This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot.

Related tags

Data AnalysissuperSFS
Overview

superSFS

This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot. It is easy-to-use and runing fast. What you should prepare is the phased vcf file containg the data of populations you intrested and the outgroup, the outgroup name file, and the annotation file. Enjoy it!!!

It has four models:

0:Using all function, from original vcf data to sfs barplot
1: Only speculate the ancestral allel and output new vcf file using speculated allel as reference
2: Only count the frequency of derived allel in each snp of each population
3: Only draw bar polt of sfs using data generated from the results of calutation of sfs

Example:

Model 0: python superSFS 0 ogdir threshold vcfdir annodir modir coutdir plotdir group
Model 1: python superSFS 1 ogdir threshold vcfdir outdir
Model 2: python superSFS 2 annodir modir coutdir
Model 3: python superSFS 3 coutdir plotdir group

Explation for each parameter:

ogdir: direction of outgroup names file
threshold: a number that if the sum of variant allel in outpgroup greater than it,the variant allel will be counted as ancestral allel
vcfdir: direction of vcf data
vannodir: direction of annotation file with sample names in first column and group name in second colum. This file should has header in first row
vmodir: assign the output direction of generated vcf file using speculated allel as reference
countdir: assign the output direction of calculation of derived allels for each snp in each group
plotdir: assign the output direction of bar plot of sfs
group: the group that you want to analysis
Business Intelligence (BI) in Python, OLAP

Open Mining Business Intelligence (BI) Application Server written in Python Requirements Python 2.7 (Backend) Lua 5.2 or LuaJIT 5.1 (OML backend) Mong

Open Mining 1.2k Dec 27, 2022
Churn prediction with PySpark

It is expected to develop a machine learning model that can predict customers who will leave the company.

3 Aug 13, 2021
In this tutorial, raster models of soil depth and soil water holding capacity for the United States will be sampled at random geographic coordinates within the state of Colorado.

Raster_Sampling_Demo (Resulting graph of this demo) Background Sampling values of a raster at specific geographic coordinates can be done with a numbe

2 Dec 13, 2022
Hidden Markov Models in Python, with scikit-learn like API

hmmlearn hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models. For supervised learning learning of HMMs and

2.7k Jan 03, 2023
Package for decomposing EMG signals into motor unit firings, as used in Formento et al 2021.

EMGDecomp Package for decomposing EMG signals into motor unit firings, created for Formento et al 2021. Based heavily on Negro et al, 2016. Supports G

13 Nov 01, 2022
Building house price data pipelines with Apache Beam and Spark on GCP

This project contains the process from building a web crawler to extract the raw data of house price to create ETL pipelines using Google Could Platform services.

1 Nov 22, 2021
BioMASS - A Python Framework for Modeling and Analysis of Signaling Systems

Mathematical modeling is a powerful method for the analysis of complex biological systems. Although there are many researches devoted on produ

BioMASS 22 Dec 27, 2022
A set of functions and analysis classes for solvation structure analysis

SolvationAnalysis The macroscopic behavior of a liquid is determined by its microscopic structure. For ionic systems, like batteries and many enzymes,

MDAnalysis 19 Nov 24, 2022
CPSPEC is an astrophysical data reduction software for timing

CPSPEC manual Introduction CPSPEC is an astrophysical data reduction software for timing. Various timing properties, such as power spectra and cross s

Tenyo Kawamura 1 Oct 20, 2021
A simple and efficient tool to parallelize Pandas operations on all available CPUs

Pandaral·lel Without parallelization With parallelization Installation $ pip install pandarallel [--upgrade] [--user] Requirements On Windows, Pandara

Manu NALEPA 2.8k Dec 31, 2022
A Python 3 library making time series data mining tasks, utilizing matrix profile algorithms

MatrixProfile MatrixProfile is a Python 3 library, brought to you by the Matrix Profile Foundation, for mining time series data. The Matrix Profile is

Matrix Profile Foundation 302 Dec 29, 2022
Import, connect and transform data into Excel

xlwings_query Import, connect and transform data into Excel. Description The concept is to apply data transformations to a main query object. When the

George Karakostas 1 Jan 19, 2022
Elementary is an open-source data reliability framework for modern data teams. The first module of the framework is data lineage.

Data lineage made simple, reliable, and automated. Effortlessly track the flow of data, understand dependencies and analyze impact. Features Visualiza

898 Jan 09, 2023
Project: Netflix Data Analysis and Visualization with Python

Project: Netflix Data Analysis and Visualization with Python Table of Contents General Info Installation Demo Usage and Main Functionalities Contribut

Kathrin Hälbich 2 Feb 13, 2022
Functional tensors for probabilistic programming

Funsor Funsor is a tensor-like library for functions and distributions. See Functional tensors for probabilistic programming for a system description.

208 Dec 29, 2022
Retentioneering 581 Jan 07, 2023
Titanic data analysis for python

Titanic-data-analysis This Repo is an analysis on Titanic_mod.csv This csv file contains some assumed data of the Titanic ship after sinking This full

Hardik Bhanot 1 Dec 26, 2021
Fast, flexible and easy to use probabilistic modelling in Python.

Please consider citing the JMLR-MLOSS Manuscript if you've used pomegranate in your academic work! pomegranate is a package for building probabilistic

Jacob Schreiber 3k Jan 02, 2023
Yet Another Workflow Parser for SecurityHub

YAWPS Yet Another Workflow Parser for SecurityHub "Screaming pepper" by Rum Bucolic Ape is licensed with CC BY-ND 2.0. To view a copy of this license,

myoung34 8 Dec 22, 2022
Unsub is a collection analysis tool that assists libraries in analyzing their journal subscriptions.

About Unsub is a collection analysis tool that assists libraries in analyzing their journal subscriptions. The tool provides rich data and a summary g

9 Nov 16, 2022