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#!/bin/bash
set -e
BLAST=blastall
FORMATDB=formatdb
if [ ! -d test_output ]; then
mkdir test_output
fi
#build databases
if [ ! -d test_output/formatted_databases ]; then
mkdir test_output/formatted_databases
fi
$FORMATDB -i test_input/test_dna_database.fasta -p F -n test_output/formatted_databases/test_dna_database.fasta
$FORMATDB -i test_input/test_protein_database.fasta -p T -n test_output/formatted_databases/test_protein_database.fasta
rm formatdb.log
#Nucleotide-nucleotide BLAST (blastn)
perl local_blast_client.pl -i test_input/test_input_dna.fasta -y $BLAST -b blastn -d test_output/formatted_databases/test_dna_database.fasta -o test_output/results_blastn.txt
#Protein-protein BLAST (blastp)
perl local_blast_client.pl -i test_input/test_input_protein.fasta -y $BLAST -b blastp -d test_output/formatted_databases/test_protein_database.fasta -o test_output/results_blastp.txt -x 1E-50
#Translated query vs protein database (blastx)
perl local_blast_client.pl -i test_input/test_input_dna.fasta -y $BLAST -b blastx -d test_output/formatted_databases/test_protein_database.fasta -o test_output/results_blastx.txt
#Protein query vs translated database (tblastn)
perl local_blast_client.pl -i test_input/test_input_protein.fasta -y $BLAST -b tblastn -d test_output/formatted_databases/test_dna_database.fasta -o test_output/results_tblastn.txt
#Translated query vs. translated database (tblastx)
perl local_blast_client.pl -i test_input/test_input_dna.fasta -y $BLAST -b tblastx -d test_output/formatted_databases/test_dna_database.fasta -o test_output/results_tblastx.txt
rm -rf test_output/formatted_databases
#compare new output to sample output
new_output=test_output
old_output=sample_output
IFS=$'\n'
new_files=($( find $new_output -type f -print0 | perl -ne 'my @files = split(/\0/, $_); foreach(@files) { if (!($_ =~ m/\.svn/)) {print "$_\n";}}'))
unset IFS
for (( i=0; i<${#new_files[@]}; i++ ));
do
old_file=${old_output}$(echo "${new_files[$i]}" | perl -nl -e 's/^[^\/]+//;' -e 'print $_')
echo "Comparing ${old_file} to ${new_files[$i]}"
set +e
if diff -u "$old_file" "${new_files[$i]}"; then
echo "No differences found"
fi
set -e
done
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