snps | tools for reading , writing , merging , and remapping SNPs | Genomics library

by apriha Python Version: 2.8.1 License: BSD-3-Clause

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

kandi X-RAY | snps Summary

snps is a Python library typically used in Artificial Intelligence, Genomics applications. snps has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install snps' or download it from GitHub, PyPI.

tools for reading, writing, merging, and remapping SNPs

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Quality

Security

License

Reuse

Support

snps has a low active ecosystem.

It has 69 star(s) with 17 fork(s). There are 5 watchers for this library.

There were 1 major release(s) in the last 12 months.

There are 20 open issues and 37 have been closed. On average issues are closed in 191 days. There are 3 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of snps is 2.8.1

Quality

snps has no bugs reported.

Security

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

License

snps 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

snps releases are available to install and integrate.

Deployable package is available in PyPI.

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

Top functions reviewed by kandi - BETA

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

Return a dict of the command - line tool
Read data from file
Extract version information from VCS
Save a Pandas DataFrame as a csv file
Get project root directory
Construct a ConfigParser from a root
Creates an analysis plot
Read the SNPs data into a dictionary
Create a vcf representation for the given task
Get reference sequences
Create reference sequences
Clear the sequence
Create the versioneer config file
Save a pandas dataframe as a csv file
Get the number of chromosomes for each chromosome
Load the contents of the opennp_datadump file
Write SNPs to file
Assign PAR SNPs
Scans the given setup py file and checks if it is missing
Loads the contents of the OpenSSnp datadump file
Read a file from a file
Return a list of OpenAPI datadump files
Load SNPs file
Duplicate heterozygous SNPs
Return the sex of the person
Compute variant name
Returns the sequence sequence
Returns the length of the sequence
End of the sequence

Get all kandi verified functions for this library.

snps Key Features

No Key Features are available at this moment for snps.

snps Examples and Code Snippets

No Code Snippets are available at this moment for snps.

Community Discussions

Trending Discussions on snps

How to extract two consecutive lines that match pattern in python

Applying Bonferroni correction to eQTL analysis done with Matrix_eQTL_engine

Change terminal labels of phylogram - plotBS function {phangorn package}

How to summerize by column(s) and value with R

Filtering haplotypes which contains AAGAGACAAG in the middle

How do I find common characters in a list of dataframes?

Unable to pass a sentence in a list of strings using extra-vars in Ansible

Fast way to compare concatenated string with values in vector

Script to make 1 random layer visible within each group [Photoshop cc2018]

How to speed up forloop grep in a large dataframe using R

QUESTION

How to extract two consecutive lines that match pattern in python

Asked 2021-Jun-11 at 10:08

I am trying to extract lines that match two different patterns from test.txt.
First I want to extract line that match >> fbat -v1 and then match the corresponding line just below p-value(2-sided).

This is the code I tried, but it only extracts the first match.

...

ANSWER

Answered 2021-Jun-10 at 15:15

import re

file = open('test.txt')
for idx, line in enumerate(file):
    match = re.findall('^>> fbat -v1', line)
    if match:
        match = re.findall('p-value(2-sided)', file[idx+1])

Source https://stackoverflow.com/questions/67923967

QUESTION

Applying Bonferroni correction to eQTL analysis done with Matrix_eQTL_engine

Asked 2021-May-17 at 18:50

I have completed an eqtl analysis using the MatrixEQTL package.

...

ANSWER

Answered 2021-May-17 at 18:50

the author of the package here.

First, I would NOT suggest using pvOutputThreshold = 1 as it can result in storing billions of p-values and make R run out of memory.

Second, Matrix eQTL returns the number of tests it has conducted, so that you can do Bonferroni correction yourself. You can get it with this line:

Source https://stackoverflow.com/questions/67574975

QUESTION

Change terminal labels of phylogram - plotBS function {phangorn package}

Asked 2021-May-13 at 16:03

I want to change terminal/taxa colour to blue, for specific taxa.

I'd like to change "Pomquet Lake", "Lake Ainslie", "Black River", "Pinchgut Lake", and "Blue Pond" to blue. is there a way to do this?

Code (figure below):

...

ANSWER

Answered 2021-May-13 at 15:52

No data are given, so that the example is not fully reproducible. The following general example using hclust may hopefully give you an idea:

Source https://stackoverflow.com/questions/67521918

QUESTION

How to summerize by column(s) and value with R

Asked 2021-Apr-24 at 17:53

In R I have a dataframe with an ID column, multiple columns with a categorical value ('AA', 'AB', 'BB') and 1 column with a numerical value. It looks like this:

SUBJID SNP1 SNP2 Concentration 1 'AA' 'BB' 20 2 'AA' 'AA' 8 3 'BB' 'BB' 19 4 'AB' 'AB' 30

Needed is the mean 'concentration' for each value per column. Can this be done with dplyr in the current dataframe or should I first transform the dataframe to a different shape for example?

I know how to get the mean value for 1 specific column: df %>% group_by(SNP1) %>% summarise(n=n(), Mean = mean)). This doesn't help me to get the mean concentration per value within a column for multiple columns.

Desired output:

Group Mean concentration SNP1 'AA' 20.5 SNP1 'AB' 22.5 SNP1 'BB' 19.8 SNP2 'AA' 20.9 SNP2 'AB' 18.9 SNP2 'BB' 15.1

Has to be done for up to 13 columns (SNPs).

...

ANSWER

Answered 2021-Apr-24 at 16:51

Is this what you are looking for? The 'trick' here is to pivot_longer:

Source https://stackoverflow.com/questions/67242677

QUESTION

Filtering haplotypes which contains AAGAGACAAG in the middle

Asked 2021-Feb-25 at 11:56

For my project, I need to find out which haplotyp (40 SNPs) is mostly causing the phenotyp.
For this I want to find out which haplotypes are associated with a very high or a very negative diplotypeffect. Because there are 294 different haplotypes, I need to select a smaller window (like 10 SNPs).

Now i want r to show me all rows where the 10 SNPs are contained in the 40 SNPs with the command:

...

ANSWER

Answered 2021-Feb-25 at 11:39

%in% tests vector membership. What you want do do is string matching. Use grepl for that:

Source https://stackoverflow.com/questions/66367611

QUESTION

How do I find common characters in a list of dataframes?

Asked 2021-Feb-23 at 19:09

I have about 70 dataframes in a list, each of them has a column named SNP. I want to find the common SNPs that exist in all dataframes. This is the code I used:

...

ANSWER

Answered 2021-Feb-23 at 19:09

Your problems appear to be two-fold:

One of your frames is missing SNP as a column name. That will often cause problems:

Source https://stackoverflow.com/questions/66339366

QUESTION

Unable to pass a sentence in a list of strings using extra-vars in Ansible

Asked 2021-Feb-17 at 01:00

Background:

I have an Ansible utility that will take new comments as extra-vars from the users and add them to /etc/motd in the comments section. These comments are first stored in local facts file in the form of an array. My code then iterates through this and writes each comment in a new line. However, this works only for a single-word comment but not for an entire sentence.

Input format:

...

ANSWER

Answered 2021-Feb-17 at 01:00

I figured out the problem. The issue was with the quotes in my input. No change in the code was required.

Note: If the input is a sentence (with spaces), make sure that you pay attention to the quotes. There is a double quote (") within the single quotes (').

Source https://stackoverflow.com/questions/66233258

QUESTION

Fast way to compare concatenated string with values in vector

Asked 2021-Feb-09 at 00:04

I have a data frame with two columns with SNP ids, 'block1' and 'block2'. In these columns, the individual ids are concatenated and separated by |, e.g. in row 1 in 'block1': "A1|A2|A3|A4|A5|A6".

For each row in 'block1', I want to check if each individual id is present in the 'SNPA' column. In the same way I want to check if each id in 'block2' is in 'SNPB' column.

If the blocks (block1 and block2) have at least two SNPs each in a row (from the column SNPA for block1, and SNPB for block2), the row should be kept. Other rows with less than two matching SNPs should be removed, e.g. rows 9 to 14.

Example:

Taking the row 10 in my df: block1 contain 4 SNPS (A31|A32|A33|A34) but only one of them (A34) is present in the column (SNPA), so this row should be removed (idem for rows 9, 11, 12, 13 and 14). Row 14: block2 contain only 1 SNP (A57) from the SNPB column , so should be removed also, ... etc.

I tried the @NelsonGon solution, but it takes a lot of time (several days on a cluster):

...

ANSWER

Answered 2021-Feb-07 at 22:39

Instead of looping over each element of list i.e. each row of the data, an option is to convert the list to a matrix after appending NA at the end (where list elements are of lesser length than the maximum length), use %in% with rowSums to do this in a vectorized way.

Source https://stackoverflow.com/questions/66093121

QUESTION

Script to make 1 random layer visible within each group [Photoshop cc2018]

Asked 2021-Feb-02 at 14:00

I'm trying to make a script that would at random select and show a single layer from all groups on Photoshop and export the result as a png.

I found this script here that seems to work:

...

ANSWER

Answered 2021-Feb-02 at 14:00

Without seeing what your PSD looks like, it's hard to tell. However, I think the code is failing on the revert function.

Try this instead:

Source https://stackoverflow.com/questions/65996782

QUESTION

How to speed up forloop grep in a large dataframe using R

Asked 2021-Jan-22 at 19:09

Please I need help.

I have I script that works well for many dataframes even if that takes several hours (on the cluster: > 100 GB memory). For some large dataframes (> 3 Million rows ) the loop for doesn't work even after two days of running. So, I need help if there is a way to speed up the for loop or replace the script with more speeder functions in R.

This is a short description of my script/data:

...

ANSWER

Answered 2021-Jan-21 at 14:52

I tried completely different approach and deliberately increased the size of your data by 500. The solution I propose is 5 times faster for 500 times larger dataset, and should be more and more faster if the size of the data increase.

Source https://stackoverflow.com/questions/65828374

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

Vulnerabilities

No vulnerabilities reported

Install snps

You can install using 'pip install snps' or download it from GitHub, PyPI.
You can use snps 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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