Michael Grünstäudl (Gruenstaeudl), PhD

Researcher at the Freie Universität Berlin

Monatsarchiv für April 2018

Few-liner: Batch download of DNA sequences from NCBI

The wonders of entrez Today I found myself in need of a script to download dozens of DNA sequences submitted to NCBI Nucleotide. The sequences in questeion were stores in file input.txt. $ cat input.txt Liriope_muscari_USACult,JX080424 Dracaena_adamii_IVORYCOAST,JX080436 … Here is how I did it: $ INF=input.txt $ for line in $(cat $INF); do SEQNAME=$(echo „$line“ […]

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Bioinformatic spring cleaning – Part II

An improved few-liner to keep the data compressed If you wish to recusively loop through a folder and its nested subfolders and automatically gzip all files greater than 1 GB, the following few-liner is for you: for file in $(LANG=C find . -size +1G -type f -print); do if [[ ! $file == *.gzip ]]; […]

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