary

yeastmine is a Python library. yeastmine has no bugs, it has no vulnerabilities and it has low support. However yeastmine build file is not available. You can download it from GitHub.

Scripts using [YeastMine] (populated by [SGD] www.yeastgenome.org/) and powered by [InterMine] to collect [Saccharomyces Genome Database] www.yeastgenome.org/) data. Running these scripts does require InterMine Python Web Service Client module be installed on the system. See notes on installing the InterMine Python Web Service Client Module. Currently (November 2020), I have a repository where you can launch MyBinder sessions where get_protein_seq_as_FASTA.py and presumably other scripts in the repository work. See [the cl_sq_demo-binder repo here] to launch such MyBinder sessions. The issue was that the current version of the intermine package installed by conda and pip is outdated at present time. The current development version fixes an issue with using templates and perhaps other things in the current Python version and so is preferably the one to use at this time, see [here] Note that to get the development branch of the intermine webservice installed, the cl_sq_demo-binder repository was updated as shown [here] That approach should be easily applied to other repositories or run %pip install in a cell in a notebook in a session. (I haven’t yet checked whether the used of %pip install is compatiable with having installed intermine from the traditional sources, which presently give an older version, prior.).

Support

Quality

Security

License

Reuse

Support

yeastmine has a low active ecosystem.

It has 4 star(s) with 3 fork(s). There are 1 watchers for this library.

It had no major release in the last 6 months.

yeastmine has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of yeastmine is current.

Quality

yeastmine has 0 bugs and 0 code smells.

Security

yeastmine has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

yeastmine code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

yeastmine does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

yeastmine releases are not available. You will need to build from source code and install.

yeastmine has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions, examples and code snippets are available.

It has 1428 lines of code, 42 functions and 14 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed yeastmine and discovered the below as its top functions. This is intended to give you an instant insight into yeastmine implemented functionality, and help decide if they suit your requirements.

Generate a data file for each gene
Generate a header text for the given month
Generate a file name
Retrieve the chromosome coordinates as a FASTA file
Generate a name based on a file name
Generate a custom track file
Generate configuration text
Generate an output file name based on a filename
Calculate the density of a residue
Generate an output file from the provided text
Replace KQE in text
Generate the density report
Calculate the balance of the given amino acid string
Generate the report of length - normalized density normalized density
Function to generate the length of the length - normalized density report
This function calculates the density of each cell in the table
Generate a dictionary of chunked chunks for each gene
Retrieve the protein sequence as a FASTA file
Retrieve the gene sequence as a FASTA file
Convert a list to text

Get all kandi verified functions for this library.

yeastmine Key Features

No Key Features are available at this moment for yeastmine.

yeastmine Examples and Code Snippets

No Code Snippets are available at this moment for yeastmine.

Community Discussions

No Community Discussions are available at this moment for yeastmine.Refer to stack overflow page for discussions.

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install yeastmine

As described at [here](http://yeastmine.yeastgenome.org/yeastmine/api.do?subtab=python) you intstall the module on your system by. (Dollar sign is used to indicate prompt. Don’t include that in your command.) You may need to do that as a superuser, i.e. include sudo at the start of that command, depending on how your system is set up. If you are choosing to use a [PythonAnywhere](https://www.pythonanywhere.com/) account, you still need to install the InterMine Python Web Service Client Module to your individual account. It is done very similarly. You just need to additionally pass the user flag `--user `, as shown below and described [here](https://www.pythonanywhere.com/wiki/InstallingNewModules).
I looked at YeastMine presently and saw the current link to the site uses https and so I tried changing the address in my script to what is shown in samples, i.e., script obtained from going to https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Transcript&scope=all and clicking link down below for python to open https://yeastmine.yeastgenome.org/yeastmine/templateAction.do .
Ran updgrade of intermine with python genes_ieasy_install --user --upgrade intermine
Still get Squid error running the sample script fro PythonAnywhere. Think it is related to fact for free PythonAnywhere accounts that things run through a proxy and the current requests package is broken for that, see https://www.pythonanywhere.com/forums/topic/761/ . That package is probably used in the intermine access or somethhing broken is. Since it is an overarching thing at the level of the popular requests package/https switch everyone is doing, maybe best to not try and make work from PythonAnywhere until the dust settles, since I think YeastMine may be working on my local Mac desktop for now. I’ll just use that in the interim.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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