Common bioinformatics database construction

Related tags

Data Analysisbiodb
Overview

biodb

Common bioinformatics database construction

1.taxonomy (Substance classification database)

  • Download the database
wget -c https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
tar -zxvf new_taxdump.tar.gz
lineage2tax.py fullnamelineage.dmp >species.taxonomy
get_taxid.py rankedlineage.dmp --kingdom Bacteria >Bacteria.taxid

2.Rfam

  • Download the database
family.txt gunzip Rfam.cm.gz cmpress Rfam.cm ">
wget -c https://ftp.ebi.ac.uk/pub/databases/Rfam/14.6/Rfam.cm.gz
wget -c https://ftp.ebi.ac.uk/pub/databases/Rfam/14.6/rfam2go/rfam2go
wget -c https://ftp.ebi.ac.uk/pub/databases/Rfam/14.6/database_files/family.txt.gz
zcat family.txt.gz |awk -F '\t' '{print $1"\t"$2"\t"$4"\t"$19"\t"$30}' >family.txt
gunzip Rfam.cm.gz
cmpress Rfam.cm
Owner
sy520
Xingguo Zhang
sy520
TheMachineScraper 🐱‍👤 is an Information Grabber built for Machine Analysis

TheMachineScraper 🐱‍👤 is a tool made purely for analysing machine data for any reason.

doop 5 Dec 01, 2022
Python tools for querying and manipulating BIDS datasets.

PyBIDS is a Python library to centralize interactions with datasets conforming BIDS (Brain Imaging Data Structure) format.

Brain Imaging Data Structure 180 Dec 18, 2022
Cold Brew: Distilling Graph Node Representations with Incomplete or Missing Neighborhoods

Cold Brew: Distilling Graph Node Representations with Incomplete or Missing Neighborhoods Introduction Graph Neural Networks (GNNs) have demonstrated

37 Dec 15, 2022
Recommendations from Cramer: On the show Mad-Money (CNBC) Jim Cramer picks stocks which he recommends to buy. We will use this data to build a portfolio

Backtesting the "Cramer Effect" & Recommendations from Cramer Recommendations from Cramer: On the show Mad-Money (CNBC) Jim Cramer picks stocks which

Gábor Vecsei 12 Aug 30, 2022
Get mutations in cluster by querying from LAPIS API

Cluster Mutation Script Get mutations appearing within user-defined clusters. Usage Clusters are defined in the clusters dict in main.py: clusters = {

neherlab 1 Oct 22, 2021
Data pipelines built with polars

valves Warning: the project is very much work in progress. Valves is a collection of functions for your data .pipe()-lines. This project aimes to host

14 Jan 03, 2023
Projects that implement various aspects of Data Engineering.

DATAWAREHOUSE ON AWS The purpose of this project is to build a datawarehouse to accomodate data of active user activity for music streaming applicatio

2 Oct 14, 2021
MapReader: A computer vision pipeline for the semantic exploration of maps at scale

MapReader A computer vision pipeline for the semantic exploration of maps at scale MapReader is an end-to-end computer vision (CV) pipeline designed b

Living with Machines 25 Dec 26, 2022
Sample code for Harry's Airflow online trainng course

Sample code for Harry's Airflow online trainng course You can find the videos on youtube or bilibili. I am working on adding below things: the slide p

102 Dec 30, 2022
This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot.

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 s

3 Dec 16, 2022
Python Library for learning (Structure and Parameter) and inference (Statistical and Causal) in Bayesian Networks.

pgmpy pgmpy is a python library for working with Probabilistic Graphical Models. Documentation and list of algorithms supported is at our official sit

pgmpy 2.2k Dec 25, 2022
Produces a summary CSV report of an Amber Electric customer's energy consumption and cost data.

Amber Electric Usage Summary This is a command line tool that produces a summary CSV report of an Amber Electric customer's energy consumption and cos

Graham Lea 12 May 26, 2022
A forecasting system dedicated to smart city data

smart-city-predictions System prognostyczny dedykowany dla danych inteligentnych miast Praca inżynierska realizowana przez Michała Stawikowskiego and

Kevin Lai 1 Nov 08, 2021
Python script for transferring data between three drives in two separate stages

Waterlock Waterlock is a Python script meant for incrementally transferring data between three folder locations in two separate stages. It performs ha

David Swanlund 13 Nov 10, 2021
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
This mini project showcase how to build and debug Apache Spark application using Python

Spark app can't be debugged using normal procedure. This mini project showcase how to build and debug Apache Spark application using Python programming language. There are also options to run Spark a

Denny Imanuel 1 Dec 29, 2021
Working Time Statistics of working hours and working conditions by industry and company

Working Time Statistics of working hours and working conditions by industry and company

Feng Ruohang 88 Nov 04, 2022
Full automated data pipeline using docker images

Create postgres tables from CSV files This first section is only relate to creating tables from CSV files using postgres container alone. Just one of

1 Nov 21, 2021
Analyze the Gravitational wave data stored at LIGO/VIRGO observatories

Gravitational-Wave-Analysis This project showcases how to analyze the Gravitational wave data stored at LIGO/VIRGO observatories, using Python program

1 Jan 23, 2022
International Space Station data with Python research 🌎

International Space Station data with Python research 🌎 Plotting ISS trajectory, calculating the velocity over the earth and more. Plotting trajector

Facundo Pedaccio 41 Jun 16, 2022