scallop | Scallop is a reference-based transcriptome assembler | Genomics library

by Kingsford-Group C++ Version: v0.10.5 License: BSD-3-Clause

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

kandi X-RAY | scallop Summary

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

Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be proved preserving all phasing paths from reads and paired-end reads, while also achieves both transcripts parsimony and coverage deviation minimization. Scallop paper has been published at Nature Biotechnology. The datasets and scripts used in this paper to compare the performance of Scallop and other assemblers are available at scalloptest. Please also checkout the podcast about Scallop (thanks Roman Cheplyaka for the interview). It is available at both the bioinformatics chat and iTunes.

Support

Quality

Security

License

Reuse

Support

scallop has a low active ecosystem.

It has 75 star(s) with 16 fork(s). There are 15 watchers for this library.

It had no major release in the last 12 months.

There are 8 open issues and 22 have been closed. On average issues are closed in 19 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of scallop is v0.10.5

Quality

scallop has 0 bugs and 0 code smells.

Security

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

scallop code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

scallop is licensed under the BSD-3-Clause License. This license is Permissive.

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

Reuse

scallop releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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scallop Key Features

No Key Features are available at this moment for scallop.

scallop Examples and Code Snippets

No Code Snippets are available at this moment for scallop.

Community Discussions

Trending Discussions on scallop

Regex captures commented rows, but nothing when try to remove commented rows

How do I add a column of abundance data by summing observations per site?

ValueError: Out of range float values are not JSON compliant error on Heroku, and WSL but not on Windows

undefined while trying to calculate price in object

Intellij Idea Code Coverage Vs Maven Jacoco

How to parallelize classification with Zero Shot Classification by Huggingface?

BigQuery SQL : Left Join with aggregate conditions

Creating multiple Modals for many different pictures

Kafka Streams 2.3 to 2.5 upgrade breaks Scala compilation

How to plot mean CPUE for multiple species with ggplot in R

QUESTION

Regex captures commented rows, but nothing when try to remove commented rows

Asked 2022-Mar-23 at 15:15

I'm trying to re-use a regex I'm using to parse another file. This file has some commented rows, and I need to make sure the commented rows aren't captured.

This is the string being parsed:

...

ANSWER

Answered 2022-Feb-22 at 04:52

Not a robust solution, it does work for the code currently posted but I do not assure this will work with the actual code you might test it on.

The regex expects a single string, hence, when testing this with your file, make sure you're using the -Raw switch.

See https://regex101.com/r/l0RLPw/2 for details.

Source https://stackoverflow.com/questions/71212777

QUESTION

How do I add a column of abundance data by summing observations per site?

Asked 2022-Mar-08 at 15:27

I have a dataframe containing observations of scallop presence/absence across multiple sites. I would like to count the number of scallops per site, using the UID (unique identifier) and the presence/absence column (binary: 0 is absent, 1 is present).

My dataframe looks like this:

UID Present.Absent Size.cm binary A-10-2021 Present 4.60 1 A-10-2021 Present 6.0 1 A-11-2021 Present 4.70 1 A-11-2021 Present 4.8 1 A-4-2021 Absent NA 0 A-5-2021 Present 5.90 1 A-5-2021 Present 6.00 1 A-5-2021 Present 6.00 1 A-5-2021 Present 3.90 1 A-5-2021 Present 5.00 1 A-6-2021 Absent NA 0

and it goes on for about ~6000 observations, with about 1500 different UIDs

I am new to R, and wasn't sure how to go about this. Is there a way to have it so there's one row per UID, with a column of abundance data? Any help is much appreciated, and if any additional information would help, I am happy to provide. Thank you!

Edit: added sample of data ; first 10 rows

...

ANSWER

Answered 2022-Mar-08 at 15:27

You can use group_by() to achieve that:

Source https://stackoverflow.com/questions/71397156

QUESTION

ValueError: Out of range float values are not JSON compliant error on Heroku, and WSL but not on Windows

Asked 2022-Feb-18 at 04:19

I'm trying to deploy a CNN model created using Tensorflow to Heroku with FastAPI. The app runs on Heroku but returns an error when trying to make model predictions. Running heroku logs --tail returns this:

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ANSWER

Answered 2022-Feb-17 at 08:30

This error usually occurs when JSON attempts to convert a NaN value and fails to do so. Probably, tensorflow returns NaN at some point. I would advise you to try debugging by looking for a NaN value

Source https://stackoverflow.com/questions/71152285

QUESTION

undefined while trying to calculate price in object

Asked 2021-Sep-12 at 07:54

I'm taking the Codecademy Javascript course. I'm tasked with making a menu. I just learned about objects and I'm still a little fuzzy on the distinction between methods and properties right now. I've been following along to their video trying to debug my code but as far as I can tell it should function the same, if not be exactly the same.

...

ANSWER

Answered 2021-Sep-12 at 07:54

Your variable name is appetizer

Source https://stackoverflow.com/questions/69149464

QUESTION

Intellij Idea Code Coverage Vs Maven Jacoco

Asked 2021-Mar-10 at 21:45

when I run my tests in Intellij idea choosing code coverage tool as JaCoCo and include my packages I see I get 80% above coverage in the report but when I run it using maven command line I get 0% in JaCoCo report below are two questions.

can I see what command Intellij Idea Ultimate version is using to run my unit tests with code coverage ?
Why my maven command mvn clean test jacoco:report is showing my coverage percentage as 0%.

This is a Scala maven project.

My POM.xml file:-

...

ANSWER

Answered 2021-Feb-03 at 22:16

Assuming that you are using JaCoCo with cobertura coverage you need to declare the dependencies and the plugin to run the command mvn cobertura:cobertura.

Source https://stackoverflow.com/questions/66032697

QUESTION

How to parallelize classification with Zero Shot Classification by Huggingface?

Asked 2021-Feb-18 at 01:31

I have around 70 categories (it can be 20 or 30 also) and I want to be able to parallelize the process using ray but I get an error:

...

ANSWER

Answered 2021-Feb-18 at 01:31

This error is happening because of sending large objects to redis. merged_df is a large dataframe and since you are calling get_meal_category 10 times, Ray will attempt to serialize merged_df 10 times. Instead if you put merged_df into the Ray object store just once, and then pass along a reference to the object, this should work.

EDIT: Since the classifier is also large, do something similar for that as well.

Can you try something like this:

Source https://stackoverflow.com/questions/66249631

QUESTION

BigQuery SQL : Left Join with aggregate conditions

Asked 2021-Feb-07 at 18:57

I have two Tables like : Table1:

...

ANSWER

Answered 2021-Feb-07 at 18:03

Try the following

Source https://stackoverflow.com/questions/66091089

QUESTION

Creating multiple Modals for many different pictures

Asked 2020-Jun-26 at 18:02

I have a modal that contains many different items(Menu items). I want to make it so when I click the heading of any specific menu item, another modal pops-up showing the image of said dish. The only issue I run into, is that I would have to create a ton of different modals for each item dish(15 of them). IS there a way I can create a function/loop fthem so they only access a soecific image attatched to said item? Should I create a seperate container for the images? Or add them to the item containers themselves and set the display to none?

Here is an example without much css or the JS with it? Any thoughts of the best way to tackle this?

...

ANSWER

Answered 2020-Jun-26 at 18:02

You don't need a separate modal for each image. You just need a one modal that will display different images.

Using javascript, you need to add a click event listener to the container of all the items. When any items is clicked, get the src attribute of the img element associated with that item and set this src attribute as the src attribute of the img in the modal.

Here's a demo in which i have 3 images which are displayed in a modal one at a time depending on which image label you clicked on.

Source https://stackoverflow.com/questions/62600067

QUESTION

Kafka Streams 2.3 to 2.5 upgrade breaks Scala compilation

Asked 2020-Jun-16 at 11:10

When upgrading from KafkaStreams library from 2.3 to 2.5, keeping the same Scala version, it breaks when running with the following error:

...

ANSWER

Answered 2020-Jun-16 at 11:10

I just had to upgrade my Scala version to the one published in the "Compiled Dependencies" section here, which is:

Source https://stackoverflow.com/questions/62395841

QUESTION

How to plot mean CPUE for multiple species with ggplot in R

Asked 2020-May-24 at 20:42

I'm trying to figure out the best way to plot mean CPUE for the top 5 most abundant species by year. I was able to plot these all separately, but it requires a lot of code and gets messy and I can't figure out how to get them all on the same figure.

This is a subset of my data

...

ANSWER

Answered 2020-May-24 at 06:58

Get the most common species according to mean CPUE value over all years

Source https://stackoverflow.com/questions/61978050

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

Vulnerabilities

No vulnerabilities reported

Install scallop

Download the source code of Scallop from here. Scallop uses additional libraries of Boost and htslib (NOTE: from v0.10.4 the dependence on Clp is optional). If they have not been installed in your system, you first need to download and install them. You might also need to export the runtime library path to certain environmental variable (for example, LD_LIBRARY_PATH, for most linux distributions). After install these dependencies, you then compile the source code of Scallop. If some of the above dependencies are not installed to the default system directories (for example, /usr/local, for most linux distributions), their corresponding installing paths should be specified to configure of Scallop.
If Boost has not been downloaded/installed, download Boost (license) from (http://www.boost.org). Uncompress it somewhere (compiling and installing are not necessary).
If htslib has not been installed, download htslib (license) from (http://www.htslib.org/) with version 1.5 or higher. Note that htslib relies on zlib. So if zlib has not been installed in your system, you need to install zlib first. To do so, download zlib (license) at (https://zlib.net/). Use the following commands to install zlib:.
NOTE: Clp will be used to solve the linear programming instances created when decomposing unsplitable vertices. An alternative algorithm is provided in Scallop from version v0.10.4 (and hence since then the installation of Clp becomes optional). Our testing shows that these two algorithms give very similar results. If Clp has not been installed in your system, download Clp (license) from (https://projects.coin-or.org/Clp). Use the following to install Clp.

Support

Scallop is, and will continue to be, freely and actively supported on a best-effort basis. If you need industrial-grade technical support, please consider the options at oceangenomics.com/support.

Find more information at: