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Get Data Files

Data for the exercises in this GitBook are available on GitHub at https://github.com/jfq3/data_sets. There are several ways of obtaining the data.

If you wil be running the tutorials using MiGA-Web, you will need to first download the data files to your computer. You can do this by going to https://github.com/jfq3/data_sets, clicking on a file name and then clicking on the download button on the right of the screen. For example, to get the miscellaneous genomes, click on the folder Miscellaneous genomes, then on the file miscellaneous.tar.gz and then on the download button. You will need to decompress the files before you can use them. Or working from the command line, you can download the data by using the instructions below.

If you will be running the tutorials from the command line, the bash script below downloads all of the data necessary for the exercises and puts them in a directory structure compatible with the example scripts. It also changes the extension of one of the pseudomonad genomes so that it may be set aside as a query genome for some of the exercises. The easiest way to get the script and data is:

cd ~/miga-data
wget https://github.com/jfq3/data_sets/raw/master/get_example_data.sh
chmod u+x get_example_data.sh
./get_example_data.sh

Or you can copy the code below, paste it into your text editor, save it as get_example_data.sh and run it as above.

#!/bin/bash

# Get example data for the MiGA tutorials
mkdir -p $HOME/miga-data/miga_genomes
cd $HOME/miga-data/miga_genomes
mkdir a_capsulatum
mkdir dehalo
mkdir misc
mkdir pseudo
cd a_capsulatum
wget https://github.com/jfq3/data_sets/raw/master/A_capsulatum_reads.fasta.gz
gzip -d A_capsulatum_reads.fasta.gz
rm A_capsulatum_reads.fasta.gz
cd ../dehalo
wget https://github.com/jfq3/data_sets/raw/master/Dehalococcoides_genomes/dehalococcoides_genomes.tar.gz
tar xzf dehalococcoides_genomes.tar.gz
rm dehalococcoides_genomes.tar.gz
cd ../misc
wget https://github.com/jfq3/data_sets/raw/master/Miscellaneous_genomes/miscellaneous.tar.gz
tar xzf miscellaneous.tar.gz
rm miscellaneous.tar.gz
cd ../pseudo
wget https://github.com/jfq3/data_sets/raw/master/Pseudomonas_genomes/pseudomonads.tar.gz
tar xzf pseudomonads.tar.gz
mv P_aeruginosa.fasta P_aeruginosa.fna
rm pseudomonads.tar.gz

The resulting files and directory structure are:

$HOME/miga-data/miga_genomes
├── a_capsulatum
│   └── A_capsulatum_reads.fasta
├── dehalo
│   ├── GCF_000011905.1_ASM1190v1_genomic.fna
│   ├── GCF_000341655.1_ASM34165v1_genomic.fna
│   ├── GCF_000341695.1_ASM34169v1_genomic.fna
│   ├── GCF_000830925.1_ASM83092v1_genomic.fna
│   ├── GCF_001010485.1_ASM101048v1_genomic.fna
│   ├── GCF_001547795.1_ASM154779v1_genomic.fna
│   ├── GCF_001610775.1_ASM161077v1_genomic.fna
│   ├── GCF_001889305.1_ASM188930v1_genomic.fna
│   ├── GCF_002007845.1_ASM200784v1_genomic.fna
│   └── GCF_004684285.1_ASM468428v1_genomic.fna
├── misc
│   ├── Acidobacterium_capsulatum.fasta
│   ├── Acinetobacter_baumanii.fasta
│   ├── Bacillus_anthracis.fasta
│   ├── Bacillus_cereus.fasta
│   ├── Bifidobacterium_bifidum.fasta
│   ├── Campylobacter_jejuni.fasta
│   ├── Cytophaga_hutchinsonii.fasta
│   ├── Gemmatimonas_aurantiaca.fasta
│   └── Lacunisphaera_limnophila.fasta
└── pseudo
    ├── P_aeruginosa.fna
    ├── P_alcaligenes.fasta
    ├── P_fluorescens.fasta
    ├── P_mendocina.fasta
    ├── P_putida.fasta
    ├── P_stutzeri.fasta
    └── P_syringae.fasta