seq | A high-performance , Pythonic language for bioinformatics | Genomics library

by seq-lang C++ Version: v0.11.0 License: Apache-2.0

X-Ray Key Features Code Snippets(3)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | seq Summary

seq is a C++ library typically used in Artificial Intelligence, Genomics applications. seq has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

A strongly-typed and statically-compiled high-performance Pythonic language!. Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing Python code, and achieves performance comparable to (and in many cases better than) C/C++. Seq is able to outperform Python code by up to 160x. Seq can further beat equivalent C/C++ code by up to 2x without any manual interventions, and also natively supports parallelism out of the box. Implementation details and benchmarks are discussed in our paper. Learn more by following the tutorial or from the cookbook.

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Support

seq has a low active ecosystem.

It has 678 star(s) with 48 fork(s). There are 21 watchers for this library.

It had no major release in the last 12 months.

There are 19 open issues and 111 have been closed. On average issues are closed in 97 days. There are 3 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of seq is v0.11.0

Quality

seq has no bugs reported.

Security

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

License

seq is licensed under the Apache-2.0 License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

seq releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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seq Key Features

No Key Features are available at this moment for seq.

seq Examples and Code Snippets

r Check if seq is a nested sequence .

python

Lines of Code : 13

License : Non-SPDX (Apache License 2.0)

Copy

def is_nested(seq):
  """Returns true if its input is a nested structure.

  Refer to [tf.nest](https://www.tensorflow.org/api_docs/python/tf/nest)
  for the definition of a nested structure.

  Args:
    seq: the value to test.

  Returns:
    True

Calculate a sub seq

java

Lines of Code : 9

License : No License

Copy

static void subseq(String p, String up) {
        if (up.isEmpty()) {
            System.out.println(p);
            return;
        }
        char ch = up.charAt(0);
        subseq(p + ch, up.substring(1));
        subseq(p, up.substring(1));
    }

Set the seq number .

java

Lines of Code : 3

License : Permissive (MIT License)

Copy

public void setSeq(long seq) {
        this.seq = seq;
    }

Community Discussions

Trending Discussions on seq

Convert Scala `Seq[Option[A]]` to `Option[Seq[A]]`

How to fit the axis title with two lines in R?

Why does Spark perform an unnecessary shuffle during a joinWith on a pre-partitioned dataframe?

In R Shiny, why do my functions not work when using the render UI function but work fine when not using render UI?

Rank selected multiple columns in a dataframe and then add rank data as new columns

Can't access Julia Array ( BoundsError: attempt to access 0-element Vector{Int64} at index [1] )

error using lapply on tibble convert from double to logical

Replaces all values with "NA" in R dataframe

How to run a Spark-Scala unit test notebook in Databricks?

Count number of fields that match in an Array of Object in mongodb

QUESTION

Convert Scala `Seq[Option[A]]` to `Option[Seq[A]]`

Asked 2021-Jun-15 at 20:35

I'm wondering what the idiomatic way in Scala would be to convert a Seq of Option[A] to an Option[Seq[A]], where the result is None if any of the input options were None.

...

ANSWER

Answered 2021-Jun-15 at 18:17

The idiomatic way is probably to use what is generally called traverse.

I'd recommend reading Cats' documentation about it: https://typelevel.org/cats/typeclasses/traverse.html

With Cats, it would be as easy as:

Source https://stackoverflow.com/questions/67991462

QUESTION

How to fit the axis title with two lines in R?

Asked 2021-Jun-15 at 13:56

I made one graph with 'two line' y-axis title using the code ylab(expression(paste()

...

ANSWER

Answered 2021-Jun-15 at 13:56

One way would be to adjust the margins giving more space to the left.

Source https://stackoverflow.com/questions/67987562

QUESTION

Why does Spark perform an unnecessary shuffle during a joinWith on a pre-partitioned dataframe?

Asked 2021-Jun-15 at 12:49

This example has been tested with Spark 2.4.x. Let's consider 2 simple dataframes:

...

ANSWER

Answered 2021-Jun-15 at 12:49

This seems like a bug introduced by a bug fix in this ticket. The result was wrong for outer joins. Hence the need to add a Project node (packing of the struct) before the Join node.

However, we end up with this kind of query plan:

Source https://stackoverflow.com/questions/67400097

QUESTION

In R Shiny, why do my functions not work when using the render UI function but work fine when not using render UI?

Asked 2021-Jun-14 at 22:51

When running the first "almost MWE" code immediately below, which uses conditional panels and a "renderUI" function in the server section, it only runs correctly when I comment out the 3rd line from the bottom, observeEvent(vector.final(periods(),yield_input()),{yield_vector.R <<- unique(vector.final(periods(),yield_input()))}). If I run the code with this line activated, it crashes and I get the error message Error in [: subscript out of bounds which per my research means it is trying to access an array out of its boundary.

...

ANSWER

Answered 2021-Jun-14 at 22:51

Replace the line you commented out with this

Source https://stackoverflow.com/questions/67975316

QUESTION

Rank selected multiple columns in a dataframe and then add rank data as new columns

Asked 2021-Jun-14 at 17:24

The example data looks like this:

...

ANSWER

Answered 2021-Jun-14 at 17:24

We can assign. Here, we used lapply to loop over the columns (in case there are some difference in type, then lapply preserves it while apply converts to matrix and there would be a single type for those)

Source https://stackoverflow.com/questions/67974456

QUESTION

Can't access Julia Array ( BoundsError: attempt to access 0-element Vector{Int64} at index [1] )

Asked 2021-Jun-14 at 17:00

Julia Code:

...

ANSWER

Answered 2021-Jun-14 at 17:00

Use:

Source https://stackoverflow.com/questions/67973473

QUESTION

error using lapply on tibble convert from double to logical

Asked 2021-Jun-14 at 16:50

Edit: It looks like this is a known issue with the "cascade" method. Results that return NA values after the first attempt don't like being converted to doubles when subsequent methods return lat/lons.

Data: I have a list of addresses that I need to geocode. I'm using lapply() to split-apply-combine, which works, but very slowly. My thought to split (further)-apply-combine is returning errors about dim names and sizes that are confusing to me.

...

ANSWER

Answered 2021-Jun-14 at 15:59

It is working with dplyr 1.0.6

Source https://stackoverflow.com/questions/67973344

QUESTION

Replaces all values with "NA" in R dataframe

Asked 2021-Jun-14 at 16:20

I have a set of data

...

ANSWER

Answered 2021-Jun-14 at 16:20

Just multiply with NA as any operation with NA results in NA and here we could either multiply or add (+) or subtract (-) or divide (/) and it still returns NA

Source https://stackoverflow.com/questions/67973787

QUESTION

How to run a Spark-Scala unit test notebook in Databricks?

Asked 2021-Jun-14 at 15:42

I am trying to write a unit test code for my Spark-Scala notebook using scalatest.funsuite but the notebook with test() is not getting executed in databricks. Could you please let me know how can I run it?

Here is the sample test code for the same.

...

ANSWER

Answered 2021-Jun-14 at 15:42

You need to explicitly create the object for that test suite & execute it. In IDE you're relying on specific runner, but it doesn't work in the notebook environment.

You can use either the .execute function of create object (docs):

Source https://stackoverflow.com/questions/67971085

QUESTION

Count number of fields that match in an Array of Object in mongodb

Asked 2021-Jun-14 at 15:40

What I have

I have a DB in MongoDB like this:

...

ANSWER

Answered 2021-Jun-14 at 15:39

$filter to iterate loop of Series array
$regexMatch to search format in seb
$size to get total elements in filtered result

Source https://stackoverflow.com/questions/67972986

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

Vulnerabilities

No vulnerabilities reported

Install seq

Pre-built binaries for Linux and macOS on x86_64 are available alongside each release. We also have a script for downloading and installing pre-built versions:.
See Building from Source.