ariba | Antimicrobial Resistance Identification By Assembly | Genomics library

by sanger-pathogens Python Version: 2.14.6 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(8)Vulnerabilities Install Support

kandi X-RAY | ariba Summary

ariba is a Python library typically used in Artificial Intelligence, Genomics applications. ariba has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can install using 'pip install ariba' or download it from GitHub, PyPI.

ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. The input is a FASTA file of reference sequences (can be a mix of genes and noncoding sequences) and paired sequencing reads. ARIBA reports which of the reference sequences were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference sequences.

Support

Quality

Security

License

Reuse

Support

ariba has a low active ecosystem.

It has 100 star(s) with 41 fork(s). There are 26 watchers for this library.

It had no major release in the last 12 months.

There are 26 open issues and 76 have been closed. On average issues are closed in 120 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of ariba is 2.14.6

Quality

ariba has 0 bugs and 0 code smells.

Security

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

ariba code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ariba is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

ariba releases are available to install and integrate.

Deployable package is available in PyPI.

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

Installation instructions, examples and code snippets are available.

It has 13611 lines of code, 800 functions and 108 files.

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

Top functions reviewed by kandi - BETA

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

Download data from card
Extract the data from a dictionary
Extract SNPs from data dictionary
Return a list of dna seqs and gene sequences
Run the assembler
Assemble reads using FASTA
Assemble spades using spades
Run bowtie2 index
Build a bowtie2 index
Finds the closest ref sequence in cluster
Load report file
Return a list of lines describing the report
Load reference data from directory
Make a directory of prepareref files
Run cdhit
Gather data from a dictionary
Convert nucmer_hits to reference coordinates
Print the flag
Download and write data files
Run IARBA
Convert a csv report to a dictionary
Download data from plasmidfinder
Load data files
Download data fromvirulencefinder
Run Picard
Download data from resfinder

Get all kandi verified functions for this library.

ariba Key Features

No Key Features are available at this moment for ariba.

ariba Examples and Code Snippets

No Code Snippets are available at this moment for ariba.

Community Discussions

Trending Discussions on ariba

[RE]Can you see my pyinstaller error. There is no EXE file

How to Replace prefixes and Namespaces in XML using XSLT

Update an existing node concatenating the ID(deeper level) before that value in XSLT

Groovy concatenate ID and description in existing description tag

Replace . with _ in json file and write it to table using python

MSSQL: Alternative Approach to the below code, this is taking too much time to get results

Error: Illegal namespace for attribute declaration: http://www.w3.org/2001/XMLSchema-instance

How do I drag and drop with in one table in UI5?

QUESTION

[RE]Can you see my pyinstaller error. There is no EXE file

Asked 2021-Mar-16 at 09:08

I want to make exe using py file which is attached. Some test py files was formed exe and worked well.(using pyinstaller)

But I don't know why attached py file do not be converted the EXE file.

So, please try convert exe file and give me a feedback which point is wrong.

(This file is do not work in your computer due to coporate site. And this is py file for automation on the web browser.)

Creating py file using PYCHARM / Making exe file using pyinstaller on the Anaconda Powershell Prompt (Anaconda3)

** I want to show you prompt error which you can see simply. But I don't know which is error is critical to make exe. So, I attach the full prompt mssgs. Thank you for your understanding.

...

ANSWER

Answered 2021-Mar-16 at 09:08

I have PyInstaller: 3.5 and Python: 3.7.4.

I created a test.py file with the source you have provided.

Then in cmd line I used command "pyinstaller test.py"

The exe and related files are created in dist folder.

Source https://stackoverflow.com/questions/66649167

QUESTION

How to Replace prefixes and Namespaces in XML using XSLT

Asked 2021-Feb-14 at 08:47

I have a source XML like the following :

...

ANSWER

Answered 2021-Feb-13 at 16:36

Use

Source https://stackoverflow.com/questions/66187195

QUESTION

Update an existing node concatenating the ID(deeper level) before that value in XSLT

Asked 2021-Jan-27 at 18:16

i'm trying with XSLT to update an existing node (ItemDescription) with the concatenation of InternalID(in deeper level) and the existing description.

Origin XML

...

ANSWER

Answered 2021-Jan-27 at 18:16

You need to add a template for each element you want to modify:

XSLT 1.0

Source https://stackoverflow.com/questions/65924846

QUESTION

Groovy concatenate ID and description in existing description tag

Asked 2021-Jan-26 at 11:11

I'm trying in Groovy to save a Hash table with the ID and Description of the xml, but cant make my work code to get the ID in the deeper level, right now i can only map correctly the Description.

Code

...

ANSWER

Answered 2021-Jan-26 at 11:11

The following code:

Source https://stackoverflow.com/questions/65894843

QUESTION

Replace . with _ in json file and write it to table using python

Asked 2020-Nov-17 at 13:20

How to replace . with _ in my json file, and push the result json file to DB table.

Tried the below code but not working:

...

ANSWER

Answered 2020-Nov-17 at 13:20

if replacing is the only issue in your code try this:

Source https://stackoverflow.com/questions/64785058

QUESTION

MSSQL: Alternative Approach to the below code, this is taking too much time to get results

Asked 2020-Sep-25 at 10:38

I want to know how simply can write the code below and also i am interested to avoid code repetition. Is there any other way. Do's are

Whatever changes in the fields of [invoices_global] table, that changes would be inserted as new records in the format of old_value, new_value, field_changed in the Change log table.
A single field may be updated by many users, so latest should take, thats why i mentioned as last_updated_datetime desc in the code.
Need to avoid repetition.
Performance improvement, since i am calling the same table again and again multiple times for single ap_work_id. It takes 18sec to fetch results - 2000 out of 40000.
FYI, system_id and ap_work_id are same.
...

ANSWER

Answered 2020-Sep-25 at 07:59

Here's an approach where you

create a derived table with the latest value for each combination of system_id and field_changed
join that derived tabled to the original api table and get the values into individual fields

It currently uses MAX(CASE()) but you could do this as a PIVOT.

Only the top part of the SQL (relevant to the problem) is included here - you'll need to do the other joins on the bottom. I also haven't tested it (without table structures etc) so I can't promise there are no typos.

Source https://stackoverflow.com/questions/64059562

QUESTION

Error: Illegal namespace for attribute declaration: http://www.w3.org/2001/XMLSchema-instance

Asked 2020-Jun-23 at 04:22

I am trying to create a new SOAP project in SOAPUI thru importing a wsdl. The initial part of wsdl looks like:

...

ANSWER

Answered 2020-Jun-23 at 01:35

If you open the path https://www.w3.org/2001/XMLSchema-instance in a webbrowser, you will get this message:

XML Schema instance namespace
[...]
This schema should never be used as such: the XML Schema Recommendation forbids the declaration of attributes in this namespace

This should explain your error.
To fix it, look for any attribute definitions with the prefix xsi: or, more likely:

Because you defined an xs:schema with a targetNamespace like

Source https://stackoverflow.com/questions/62525519

QUESTION

How do I drag and drop with in one table in UI5?

Asked 2020-Feb-18 at 10:25

I noticed on the documentation you can drag and drop between two tables https://sapui5.hana.ondemand.com/#/entity/sap.m.Table/sample/sap.m.sample.TableDnD. But is there a way to drag and drop on the one table (same table). I have written the code for drag and drop but the drag and drop event isn't triggered when I try to drop in the same table.

...

ANSWER

Answered 2020-Feb-18 at 10:25

Try this:

Source https://stackoverflow.com/questions/60191950

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

Vulnerabilities

No vulnerabilities reported

Install ariba

Get reference data, for instance from CARD. See getref for a full list.
If you encounter an issue when installing ARIBA please contact your local system administrator. If you encounter a bug you can log it here.

Support

We currently do not have the resources to provide support for Ariba. However, the community might be able to help you out if you report any issues about usage of the software to the issues page.

Find more information at: