SALSA | scaffold long read assemblies with Hi-C data | Genomics library

by marbl Python Version: Current License: MIT

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

kandi X-RAY | SALSA Summary

SALSA is a Python library typically used in Artificial Intelligence, Genomics applications. SALSA has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However SALSA build file is not available. You can download it from GitHub.

SALSA: A tool to scaffold long read assemblies with Hi-C data

Support

Quality

Security

License

Reuse

Support

SALSA has a low active ecosystem.

It has 125 star(s) with 35 fork(s). There are 20 watchers for this library.

It had no major release in the last 6 months.

There are 18 open issues and 108 have been closed. On average issues are closed in 120 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of SALSA is current.

Quality

SALSA has 0 bugs and 0 code smells.

Security

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

SALSA code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

SALSA is licensed under the MIT License. This license is Permissive.

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

Reuse

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

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

Installation instructions are not available. Examples and code snippets are available.

SALSA saves you 812 person hours of effort in developing the same functionality from scratch.

It has 1961 lines of code, 32 functions and 10 files.

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

Top functions reviewed by kandi - BETA

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

Convert a name to a pre - cleaned name and coordinates
Parse a fasta file
Parse a contig file
Get the maximum weight between start and end
Find the maximum reachability between start and end

Get all kandi verified functions for this library.

SALSA Key Features

No Key Features are available at this moment for SALSA.

SALSA Examples and Code Snippets

No Code Snippets are available at this moment for SALSA.

Community Discussions

Trending Discussions on SALSA

What does this higher-ranked trait bound mean?

Change string values with new values contain in another data frame

How to clear the screen in kivy

Using Tab Complete After an Established Parameter in Powershell

PySpark SQL Joining Tables

How to replace any string, of a column, in a data frame to a empty string

Can install Python 2 `gtop` module in virtual environment

Passing a function through list of columns with numpy.vectorize or DataFrame.apply?

How to align icons on website header? (CSS + HTML)

The method getType() is undefined for the type Ingredient

QUESTION

What does this higher-ranked trait bound mean?

Asked 2022-Jan-08 at 03:46

In Salsa, there is a higher-ranked trait bound on a trait. I've seen HRTBs on function definitions but not on a trait. What does it mean?

...

ANSWER

Answered 2022-Jan-03 at 19:41

It has to do with the type in the argument for query_storage:

Source https://stackoverflow.com/questions/70557666

QUESTION

Change string values with new values contain in another data frame

Asked 2022-Jan-06 at 19:08

I have a csv with thousand of rows with sales data as follows:

...

ANSWER

Answered 2022-Jan-06 at 17:41

You can use the replace function:

Source https://stackoverflow.com/questions/70611263

QUESTION

How to clear the screen in kivy

Asked 2021-Dec-20 at 14:42

I am making a simple app where it displays some recipes and you can go into an individual 'recipe screen' which shows an image/ingredients and instructions for making the recipe. However I am now trying to make a button which returns you to the recipe list. The button works however the recipe screen and the recipe list which I am returning to seem to overlap, therefore I need to figure out how to clear the recipe screen before moving to the recipe list screen. However, for some reason the clear_canvas() or clear_screen() functions do not work. What should i do instead in order to clear the kivy screen?

This is an image of the overlapping screens:

Python code:

...

ANSWER

Answered 2021-Dec-20 at 14:42

Since you add stuff to the RecipeWindow using the on_enter() method, just add an on_leave() method to clear it:

Source https://stackoverflow.com/questions/70420628

QUESTION

Using Tab Complete After an Established Parameter in Powershell

Asked 2021-Dec-09 at 03:18

I found some code that allows you to output text one character at a time and I am trying to make it fit my use case better by allowing you to select the foreground color as well. I have already added the foreground color to my parameters and it responds correctly, but the tab complete does not cycle trough the colors as it does for Write-Host.

...

ANSWER

Answered 2021-Dec-09 at 03:18

You have 2 options, that I'm aware of, to accomplish this. Both will allow you to cycle through the set with the Tab key:

ValidateSet attribute: This one will validate and throw an exception if the argument used is not in the set.

Source https://stackoverflow.com/questions/70061330

QUESTION

PySpark SQL Joining Tables

Asked 2021-Nov-17 at 16:39

I have to provide the names of the top 10 users who provided the most tips from the Yelp dataset using the tip and user tables. When I run tip.printSchema() I get:

...

ANSWER

Answered 2021-Nov-17 at 16:39

The SQL logic first finds the top 10 users with the most tips from the tip table and joins it with the user table. Left or right side of a SQL join can be another SQL expression.

Example

The examples creates dataframes with minimal information needed to illustrate query working.

Source https://stackoverflow.com/questions/70007309

QUESTION

How to replace any string, of a column, in a data frame to a empty string

Asked 2021-Nov-15 at 16:46

So I have this function which drops a row in my DF, if any string is contained inside a cell within a column called 'Aborted Reason'.

Now the only thing is, I need to change some of the logic. This column now contains a load of free text that changes for every row. Is there away that I can replace ANY string in the cell to a empty string aka ''.

Without dropping the whole row.

...

ANSWER

Answered 2021-Nov-15 at 16:46

Here it is:

Source https://stackoverflow.com/questions/69946200

QUESTION

Can install Python 2 `gtop` module in virtual environment

Asked 2021-Oct-25 at 17:38

I'm trying to run the benchmarks game repo bencher script which was written in python 2 and requires the gtop module, NOT the pygtop module. After searching everywhere and even following their README.md I could not figure out how to get this in my python 2.7.18 virtual environment (created and maintained using pyenv).

I decided to have a look at my system version of python 2.7.18 as I followed the guide from this SO reply and the packages downloaded/installed successfully. My system version of python can import the module just fine:

...

ANSWER

Answered 2021-Oct-25 at 17:38

Thank you to @SamBob for suggesting the SO reply that led to the answer.

What I've been mistakenly doing is copying the gtk-2.0 directory into my virtualenvs site-packages such that:

Source https://stackoverflow.com/questions/69700644

QUESTION

Passing a function through list of columns with numpy.vectorize or DataFrame.apply?

Asked 2021-Oct-13 at 05:46

I've got the following data frame

...

ANSWER

Answered 2021-Oct-13 at 05:46

Series.apply applies the function to each cell (row) in the Series since there is a single dimension. However, DataFrame.apply passes the entire column to the function by default. However, translate expects text not a collection.

The function to apply a function to each cell in a DataFrame is applymap and can be used as such:

Source https://stackoverflow.com/questions/69549888

QUESTION

How to align icons on website header? (CSS + HTML)

Asked 2021-Sep-13 at 12:59

So, recently I've been learning some coding for my course.

I've experimented with a few ideas, and I'm currently making this top header ("topbar") that acts as a mini-header just above the actual header, which displays some extra info.

Unfortunately, I'm a bit of a coding noob and I can't figure out what's going wrong in this code. If you run it, you'll see the social media icons on the right (I'm using Font Awesome) aren't in the header and it's a pain to try and get them there. They should be in line with the elements on the left (middle of the topbar in terms of height, and 30px inwards from the right).

I've played around with padding, margin, align and a bunch of other things but I just can't figure it out. Any help?

HTML CODE:

...

ANSWER

Answered 2021-Sep-12 at 19:02

The reason your social media icons aren't in line with everything else is because they are actually going below it.

Take a look at this image:

As you can see, the dashed blue line is your .social-links div, and it is going below the other items in your menu.

Why is this happening?

The reason this is happening is because by default a div has a display property of block

display: block means that the element should start on a new line, and take up the entire width of it's parent.

So, long story short, to fix your problem you could add something like:

Source https://stackoverflow.com/questions/69154058

QUESTION

The method getType() is undefined for the type Ingredient

Asked 2021-Sep-12 at 20:03

package tacos.web;

import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.ModelAttribute;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.SessionAttributes;
import java.lang.reflect.Field;
import lombok.extern.slf4j.Slf4j;
import tacos.Ingredient;
import tacos.Ingredient.Type;
import tacos.Taco;

@Slf4j
@Controller
@RequestMapping("/design")
@SessionAttributes("tacoOrder")
public class DesignTacoController {

@ModelAttribute
public void addIngredientsToModel(Model model) {
        List ingredients = Arrays.asList(
          new Ingredient("FLTO", "Flour Tortilla", Type.WRAP),
          new Ingredient("COTO", "Corn Tortilla", Type.WRAP),
          new Ingredient("GRBF", "Ground Beef", Type.PROTEIN),
          new Ingredient("CARN", "Carnitas", Type.PROTEIN),
          new Ingredient("TMTO", "Diced Tomatoes", Type.VEGGIES),
          new Ingredient("LETC", "Lettuce", Type.VEGGIES),
          new Ingredient("CHED", "Cheddar", Type.CHEESE),
          new Ingredient("JACK", "Monterrey Jack", Type.CHEESE),
          new Ingredient("SLSA", "Salsa", Type.SAUCE),
          new Ingredient("SRCR", "Sour Cream", Type.SAUCE)
        );

        Type[] types = Ingredient.Type.values();
        for (Type type : types) {
          model.addAttribute(type.toString().toLowerCase(),
              filterByType(ingredients, type));
        }
}
  @GetMapping
  public String showDesignForm(Model model) {
    model.addAttribute("taco", new Taco());
    return "design";
  }

  private Iterable filterByType(
      List ingredients, Type type) {
    return ingredients
              .stream()
              .filter(x -> x.getType().equals(type))
              .collect(Collectors.toList());
  }

}

...

ANSWER

Answered 2021-Sep-12 at 20:03

Seems you are not the first person who faced with this issue https://coderanch.com/t/730026/java/lombok

In addIngredientsToModel of class DesignTacoController the flagged error is "The constructor Ingredient(String, String, Ingredient.Type) is undefined". Also, in method filterByType the flagged error is "The method getType() is undefined for the type Ingredient". It zappears that lombok is just not working. But I have lombok in the pom:

Answer:

Just adding Lombok as a dependency does not make Eclipse recognize it, you'll need a plugin for that. See https://www.baeldung.com/lombok-ide for instructions on installing Lombok into Eclipse (and IntelliJ for those who prefer it).

Source https://stackoverflow.com/questions/69152843

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

Vulnerabilities

No vulnerabilities reported

Install SALSA

You can download it from GitHub.
You can use SALSA 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

This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch.

Find more information at: