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#!/bin/bash
# Test that the indexes genomes are identical to the ones retrieved using the
# get option from crac-index
if [ -z "$abs_top_builddir" ]; then
abs_top_builddir=..
fi
if [ -z "$abs_builddir" ]; then
abs_builddir=.
fi
compare_dna_seq() {
raw_seq1=$(mktemp)
raw_seq2=$(mktemp)
(grep -v '^>' $1 | tr -dc 'ACGTTacgtn ' | tr 'acgtn ' 'ACGTNN'; echo) > $raw_seq1
(grep -v '^>' $2 | tr -dc 'ACGTTacgtn ' | tr 'acgtn ' 'ACGTNN'; echo) > $raw_seq2
diff=$(cmp -b -l $raw_seq1 $raw_seq2 | awk 'BEGIN{c=0} $3 != "N" && $5 != "N"{c++} END {print c}')
rm -f $raw_seq1 $raw_seq2
echo $diff
}
error=0
TEMP=$(mktemp)
nb_files=$(find $abs_builddir -name "*.ssa" | wc -l)
i=1
error=0
{
echo "1..$nb_files"
for file in $(find $abs_builddir -name "*.ssa"); do
file=${file%.ssa}
$LAUNCHER $abs_top_builddir/src/crac-index get $TEMP $file
orig_fasta="."${file#$abs_builddir}
orig_fasta=${orig_fasta}.fa*
if [ -f $orig_fasta ]; then
orig_fasta=$(ls $orig_fasta)
if [ $(compare_dna_seq $TEMP $orig_fasta) -gt 0 ]; then
echo -n "not "
fi
else
echo -n "not "
error=$((error+1))
fi
echo "ok $i - file "$orig_fasta
i=$((i+1))
done
} > ${0%.sh}".tap"
rm -f $TEMP
[ $error -eq 0 ]
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