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
pandas: powerful Python data analysis toolkit

pandas is a Python package that provides fast, flexible, and expressive data structures designed to make working with "relational" or "labeled" data both easy and intuitive.

pandas 36.4k Jan 03, 2023
MoRecon - A tool for reconstructing missing frames in motion capture data.

MoRecon - A tool for reconstructing missing frames in motion capture data.

Yuki Nishidate 38 Dec 03, 2022
Python utility to extract differences between two pandas dataframes.

Python utility to extract differences between two pandas dataframes.

Jaime Valero 8 Jan 07, 2023
Hue Editor: Open source SQL Query Assistant for Databases/Warehouses

Hue Editor: Open source SQL Query Assistant for Databases/Warehouses

Cloudera 759 Jan 07, 2023
A simplified prototype for an as-built tracking database with API

Asbuilt_Trax A simplified prototype for an as-built tracking database with API The purpose of this project is to: Model a database that tracks constru

Ryan Pemberton 1 Jan 31, 2022
INFO-H515 - Big Data Scalable Analytics

INFO-H515 - Big Data Scalable Analytics Jacopo De Stefani, Giovanni Buroni, Théo Verhelst and Gianluca Bontempi - Machine Learning Group Exercise clas

Yann-Aël Le Borgne 58 Dec 11, 2022
ped-crash-techvol: Texas Ped Crash Tech Volume Pack

ped-crash-techvol: Texas Ped Crash Tech Volume Pack In conjunction with the Final Report "Identifying Risk Factors that Lead to Increase in Fatal Pede

Network Modeling Center; Center for Transportation Research; The University of Texas at Austin 2 Sep 28, 2022
Tools for analyzing data collected with a custom unity-based VR for insects.

unityvr Tools for analyzing data collected with a custom unity-based VR for insects. Organization: The unityvr package contains the following submodul

Hannah Haberkern 1 Dec 14, 2022
PyIOmica (pyiomica) is a Python package for omics analyses.

PyIOmica (pyiomica) This repository contains PyIOmica, a Python package that provides bioinformatics utilities for analyzing (dynamic) omics datasets.

G. Mias Lab 13 Jun 29, 2022
Open source platform for Data Science Management automation

Hydrosphere examples This repo contains demo scenarios and pre-trained models to show Hydrosphere capabilities. Data and artifacts management Some mod

hydrosphere.io 6 Aug 10, 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
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
NumPy aware dynamic Python compiler using LLVM

Numba A Just-In-Time Compiler for Numerical Functions in Python Numba is an open source, NumPy-aware optimizing compiler for Python sponsored by Anaco

Numba 8.2k Jan 07, 2023
Statistical package in Python based on Pandas

Pingouin is an open-source statistical package written in Python 3 and based mostly on Pandas and NumPy. Some of its main features are listed below. F

Raphael Vallat 1.2k Dec 31, 2022
wikirepo is a Python package that provides a framework to easily source and leverage standardized Wikidata information

Python based Wikidata framework for easy dataframe extraction wikirepo is a Python package that provides a framework to easily source and leverage sta

Andrew Tavis McAllister 35 Jan 04, 2023
Python-based Space Physics Environment Data Analysis Software

pySPEDAS pySPEDAS is an implementation of the SPEDAS framework for Python. The Space Physics Environment Data Analysis Software (SPEDAS) framework is

SPEDAS 98 Dec 22, 2022
Port of dplyr and other related R packages in python, using pipda.

Unlike other similar packages in python that just mimic the piping syntax, datar follows the API designs from the original packages as much as possible, and is tested thoroughly with the cases from t

179 Dec 21, 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
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