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generate-test-data.sh
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#!/usr/bin/env sh
DATA_DIR=dammit/tests/test-data
TEST_FILE=pom.50.fa
TEST_PEP=pep.fa
dammit annotate $DATA_DIR/$TEST_FILE
dammit annotate $DATA_DIR/$TEST_FILE --full -o $TEST_FILE.dammit.full
#dammit annotate $DATA_DIR/$TEST_FILE --nr -o $TEST_FILE.dammit.nr
dammit annotate --evalue 10.0 $DATA_DIR/$TEST_FILE -o $TEST_FILE.dammit.evalue10
dammit annotate $DATA_DIR/$TEST_FILE --quick --user-databases $DATA_DIR/$TEST_PEP -o $TEST_FILE.dammit.udb
dammit annotate $DATA_DIR/$TEST_FILE --no-rename -o $TEST_FILE.dammit.norename
cp $TEST_FILE.dammit/$TEST_FILE.dammit.fasta $DATA_DIR/
cp $TEST_FILE.dammit/$TEST_FILE.dammit.gff3 $DATA_DIR/
cp $TEST_FILE.dammit.evalue10/$TEST_FILE.dammit.fasta $DATA_DIR/$TEST_FILE.dammit.fasta.evalue10
cp $TEST_FILE.dammit.evalue10/$TEST_FILE.dammit.gff3 $DATA_DIR/$TEST_FILE.dammit.gff3.evalue10
cp $TEST_FILE.dammit.udb/$TEST_FILE.dammit.fasta $DATA_DIR/$TEST_FILE.dammit.fasta.udb
cp $TEST_FILE.dammit.udb/$TEST_FILE.dammit.gff3 $DATA_DIR/$TEST_FILE.dammit.gff3.udb
cp $TEST_FILE.dammit.full/$TEST_FILE.dammit.fasta $DATA_DIR/$TEST_FILE.dammit.fasta.full
cp $TEST_FILE.dammit.full/$TEST_FILE.dammit.gff3 $DATA_DIR/$TEST_FILE.dammit.gff3.full
#cp $TEST_FILE.dammit.nr/$TEST_FILE.dammit.fasta $DATA_DIR/$TEST_FILE.dammit.fasta.nr
#cp $TEST_FILE.dammit.nr/$TEST_FILE.dammit.gff3 $DATA_DIR/$TEST_FILE.dammit.gff3.nr
cp $TEST_FILE.dammit.norename/$TEST_FILE.dammit.fasta $DATA_DIR/$TEST_FILE.dammit.fasta.norename
cp $TEST_FILE.dammit.norename/$TEST_FILE.dammit.gff3 $DATA_DIR/$TEST_FILE.dammit.gff3.norename