22 lines
658 B
Bash
22 lines
658 B
Bash
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#!/bin/bash
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DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
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cd $DIR/..
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# Download
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if [ ! -f data/swissprot.fasta ]; then
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wget ftp://ftp.ncbi.nih.gov/blast/db/FASTA/swissprot.gz
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gunzip swissprot.gz
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mv swissprot data/swissprot.fasta
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rm -f swissprot.gz
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else
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echo skipped: data/swissprot.fasta already exists
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fi
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# if [ ! -f data/swissprot.fasta.pdb ]; then
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# makeblastdb -in data/swissprot.fasta -input_type fasta -title swissprot -dbtype prot
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# else
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# echo skipped: swissprot DB already exists
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# fi
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(cd data && blastp -query brca1.fasta -db swissprot.fasta -outfmt 5 > ../output/brca1_swissprot_out.xml)
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