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#!/bin/bash
set -e
formatdb=/usr/bin/formatdb
scripts_path=/usr/share/cct/lib
wd=`pwd`
if [ ! -d test_output ]; then
mkdir test_output
fi
if [ ! -d db ]; then
mkdir db
fi
cd db
if [ ! -f myva ]; then
wget http://ftp.ncbi.nih.gov/pub/COG/COG/myva
fi
if [ ! -f whog ]; then
wget http://ftp.ncbi.nih.gov/pub/COG/COG/whog
fi
if [ ! -f myva.phr ]; then
formatdb -p T -i myva -o T
fi
cd $wd
perl assign_cogs.pl -i test_input/sample_1.gbk \
-o test_output/sample_1.gff -s cds \
-myva db/myva -whog db/whog \
-get_orfs $scripts_path/get_orfs/get_orfs.pl \
-get_cds $scripts_path/get_cds/get_cds.pl \
-local_bl $scripts_path/local_blast_client/local_blast_client.pl \
-blastall /usr/bin/blastall -v
perl assign_cogs.pl -i test_input/sample_1.gbk \
-o test_output/sample_1b.gff -s cds \
-myva db/myva -whog db/whog \
-get_orfs $scripts_path/get_orfs/get_orfs.pl \
-get_cds $scripts_path/get_cds/get_cds.pl \
-local_bl $scripts_path/local_blast_client/local_blast_client.pl \
-blastall /usr/bin/blastall \
-a -e 0.0000001 -p 0.60 -v
perl assign_cogs.pl -i test_input/sample_2.fna \
-o test_output/sample_2.gff -s orfs \
-myva db/myva -whog db/whog \
-get_orfs $scripts_path/get_orfs/get_orfs.pl \
-get_cds $scripts_path/get_cds/get_cds.pl \
-local_bl $scripts_path/local_blast_client/local_blast_client.pl \
-blastall /usr/bin/blastall -v
perl assign_cogs.pl -i test_input/sample_2.fna \
-o test_output/sample_2b.gff -s orfs \
-myva db/myva -whog db/whog \
-get_orfs $scripts_path/get_orfs/get_orfs.pl \
-get_cds $scripts_path/get_cds/get_cds.pl \
-local_bl $scripts_path/local_blast_client/local_blast_client.pl \
-blastall /usr/bin/blastall \
-a -e 0.0000001 -p 0.60 -v
perl assign_cogs.pl -i test_input/sample_3.fna \
-o test_output/sample_3.gff -s orfs \
-myva db/myva -whog db/whog \
-get_orfs $scripts_path/get_orfs/get_orfs.pl \
-get_cds $scripts_path/get_cds/get_cds.pl \
-local_bl $scripts_path/local_blast_client/local_blast_client.pl \
-blastall /usr/bin/blastall -v
#compare new output to sample output
new_output=test_output
old_output=sample_output
new_files=($( find $new_output -type f -print0 | perl -ne 'my @files = split(/\0/, $_); foreach(@files) { if (!($_ =~ m/\.svn/)) {print "$_\n";}}'))
for (( i=0; i<${#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
diff -u $old_file ${new_files[$i]}
if [ $? -eq 0 ]; then
echo "No differences found"
fi
set -e
done
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