khmer | memory nucleotide sequence k-mer counting | Genomics library

by dib-lab Python Version: v2.1.2 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | khmer Summary

khmer is a Python library typically used in Artificial Intelligence, Genomics applications. khmer has no bugs, it has no vulnerabilities, it has build file available and it has low support. However khmer has a Non-SPDX License. You can download it from GitHub.

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Support

Quality

Security

License

Reuse

Support

khmer has a low active ecosystem.

It has 647 star(s) with 309 fork(s). There are 65 watchers for this library.

It had no major release in the last 12 months.

There are 302 open issues and 720 have been closed. On average issues are closed in 136 days. There are 45 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of khmer is v2.1.2

Quality

khmer has 0 bugs and 0 code smells.

Security

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

khmer code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

khmer 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

khmer releases are available to install and integrate.

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

Top functions reviewed by kandi - BETA

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

Return a dict containing the cmdclass for the versioneer
Extract version information
Return the project root directory
Return a ConfigParser instance from a root
Return parser
Build command line arguments
Build node graph arguments
Add threading arguments to the given parser
Create the versioneer config file
Extract version information from VCS
Yield read pairs from screed stream
Normalize reads by median
Iterate through two reads
Trim a read - only record
Check if input files exist
R Check the free space of input files
Print usage information for graphsize
Extract paired reads from a stream
Scans the setup py py file and checks for missing values
Create a countgraph object
Check if a graph is available on disk
Print out information about configuration
Use setuptools
Removes a single read from the counts
Determines how many sequences are in the same length
Start worker threads
Log information about a script

Get all kandi verified functions for this library.

khmer Key Features

No Key Features are available at this moment for khmer.

khmer Examples and Code Snippets

No Code Snippets are available at this moment for khmer.

Community Discussions

Trending Discussions on khmer

Mysql crosstab fixed column query does not display certain multi language characters

get second JSON value knowing the first one

Static file not found in Django production

Generate CRC16 CCITT False with Javascript?

googletrans stopped working with detecting all languages as English

how can I access Django rest framework using ajax

Faster way to do this comparison of string in perl for foreign charsets

Decoding result with Mojo::UserAgent for regex match

How can I refresh data on click in Leaflet map?

Sklearn text classification: Why is accuracy so low?

QUESTION

Mysql crosstab fixed column query does not display certain multi language characters

Asked 2021-Nov-02 at 19:09

I am looking for help in understanding the issue with retrieving certain characters in MYSQL. I have a table which contains international numerals in unicode for each numeral system (e.g. Roman, Hebrew, Thai, Khmer, Lao, etc). The character set of the table is utf8 and collation is utf8_general_ci.

The table is organised as follows:

NUM_SYS_NAME NUM_ID TEXT Roman 1 I Roman 2 II Roman 3 III Roman 5 V Thai 5 ๕ Ethiopic 500 ፭፻

etc, there are 18 numbers for each numeral system, from 0 to 10, also 50, 100, 500, 1000, 10000.

The MySql query is this:

...

ANSWER

Answered 2021-Nov-02 at 19:09

The encoding isn't the issue, it's about using MAX()

max(case when NUM_ID = 4 then TEXT else 'N/A' end) as '4', <-- the string 'N/A' is greater than the string 'IV', in alphabetic order, and then, the 'N/A' is selected over the 'IV', or anything that has sorting order lesser than 'N/A'. That's why the letter 'O' works, because it's after 'N'.

A workaround would be to replace the string 'N/A' by the value NULL :

Source https://stackoverflow.com/questions/69811465

QUESTION

get second JSON value knowing the first one

Asked 2021-Apr-02 at 14:29

I've got the following JSON file, translation.json, containing a key called "greeting" and a value containing the language the greeting is written in.

...

ANSWER

Answered 2021-Apr-01 at 10:59

Here's what you're looking for.

Source https://stackoverflow.com/questions/66903000

QUESTION

Static file not found in Django production

Asked 2021-Mar-13 at 12:58

I am trying to deploy my Django project using Ubuntu and apache webserver. When I transferred my project to the Ubuntu web server and tested it in development, everything went fine. However when changed to production, I experienced file not found problem and I suspect this problem is related to my setings.py, but I am unable to troubleshoot it further. The error I see in production when accessing my site is:

...

ANSWER

Answered 2021-Mar-13 at 12:58

It is as commented by Ivan Starostin that one should give the absolute path in to the file in the production environment. Also using reverse url can also work in this case as suggested in the comment.

Source https://stackoverflow.com/questions/66610969

QUESTION

Generate CRC16 CCITT False with Javascript?

Asked 2021-Mar-05 at 06:18

As i input english letter, it returns correct crc. However, i input "ក" (Khmer language), the result is far far different.

This is the checksum i've been comparing https://crccalc.com/

Is there a way that we could convert these code for better result??

...

ANSWER

Answered 2021-Mar-05 at 06:18

charCodeAt() gives you the UTF-16 character code, which is a 16-bit value. That is not a byte. Your CRC code takes bytes. What you're doing discards the high eight bits of each character code, which makes no sense.

The sequence of bytes that gives the CRC f1f1 is e1 9e 80, which is the UTF-8 representation of ក. You need to convert the character to UTF-8 and then compute the CRC on that sequence of bytes.

Source https://stackoverflow.com/questions/66486088

QUESTION

googletrans stopped working with detecting all languages as English

Asked 2020-Dec-30 at 19:22

The problem I have here is googletrans API suddenly stopped working, just like this:

...

ANSWER

Answered 2020-Dec-30 at 19:22

According to the documentation googletrans, https://pypi.org/project/googletrans/, "is an unofficial library using the web API of translate.google.com".

They specifically state:

Due to limitations of the web version of google translate, this API does not guarantee that the library would work properly at all times (so please use this library if you don’t care about stability)

and suggest to use the official Google Translate API (click here).

For further reading I highly suggest the following sources:

GoogleTrans Python not translating
https://pypi.org/project/googletrans/
https://py-googletrans.readthedocs.io/en/latest/
If you decide to switch to the official API check out: https://cloud.google.com/translate/docs

Source https://stackoverflow.com/questions/65511216

QUESTION

how can I access Django rest framework using ajax

Asked 2020-Dec-24 at 18:45

I am trying to get a form from the rest framework using ajax I already tried the ajax get method on other thing and it worked for me now I am trying to use the POST method to grab the form but i am facing difficulties my current HTML code:

...

ANSWER

Answered 2020-Dec-24 at 18:45

The data sent in your ajax request cannot be understood by Django rest.

Response from Django:

Source https://stackoverflow.com/questions/65440992

QUESTION

Faster way to do this comparison of string in perl for foreign charsets

Asked 2020-Nov-29 at 07:22

I have the following code which works well:

...

ANSWER

Answered 2020-Nov-28 at 14:38

The only way I could seem to get it to work, was with:

Source https://stackoverflow.com/questions/65047822

QUESTION

Decoding result with Mojo::UserAgent for regex match

Asked 2020-Nov-02 at 10:41

I'm trying to work out why this won't work:

...

ANSWER

Answered 2020-Nov-02 at 09:52

The title is in charset=gb2312 which requires to be decoded into perl internal representation.

Following code demonstrates decoding and output to console the title for this particular website.

Source https://stackoverflow.com/questions/64641309

QUESTION

How can I refresh data on click in Leaflet map?

Asked 2020-May-25 at 11:02

...

ANSWER

Answered 2020-May-25 at 11:02

I'm not sure this is the exact answer to the OP but here is my two-cents. In my opinion it is better to keep the geographical data separate from the non geographical data. So first I created some function stateNGData (non geographical data). This function return an object with a method shufffle for easy shuffling of the state language. I then created the object data. In this way it is easy to retrieve|update what ever information about the state in question.

Source https://stackoverflow.com/questions/61964539

QUESTION

Sklearn text classification: Why is accuracy so low?

Asked 2020-May-10 at 23:09

Alright, Im following https://medium.com/@phylypo/text-classification-with-scikit-learn-on-khmer-documents-1a395317d195 and https://scikit-learn.org/stable/tutorial/text_analytics/working_with_text_data.html trying to classify text based on category. My dataframe is laid out like this and named result:

...

ANSWER

Answered 2020-May-10 at 08:05

What you are doing

The mistake I believe is in these lines:

Source https://stackoverflow.com/questions/61703947

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

Vulnerabilities

No vulnerabilities reported

Install khmer

You can download it from GitHub.
You can use khmer 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: