bioservices | Access to Biological Web Services from Python | Genomics library

by cokelaer Python Version: 1.11.2 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(4)Vulnerabilities Install Support

kandi X-RAY | bioservices Summary

bioservices is a Python library typically used in Artificial Intelligence, Genomics applications. bioservices has no bugs, it has no vulnerabilities, it has build file available and it has high support. However bioservices has a Non-SPDX License. You can install using 'pip install bioservices' or download it from GitHub, PyPI.

Access to Biological Web Services from Python.

Support

Quality

Security

License

Reuse

Support

bioservices has a highly active ecosystem.

It has 248 star(s) with 61 fork(s). There are 16 watchers for this library.

It had no major release in the last 12 months.

There are 10 open issues and 192 have been closed. On average issues are closed in 117 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of bioservices is 1.11.2

Quality

bioservices has 0 bugs and 0 code smells.

Security

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

bioservices code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

bioservices has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

bioservices releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

bioservices saves you 5644 person hours of effort in developing the same functionality from scratch.

It has 11812 lines of code, 1246 functions and 117 files.

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

Top functions reviewed by kandi - BETA

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

Runs the specified program
Get a specific parameter
Generate the user agent string
Parse a KML pathway
Parse an entry
Get database entry
Run a single run
Get a specific parameter
Search PubMed API
Convert a Python object to XML
Download an Accession
Get valid attributes
Download a fasta file
List all classes in a class
Highlight a pathway diagram
Get the result of a job
Read the config file and update the params attribute
Get data by id
Find a molecule
Get a VPs for a given region
Query all databases
Get a list of paths from source to target
Fetch a query
Download files from ensembl genome
Gets all paths between source and source
Extract data from BioDBNet

Get all kandi verified functions for this library.

bioservices Key Features

No Key Features are available at this moment for bioservices.

bioservices Examples and Code Snippets

No Code Snippets are available at this moment for bioservices.

Community Discussions

Trending Discussions on bioservices

How to retrieve all ChEBI IDs for a given KEGG compound?

How to retrieve InChI key for KEGG compound?

Do not write line that begins with certain string

If statement and writing to file

QUESTION

How to retrieve all ChEBI IDs for a given KEGG compound?

Asked 2018-Apr-05 at 14:19

Let's say I want to map a KEGG ID to a ChEBI ID using bioservices, I can do:

...

ANSWER

Answered 2017-Oct-23 at 08:43

In short, I do not have the answer but here are some information that may help you.

The C00033 entry shows two related entities in the CHEBI database: 15366 and 30089. Now, if we look at CHEBI website, we can see that those two entries correspond to :

15366 acetic acid
30089 acetate

acetate is the ion resulting from loss of H+ from the acetic acid.

why KEGG decided to provide the two entries: I do not know.

Using the kegg_con.conv , we can see that C00033 maps to only one result in chebi, which seems sensible to me (but confusing I agree) since 30089 is just the ion form of acetic acid (15366).

For completeness, note that using the ChEBI service (from bioservices), we can map back the two ChEBI entries to KEGG and we see that:

Source https://stackoverflow.com/questions/46005142

QUESTION

How to retrieve InChI key for KEGG compound?

Asked 2017-Oct-25 at 09:15

I would like to retrieve the InChI representation for a given KEGG compound but I fail to find a direct solution for this.

One could do it via ChEBI like this:

...

ANSWER

Answered 2017-Oct-25 at 09:15

I'm not aware of a functionality in the KEGG service that would allow you to do that directly. I believe your solution (using e.g. ChEBI) is A correct one. You may have other useful service such as unichem, chemspider (you would need a login though for that one) could help as well. (disclaimer: I'm the bioservices main author)

Source https://stackoverflow.com/questions/45996496

QUESTION

Do not write line that begins with certain string

Asked 2017-Feb-18 at 18:41

I'm trying to omit writing the lines that begin with "KO", however when I run the code the lines still are written to the output file. I tried calling a a boolean expression to see if "KO" was in geneData and it comes back as true. I'm stuck with just that part.

...

ANSWER

Answered 2017-Feb-18 at 18:41

Your genedata variable is a single string. When you iterate over it, you are dealing with the individual characters of the string; your line variable is horribly misnamed. The two-character string 'KO' is obviously not contained within any of these single characters, thus your boolean condition is always True.

With no example input data, nor any expected output data, I can't tell what you're trying to do well enough to suggest a solution.

Source https://stackoverflow.com/questions/42318867

QUESTION

If statement and writing to file

Asked 2017-Feb-18 at 03:38

I am using the KEGG API to download genomic data and writing it to a file. There are 26 files total and some of of them contain the the dictionary 'COMPOUND'. I would like to assign these to CompData and write them to the output file. I tried writing it as an if True statement but this does not work.

...

ANSWER

Answered 2017-Feb-18 at 03:38

I guess that by

Source https://stackoverflow.com/questions/42310637

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

Vulnerabilities

No vulnerabilities reported

Install bioservices

You can install using 'pip install bioservices' or download it from GitHub, PyPI.
You can use bioservices like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

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 .

Find more information at: