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
Minimal working example of data acquisition with nidaqmx python API

Data Aquisition using NI-DAQmx python API Based on this project It is a minimal working example for data acquisition using the NI-DAQmx python API. It

Pablo 1 Nov 05, 2021
Python package for processing UC module spectral data.

UC Module Python Package How To Install clone repo. cd UC-module pip install . How to Use uc.module.UC(measurment=str, dark=str, reference=str, heade

Nicolai Haaber Junge 1 Oct 20, 2021
INF42 - Topological Data Analysis

TDA INF421(Conception et analyse d'algorithmes) Projet : Topological Data Analysis SphereMin Etant donné un nuage des points, ce programme contient de

2 Jan 07, 2022
Created covid data pipeline using PySpark and MySQL that collected data stream from API and do some processing and store it into MYSQL database.

Created covid data pipeline using PySpark and MySQL that collected data stream from API and do some processing and store it into MYSQL database.

2 Nov 20, 2021
Python Project on Pro Data Analysis Track

Udacity-BikeShare-Project: Python Project on Pro Data Analysis Track Basic Data Exploration with pandas on Bikeshare Data Basic Udacity project using

Belal Mohammed 0 Nov 10, 2021
simple way to build the declarative and destributed data pipelines with python

unipipeline simple way to build the declarative and distributed data pipelines. Why you should use it Declarative strict config Scaffolding Fully type

aliaksandr-master 0 Jan 26, 2022
ICLR 2022 Paper submission trend analysis

Visualize ICLR 2022 OpenReview Data

Jintang Li 75 Dec 06, 2022
Helper tools to construct probability distributions built from expert elicited data for use in monte carlo simulations.

Elicited Helper tools to construct probability distributions built from expert elicited data for use in monte carlo simulations. Credit to Brett Hoove

Ryan McGeehan 3 Nov 04, 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
PostQF is a user-friendly Postfix queue data filter which operates on data produced by postqueue -j.

PostQF Copyright © 2022 Ralph Seichter PostQF is a user-friendly Postfix queue data filter which operates on data produced by postqueue -j. See the ma

Ralph Seichter 11 Nov 24, 2022
Pypeln is a simple yet powerful Python library for creating concurrent data pipelines.

Pypeln Pypeln (pronounced as "pypeline") is a simple yet powerful Python library for creating concurrent data pipelines. Main Features Simple: Pypeln

Cristian Garcia 1.4k Dec 31, 2022
Multiple Pairwise Comparisons (Post Hoc) Tests in Python

scikit-posthocs is a Python package that provides post hoc tests for pairwise multiple comparisons that are usually performed in statistical data anal

Maksim Terpilowski 264 Dec 30, 2022
Improving your data science workflows with

Make Better Defaults Author: Kjell Wooding [email protected] This is the git re

Kjell Wooding 18 Dec 23, 2022
Spectral Analysis in Python

SPECTRUM : Spectral Analysis in Python contributions: Please join https://github.com/cokelaer/spectrum contributors: https://github.com/cokelaer/spect

Thomas Cokelaer 280 Dec 16, 2022
Data-sets from the survey and analysis

bachelor-thesis "Umfragewerte.xlsx" contains the orginal survey results. "umfrage_alle.csv" contains the survey results but one participant is cancele

1 Jan 26, 2022
Useful tool for inserting DataFrames into the Excel sheet.

PyCellFrame Insert Pandas DataFrames into the Excel sheet with a bunch of conditions Install pip install pycellframe Usage Examples Let's suppose that

Luka Sosiashvili 1 Feb 16, 2022
Pyspark Spotify ETL

This is my first Data Engineering project, it extracts data from the user's recently played tracks using Spotify's API, transforms data and then loads it into Postgresql using SQLAlchemy engine. Data

16 Jun 09, 2022
Top 50 best selling books on amazon

It's a dashboard that shows the detailed information about each book in the top 50 best selling books on amazon over the last ten years

Nahla Tarek 1 Nov 18, 2021
Finding project directories in Python (data science) projects, just like there R rprojroot and here packages

Find relative paths from a project root directory Finding project directories in Python (data science) projects, just like there R here and rprojroot

Daniel Chen 102 Nov 16, 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