ngsphy | NGSphy : phylogenomic simulation of next-generation | Genomics library

by merlyescalona Python Version: 1.0.9 License: GPL-3.0

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

kandi X-RAY | ngsphy Summary

ngsphy is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. ngsphy has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can install using 'pip install ngsphy' or download it from GitLab, GitHub, PyPI.

NGSphy is a Python open-source tool for the genome-wide simulation of NGS data (read counts or Illumina reads) obtained from thousands of gene families evolving under a common species tree, with multiple haploid and/or diploid individuals per species, where sequencing coverage (depth) heterogeneity can vary among species, individuals and loci, including off-target and uncaptured loci.

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Support

ngsphy has a low active ecosystem.

It has 12 star(s) with 7 fork(s). There are 2 watchers for this library.

It had no major release in the last 12 months.

ngsphy has no issues reported. On average issues are closed in 102 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of ngsphy is 1.0.9

Quality

ngsphy has 0 bugs and 0 code smells.

Security

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

ngsphy code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ngsphy is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

ngsphy releases are available to install and integrate.

Deployable package is available in PyPI.

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

Installation instructions, examples and code snippets are available.

It has 4143 lines of code, 136 functions and 14 files.

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

Top functions reviewed by kandi - BETA

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

Calculate the coverage matrix
Write the coverage matrix for a given replication matrix
Returns the value of the parameter
Format log record
Checks for indels for indels
Checks the arguments
Check all the files within the replicates
Check if Ploidy - tree relation exists
Check Ploidy s ploidy data
Handles command line arguments
Create a log file
Run the main loop
Retrieve the mating commands from the database
Launches a command
Add line to file
Copies the ancestral sequence file to the output folder
Parse a FASTA file and return a dictionary of sequences
Calculates ancestral sequence base frequencies
Check for Ploidy s ploidy
Validate the coverage distribution
Write script to SGE
Root the gene tree
Write the tree to disk
Iterate over replicates
Create folder structure
Run the indelible control file

Get all kandi verified functions for this library.

ngsphy Key Features

No Key Features are available at this moment for ngsphy.

ngsphy Examples and Code Snippets

No Code Snippets are available at this moment for ngsphy.

Community Discussions

Trending Discussions on Genomics

search for regex match between two files using python

Is there a way to permute inside using to variables in bash?

BigQuery Regex to extract string between two substrings

how to stop letter repeating itself python

Split multiallelic to biallelic in vcf by plink 1.9 and its variant name

Delete specific letter in a FASTA sequence

How to get the words within the first single quote in r using regex?

Does Apache Spark 3 support GPU usage for Spark RDDs?

Aggregating and summing columns across 1500 files by matching IDs in R (or bash)

Usage of compression IO functions in apache arrow

QUESTION

search for regex match between two files using python

Asked 2022-Apr-09 at 00:49

I´m working with two text files that look like this: File 1

...

ANSWER

Answered 2022-Apr-09 at 00:49

Perhaps you are after this?

Source https://stackoverflow.com/questions/71789818

QUESTION

Is there a way to permute inside using to variables in bash?

Asked 2021-Dec-09 at 23:50

I'm using the software plink2 (https://www.cog-genomics.org/plink/2.0/) and I'm trying to iterate over 3 variables.

This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file.

The idea is to iterate over the input files and then over exclude files to generate single outputfiles.

Input files: Highland.ped - Midland.ped - Lowland.ped
Exclude-map files: HighlandMidland.txt - HighlandLowland.txt - MidlandLowland.txt
Output files: HighlandMidland - HighlandLowland - MidlandHighland - MidlandLowland - LowlandHighland - LowlandMidland

The general code is:

...

ANSWER

Answered 2021-Dec-09 at 23:50

Honestly, I think your current code is quite clear; but if you really want to write this as a loop, here's one possibility:

Source https://stackoverflow.com/questions/70298074

QUESTION

BigQuery Regex to extract string between two substrings

Asked 2021-Dec-09 at 01:11

From this example string:

...

ANSWER

Answered 2021-Dec-09 at 01:11

use regexp_extract(col, r"&q;Stockcode&q;:([^/$]*?),&q;.*")

if applied to sample data in your question - output is

Source https://stackoverflow.com/questions/70283253

QUESTION

how to stop letter repeating itself python

Asked 2021-Nov-25 at 18:33

I am making a code which takes in jumble word and returns a unjumbled word , the data.json contains a list and here take a word one-by-one and check if it contains all the characters of the word and later checking if the length is same , but the problem is when i enter a word as helol then the l is checked twice and giving me some other outputs including the main one(hello). i know why does it happen but i cant get a fix to it

...

ANSWER

Answered 2021-Nov-25 at 18:33

As I understand it you are trying to identify all possible matches for the jumbled string in your list. You could sort the letters in the jumbled word and match the resulting list against sorted lists of the words in your data file.

Source https://stackoverflow.com/questions/70112201

QUESTION

Split multiallelic to biallelic in vcf by plink 1.9 and its variant name

Asked 2021-Nov-17 at 13:56

I am trying to use plink1.9 to split multiallelic into biallelic. The input is that

...

ANSWER

Answered 2021-Nov-17 at 09:45

I used bcftools to complete the task.

https://github.com/samtools/bcftools/issues/1193

Source https://stackoverflow.com/questions/70001737

QUESTION

Delete specific letter in a FASTA sequence

Asked 2021-Oct-12 at 21:00

I have a FASTA file that has about 300000 sequences but some of the sequences are like these

...

ANSWER

Answered 2021-Oct-12 at 20:28

You can match your non-X containing FASTA entries with the regex >.+\n[^X]+\n. This checks for a substring starting with > having a first line of anything (the FASTA header), which is followed by characters not containing an X until you reach a line break.

For example:

Source https://stackoverflow.com/questions/69545912

QUESTION

How to get the words within the first single quote in r using regex?

Asked 2021-Oct-04 at 22:27

For example, I have two strings:

...

ANSWER

Answered 2021-Oct-04 at 22:27

For your example your pattern would be:

Source https://stackoverflow.com/questions/69442717

QUESTION

Does Apache Spark 3 support GPU usage for Spark RDDs?

Asked 2021-Sep-23 at 05:53

I am currently trying to run genomic analyses pipelines using Hail(library for genomics analyses written in python and Scala). Recently, Apache Spark 3 was released and it supported GPU usage.

I tried spark-rapids library start an on-premise slurm cluster with gpu nodes. I was able to initialise the cluster. However, when I tried running hail tasks, the executors keep getting killed.

On querying in Hail forum, I got the response that

That’s a GPU code generator for Spark-SQL, and Hail doesn’t use any Spark-SQL interfaces, only the RDD interfaces.

So, does Spark3 not support GPU usage for RDD interfaces?

...

ANSWER

Answered 2021-Sep-23 at 05:53

As of now, spark-rapids doesn't support GPU usage for RDD interfaces.

Source: Link

Apache Spark 3.0+ lets users provide a plugin that can replace the backend for SQL and DataFrame operations. This requires no API changes from the user. The plugin will replace SQL operations it supports with GPU accelerated versions. If an operation is not supported it will fall back to using the Spark CPU version. Note that the plugin cannot accelerate operations that manipulate RDDs directly.

Here, an answer from spark-rapids team

Source: Link

We do not support running the RDD API on GPUs at this time. We only support the SQL/Dataframe API, and even then only a subset of the operators. This is because we are translating individual Catalyst operators into GPU enabled equivalent operators. I would love to be able to support the RDD API, but that would require us to be able to take arbitrary java, scala, and python code and run it on the GPU. We are investigating ways to try to accomplish some of this, but right now it is very difficult to do. That is especially true for libraries like Hail, which use python as an API, but the data analysis is done in C/C++.

Source https://stackoverflow.com/questions/69273205

QUESTION

Aggregating and summing columns across 1500 files by matching IDs in R (or bash)

Asked 2021-Sep-07 at 13:09

I have 1500 files with the same format (the .scount file format from PLINK2 https://www.cog-genomics.org/plink/2.0/formats#scount), an example is below:

...

ANSWER

Answered 2021-Sep-07 at 11:10

a tidyverse solution

Source https://stackoverflow.com/questions/69086946

QUESTION

Usage of compression IO functions in apache arrow

Asked 2021-Jun-02 at 18:58

I have been implementing a suite of RecordBatchReaders for a genomics toolset. The standard unit of work is a RecordBatch. I ended up implementing a lot of my own compression and IO tools instead of using the existing utilities in the arrow cpp platform because I was confused about them. Are there any clear examples of using the existing compression and file IO utilities to simply get a file stream that inflates standard zlib data? Also, an object diagram for the cpp platform would be helpful in ramping up.

...

ANSWER

Answered 2021-Jun-02 at 18:58

Here is an example program that inflates a compressed zlib file and reads it as CSV.

Source https://stackoverflow.com/questions/67799265

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

Vulnerabilities

No vulnerabilities reported

Install ngsphy

NGSphy simulates reads (or read counts) from alignments originated from single gene trees or gene-tree distributions (originated from species-tree distributions). It is designed to read directly from SimPhy (a simulator of gene family evolution) in the case of gene-tree distributions, but it can also be fed with gene trees directly. These trees can contain orthologs, paralogs and xenologs. Alignments are simulated using INDELible and can represent multiple haploid and/or diploid individuals per species. Then, either Illumina reads (using ART) or read counts are simulated for each individual, with the depth of coverage allowed to vary between species, individuals and loci. This flexibility allows for the simulation of both off-target (captured but not targeted) and uncaptured (targeted but not captured) loci. You will need a NGSphy settings file and the required files according to the input mode selected (see bellow).
Examples of setting files can be found here.
For installation please go here
For detailed explanations please search in the full manual.
In the Wiki you can find: tutorials for each of the possible input modes a validation test a use case test

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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