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
PATC: Introduction to Big Data Analytics. Practical Data Analytics for Solving Real World Problems

PATC: Introduction to Big Data Analytics. Practical Data Analytics for Solving Real World Problems

1 Feb 07, 2022
PyTorch implementation for NCL (Neighborhood-enrighed Contrastive Learning)

NCL (Neighborhood-enrighed Contrastive Learning) This is the official PyTorch implementation for the paper: Zihan Lin*, Changxin Tian*, Yupeng Hou* Wa

RUCAIBox 73 Jan 03, 2023
This repository contains some analysis of possible nerdle answers

Nerdle Analysis https://nerdlegame.com/ This repository contains some analysis of possible nerdle answers. Here's a quick overview: nerdle.py contains

0 Dec 16, 2022
NumPy and Pandas interface to Big Data

Blaze translates a subset of modified NumPy and Pandas-like syntax to databases and other computing systems. Blaze allows Python users a familiar inte

Blaze 3.1k Jan 05, 2023
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
Pandas and Spark DataFrame comparison for humans

DataComPy DataComPy is a package to compare two Pandas DataFrames. Originally started to be something of a replacement for SAS's PROC COMPARE for Pand

Capital One 259 Dec 24, 2022
MS in Data Science capstone project. Studying attacks on autonomous vehicles.

Surveying Attack Models for CAVs Guide to Installing CARLA and Collecting Data Our project focuses on surveying attack models for Connveced Autonomous

Isabela Caetano 1 Dec 09, 2021
BErt-like Neurophysiological Data Representation

BENDR BErt-like Neurophysiological Data Representation This repository contains the source code for reproducing, or extending the BERT-like self-super

114 Dec 23, 2022
An interactive grid for sorting, filtering, and editing DataFrames in Jupyter notebooks

qgrid Qgrid is a Jupyter notebook widget which uses SlickGrid to render pandas DataFrames within a Jupyter notebook. This allows you to explore your D

Quantopian, Inc. 2.9k Jan 08, 2023
A Numba-based two-point correlation function calculator using a grid decomposition

A Numba-based two-point correlation function (2PCF) calculator using a grid decomposition. Like Corrfunc, but written in Numba, with simplicity and hackability in mind.

Lehman Garrison 3 Aug 24, 2022
Galvanalyser is a system for automatically storing data generated by battery cycling machines in a database

Galvanalyser is a system for automatically storing data generated by battery cycling machines in a database, using a set of "harvesters", whose job it

Battery Intelligence Lab 20 Sep 28, 2022
A fast, flexible, and performant feature selection package for python.

linselect A fast, flexible, and performant feature selection package for python. Package in a nutshell It's built on stepwise linear regression When p

88 Dec 06, 2022
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
4CAT: Capture and Analysis Toolkit

4CAT: Capture and Analysis Toolkit 4CAT is a research tool that can be used to analyse and process data from online social platforms. Its goal is to m

Digital Methods Initiative 147 Dec 20, 2022
🌍 Create 3d-printable STLs from satellite elevation data 🌏

mapa 🌍 Create 3d-printable STLs from satellite elevation data Installation pip install mapa Usage mapa uses numpy and numba under the hood to crunch

Fabian Gebhart 13 Dec 15, 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
PyNHD is a part of HyRiver software stack that is designed to aid in watershed analysis through web services.

A part of HyRiver software stack that provides access to NHD+ V2 data through NLDI and WaterData web services

Taher Chegini 23 Dec 14, 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
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
Statistical Analysis 📈 focused on statistical analysis and exploration used on various data sets for personal and professional projects.

Statistical Analysis 📈 This repository focuses on statistical analysis and the exploration used on various data sets for personal and professional pr

Andy Pham 1 Sep 03, 2022