ALEC | NonCommercial 3.0 United States license | Genomics library

by scottlab Python Version: Current License: Non-SPDX

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

kandi X-RAY | ALEC Summary

ALEC is a Python library typically used in Telecommunications, Media, Advertising, Marketing, Artificial Intelligence, Genomics applications. ALEC has no bugs, it has no vulnerabilities and it has low support. However ALEC build file is not available and it has a Non-SPDX License. You can download it from GitHub.

Amplicon Long-read Error Correction (ALEC) was developed to correct sequencing and alignment errors [substitutionsandinsertion/deletions (indels)] generated by targeted amplicon sequencing with the PacBio RS platform. This script has been developed usingPacBio single molecule real time (SMRT) full-gene sequencing of the CYP2D6 gene (5.0 kb)according to the P6-C4 Pacific Biosciences protocol. ALEC was further tested using a 9.2kb amplicon and long-read PacBio SMRT sequencing of the RYR2 gene. ALEC may have utility withother long-read sequencing platforms (e.g., Oxford Nanopore), and/or other sequencing chemistries; however, optimizing the error correction parameters may be necessary to achieve ideal sequence correction and output for genes and sequencing platforms other than those noted above. Four types of sequencing errors can be corrected after applying ALEC: 1) random substitutions; 2) random indels; 3) indels within homopolymers; and 4) indels near sequence variants.

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Quality

Security

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Support

ALEC has a low active ecosystem.

It has 9 star(s) with 2 fork(s). There are 5 watchers for this library.

It had no major release in the last 6 months.

There are 2 open issues and 0 have been closed. On average issues are closed in 1059 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of ALEC is current.

Quality

ALEC has no bugs reported.

Security

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

License

ALEC 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

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

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

Top functions reviewed by kandi - BETA

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

Parse a Seq
Performs the correct correction of the reads .
Argument parser .
Calculates long distances .
Check if the insertion rate is correct
Fix deletion .
Parse a fasta file
Calculates allele frequency frequencies .
Calculate consensus insert frequency .
Extract the feature matrix from the given reads .

Get all kandi verified functions for this library.

ALEC Key Features

No Key Features are available at this moment for ALEC.

ALEC Examples and Code Snippets

No Code Snippets are available at this moment for ALEC.

Community Discussions

Trending Discussions on ALEC

Why does the cte return the error that it does not exist?

How to delete rows after the item which equals to exact value?

When is a C# List not an IEnumerable?

Mongodb query to Display the number of movies based on the number of directors a movie has using split

Unable to insert into 2d list in python

Most efficient way to order by the average of a column in postgres

How to sort dictionaries and create a dictionaries based on the values in the list inside the dictionary

express validator: separating logic

Accessing a nested JSON file in Flutter

Burger menu won't open when toggled

QUESTION

Why does the cte return the error that it does not exist?

Asked 2021-Jun-14 at 22:04

Here is my code

...

ANSWER

Answered 2021-Jun-14 at 21:50

Create a CTE that returns for each Block_id the step of the first John.
Then join the table to the CTE:

Source https://stackoverflow.com/questions/67977325

QUESTION

How to delete rows after the item which equals to exact value?

Asked 2021-Jun-14 at 14:46

I have the following dataframe

...

ANSWER

Answered 2021-Jun-14 at 14:44

One method uses an updatable CTE:

Source https://stackoverflow.com/questions/67972334

QUESTION

When is a C# List not an IEnumerable?

Asked 2021-Jun-11 at 15:31

I want to be able to determine if a passed argument is an IEnumerable.

...

ANSWER

Answered 2021-Jun-11 at 15:31

It isn't IEnumerable, because KeyValuePair is a value-type (struct), and generic variance rules doesn't allow for value-types and object to be interchangeable during type tests (as a conversion - boxing - is required).


So: while it isn't IEnumerable, it is, however, IEnumerable in the non-generic sense.

Source https://stackoverflow.com/questions/67939681

QUESTION

Mongodb query to Display the number of movies based on the number of directors a movie has using split

Asked 2021-Apr-28 at 11:45

I have a movieDetails.json database and the collection name is a movie then our teacher wants us to Display the number of movies based on the number of directors a movie has a. Hint you might have to use the javascript function split Since the director is not an array, it is only a string so I can't count how many directors are there because it will always come out as 1 since its a string so I want to split that string so that I can get an array so that I can count it. But unfortunately, I don't know the query that will solve this problem. ex. of expected output:

...

ANSWER

Answered 2021-Apr-28 at 11:45

Demo - https://mongoplayground.net/p/y3kvFnocWKn

Use aggregation query

Read the below links for better understanding

Source https://stackoverflow.com/questions/67298166

QUESTION

Unable to insert into 2d list in python

Asked 2021-Apr-25 at 14:48

I am trying to insert an element into the first column of each row in a table of data read from a text file.

...

ANSWER

Answered 2021-Apr-25 at 14:48

You need to use for loop using index rather then comprehension

Source https://stackoverflow.com/questions/67249465

QUESTION

Most efficient way to order by the average of a column in postgres

Asked 2021-Apr-21 at 18:36

I know there's A way to do this, but I'm curious to know if there is a "best" way of doing this...

Let's say I have this table

Name Date Value Troy 2021-04-21 1 Troy 2021-04-20 2 Troy 2021-04-19 3 Alec 2021-04-21 3 Alec 2021-04-20 4 Alec 2021-04-19 5

I want to reorder the table based on the average of the "Value" column for each person.

Here is the expected output:

Name Date Value Alec 2021-04-21 3 Alec 2021-04-20 4 Alec 2021-04-19 5 Troy 2021-04-21 1 Troy 2021-04-20 2 Troy 2021-04-19 3

Is there a most efficient way of executing this?

...

ANSWER

Answered 2021-Apr-21 at 18:36

The calculation of the average value can be done either by aggregation in a query that groups by person and then it is joined to the table, or with AVG() window function which can be used directly in the ORDER BY clause and I believe is better for performance:

Source https://stackoverflow.com/questions/67201501

QUESTION

How to sort dictionaries and create a dictionaries based on the values in the list inside the dictionary

Asked 2021-Apr-10 at 19:04

This is a challenging one for me tried for hours as I am learning but I am not sure if my logic is correct at all.

Define a function called stars that takes in two dictionaries:

movies: a dictionary where the keys are movie titles and the values are lists of major performers in the movie.
For example:

...

ANSWER

Answered 2021-Apr-10 at 19:04

I believe you need.

Source https://stackoverflow.com/questions/67037952

QUESTION

express validator: separating logic

Asked 2021-Mar-17 at 21:09

This question is more about code organisation rather than an error/bug problem.

I am working on request body validation, json has structure like:

...

ANSWER

Answered 2021-Mar-17 at 21:09

the good practice here is that you are validating inputs ✅

the downside of your current approach is that it is hard to maintain long term ❌

you could go down the middleware way, and create multiple middlewares for each route/body that you need to validate. It works, but, the amount of work and maintenance burden will increase over time.

one approach you can follow is to create an expected schema of your input (e.g. a model definition describing the fields and values expected), and use a validator to check the current input based on the schema you created.

for Node.js we have multiple tools for that like: AJV, JOI, YUP.

using a sample example with JOI, you could replace your validation flow by doing:

Source https://stackoverflow.com/questions/66681048

QUESTION

Accessing a nested JSON file in Flutter

Asked 2020-Oct-28 at 14:54

I am trying to access the 'title' from the following list but it keeps throwing error.

...

ANSWER

Answered 2020-Oct-28 at 14:54

You need to make a cast on the element of your movie list.

Source https://stackoverflow.com/questions/64575231

QUESTION

Burger menu won't open when toggled

Asked 2020-Sep-19 at 15:31

the burger menu I've created using plain HTML, CSS, and JS does not open when clicked and I am at a loss for what to try next. The goal is for the burger menu to show up in mobile view and use 100% of the screens width to display the navigation when toggled. Here is a codepen with my code as well. https://codepen.io/alec-johnson/pen/dyMgKeN

...

ANSWER

Answered 2020-Sep-19 at 15:29

Remove .navabr-links here

.navabr-links.active {display: flex;} so it will be .active {display: flex;}

Source https://stackoverflow.com/questions/63970350

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

Vulnerabilities

No vulnerabilities reported

Install ALEC

You can download it from GitHub.
You can use ALEC 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.