FUSTA: leveraging FUSE for manipulation of multiFASTA files at scale.

Abstract

FASTA files are the de facto standard for sharing, manipulating and storing biological sequences, while concatenated in multiFASTA they tend to be unwieldy for two main reasons: (i) they can become big enough that their manipulation with standard text-editing tools is unpractical, either due to slowness or memory consumption; (ii) by mixing metadata (headers) and data (sequences), bulk operations using standard text streaming tools (such as sed or awk) are impossible without including a parsing step, which may be error-prone and introduce friction in the development process. Here, we present FUSTA (FUse for faSTA), a software utility which makes use of the FUSE technology to expose a multiFASTA file as a hierarchy of virtual files, letting users operate directly on the sequences as independent virtual files through classical file manipulation methods. FUSTA is freely available under the CeCILL-C (LGPLv3-compatible) license at https://github.com/delehef/fusta. Supplementary data are available at Bioinformatics Advances online.