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
MotorcycleParts DataAnalysis python

We work with the accounting department of a company that sells motorcycle parts. The company operates three warehouses in a large metropolitan area.

NASEEM A P 1 Jan 12, 2022
Intercepting proxy + analysis toolkit for Second Life compatible virtual worlds

Hippolyzer Hippolyzer is a revival of Linden Lab's PyOGP library targeting modern Python 3, with a focus on debugging issues in Second Life-compatible

Salad Dais 6 Sep 01, 2022
PyEmits, a python package for easy manipulation in time-series data.

PyEmits, a python package for easy manipulation in time-series data. Time-series data is very common in real life. Engineering FSI industry (Financial

Thompson 5 Sep 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
A library to create multi-page Streamlit applications with ease.

A library to create multi-page Streamlit applications with ease.

Jackson Storm 107 Jan 04, 2023
General Assembly's 2015 Data Science course in Washington, DC

DAT8 Course Repository Course materials for General Assembly's Data Science course in Washington, DC (8/18/15 - 10/29/15). Instructor: Kevin Markham (

Kevin Markham 1.6k Jan 07, 2023
Describing statistical models in Python using symbolic formulas

Patsy is a Python library for describing statistical models (especially linear models, or models that have a linear component) and building design mat

Python for Data 866 Dec 16, 2022
CS50 pset9: Using flask API to create a web application to exchange stocks' shares.

C$50 Finance In this guide we want to implement a website via which users can “register”, “login” “buy” and “sell” stocks, like below: Background If y

1 Jan 24, 2022
Exploratory data analysis

Exploratory data analysis An Exploratory data analysis APP TAPIWA CHAMBOKO 🚀 About Me I'm a full stack developer experienced in deploying artificial

tapiwa chamboko 1 Nov 07, 2021
Pipeline to convert a haploid assembly into diploid

HapDup (haplotype duplicator) is a pipeline to convert a haploid long read assembly into a dual diploid assembly. The reconstructed haplotypes

Mikhail Kolmogorov 50 Jan 05, 2023
Find exposed data in Azure with this public blob scanner

BlobHunter A tool for scanning Azure blob storage accounts for publicly opened blobs. BlobHunter is a part of "Hunting Azure Blobs Exposes Millions of

CyberArk 250 Jan 03, 2023
Detailed analysis on fraud claims in insurance companies, gives you information as to why huge loss take place in insurance companies

Insurance-Fraud-Claims Detailed analysis on fraud claims in insurance companies, gives you information as to why huge loss take place in insurance com

1 Jan 27, 2022
NFCDS Workshop Beginners Guide Bioinformatics Data Analysis

Genomics Workshop FIXME: overview of workshop Code of Conduct All participants s

Elizabeth Brooks 2 Jun 13, 2022
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
Accurately separate the TLD from the registered domain and subdomains of a URL, using the Public Suffix List.

tldextract Python Module tldextract accurately separates the gTLD or ccTLD (generic or country code top-level domain) from the registered domain and s

John Kurkowski 1.6k Jan 03, 2023
Stochastic Gradient Trees implementation in Python

Stochastic Gradient Trees - Python Stochastic Gradient Trees1 by Henry Gouk, Bernhard Pfahringer, and Eibe Frank implementation in Python. Based on th

John Koumentis 2 Nov 18, 2022
A probabilistic programming library for Bayesian deep learning, generative models, based on Tensorflow

ZhuSuan is a Python probabilistic programming library for Bayesian deep learning, which conjoins the complimentary advantages of Bayesian methods and

Tsinghua Machine Learning Group 2.2k Dec 28, 2022
PyPDC is a Python package for calculating asymptotic Partial Directed Coherence estimations for brain connectivity analysis.

Python asymptotic Partial Directed Coherence and Directed Coherence estimation package for brain connectivity analysis. Free software: MIT license Doc

Heitor Baldo 3 Nov 26, 2022
A notebook to analyze Amazon Recommendation Review Dataset.

Amazon Recommendation Review Dataset Analyzer A notebook to analyze Amazon Recommendation Review Dataset. Features Calculates distinct user count, dis

isleki 3 Aug 22, 2022
Python data processing, analysis, visualization, and data operations

Python This is a Python data processing, analysis, visualization and data operations of the source code warehouse, book ISBN: 9787115527592 Descriptio

FangWei 1 Jan 16, 2022