aldy | Allelic decomposition and exact genotyping | Genomics library

by 0xTCG Python Version: Current License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(4)Vulnerabilities Install Support

kandi X-RAY | aldy Summary

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

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Support

Quality

Security

License

Reuse

Support

aldy has a low active ecosystem.

It has 19 star(s) with 12 fork(s). There are 4 watchers for this library.

It had no major release in the last 6 months.

There are 4 open issues and 17 have been closed. On average issues are closed in 107 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of aldy is current.

Quality

aldy has no bugs reported.

Security

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

License

aldy 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

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

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

Top functions reviewed by kandi - BETA

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

Load long sam file
Return chr prefix
Return a samtools representation of this region
Return the script path for a resource key
Calculate the consensus alignment of two reads
Calculate consensus consensus data
Calculate the consensus base based on the given locus
Extract locus from a list of locus
Phase each variant in the target
Calculate the loss for a given index
Calculate the peak of a contig
Calculate the end point of a contig
Check if the query matches the given indel type
Check if two sequences are equal
Check if the end of the sequence contains repeats
Calculate the consensus sequence
Return the character in the sequence at i
Load a sam file
Check if a read is in a region
Load a VCF file
Load the CN - neutral region
Calculate the coverage ratio of the CN - neutral region
Dump the coverage information
Add a new variable to the model
Return the version number
Adds a constraint to the model

Get all kandi verified functions for this library.

aldy Key Features

No Key Features are available at this moment for aldy.

aldy Examples and Code Snippets

No Code Snippets are available at this moment for aldy.

Community Discussions

Trending Discussions on aldy

System.Linq.Dynamic.Core cannot compare 'object' type

for-loop in loop syntax error: unexpected end of file

Why kafka throw Received -1 when reading from channel, socket has likely been closed, when spark streaming to secured kafka?

Incomparable types: String and class name

QUESTION

System.Linq.Dynamic.Core cannot compare 'object' type

Asked 2020-Nov-12 at 04:00

I'm trying to run a dynamic query with a model as below:

...

ANSWER

Answered 2020-Nov-12 at 04:00

It is possible if you use .Equals(), which will first check to see if the types are identical and, if they are not, will perform a cast to the run-time type.

Source https://stackoverflow.com/questions/64797434

QUESTION

for-loop in loop syntax error: unexpected end of file

Asked 2020-Apr-02 at 15:53

I'm trying to run a program called aldy on several .json files with a list of items (A, B, C, D)

I want to use the file name without the extension
like bob in bob.json, amy in amy.json

The desired output would be
bob.a.txt, bob.b.txt, ...
amy.a.txt, amy.b.txt, ...

The code I have

...

ANSWER

Answered 2020-Apr-02 at 15:53

Make the following corrections:

for i in "${LIST[@]}"; do. That's how you get all elements of an array.
outfile=${filename}.${i}.txt.
1. There may be no spaces around = in assignments.
2. Concatenating variables is done by placing them next to one another. You can use braces (as in ${expandthis}butnotthis) to delimit them, but in your case simply $filename.$i.txt would do (. serves as delimiter).
aldy -g "$i" -o "$outfile" "$file". Quote your variables when expanding them. If you always do it, either the quotes will be redundant, or (in most cases) they will prevent problems caused by word splitting and globbing.

Source https://stackoverflow.com/questions/60995340

QUESTION

Why kafka throw Received -1 when reading from channel, socket has likely been closed, when spark streaming to secured kafka?

Asked 2018-Nov-28 at 06:07

I'm getting this error when trying to stream from spark (using Java) to secured Kafka (with SASL PLAINTEXT mechanism).

more detailed error message:

...

ANSWER

Answered 2017-Jul-07 at 09:33

i've been resolved my problem with following guide from https://spark.apache.org/docs/latest/streaming-kafka-0-10-integration.html.

i replaced my spark-streaming-kafka_2.11 in my pom.xml to spark-streaming-kafka-0-10_2.11 and version 2.11.

based on error logs above in question. Im curious that the error throwed by SimpleConsumer, which SimpleConsumer is determined as an old consumer. Then i replace my pom dependencies as i said above, and change my code into following spark streaming integration guide above. Now i can stream into secured sasl plain kafka.

Source https://stackoverflow.com/questions/44965604

QUESTION

Incomparable types: String and class name

Asked 2017-Mar-17 at 18:53

I want to make a program that can search for books in a library. But i found the error on if part for search a book in that list:

...

ANSWER

Answered 2017-Mar-17 at 18:31

String cari;
System.out.println("Masukkan buku yang ingin dicari: ");
cari = in.nextLine();
if(cari == buku1.Perpus[1])

Source https://stackoverflow.com/questions/42864606

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

Vulnerabilities

No vulnerabilities reported

Install aldy

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

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