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Convert a ClearLabs fasta tarball on Linux

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This commit is contained in:
Thomas A. Christensen II 2021-03-17 21:54:38 -06:00
parent 09c08c9de1
commit 7065e22ab3
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 18 additions and 0 deletions
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convert-fastas.sh Executable file
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#!/bin/bash
# Untars the ClearLabs bulk download and converts it to a single FASTA suitable
# for online sequence analyzers
# Pull in the tarball name
FASTAFILE=${1}
# Determine what the nasty name is
FASTANAME=$(basename -s .fastas.tar "$FASTAFILE")
# Make a new folder to put everything in
mkdir "$FASTANAME"
# Untar the tarball
tar -xf "$FASTAFILE" -C "$FASTANAME"
# Smash all of the FASTAs together into a single file
cat "$FASTANAME"/*.fasta > "$FASTANAME"/"$FASTANAME".fasta