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August 21, 2010 17:18
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#!/bin/sh | |
# | |
set -e | |
check_requirements() | |
{ | |
[ ! -f $s2f_bin ] && error "bfast solid2fastq not found." | |
[ ! -f $bwa_s2f ] && error "bwa solid2fastq not found." | |
[ ! -x $s2f_bin ] && error "bfast solid2fastq not executable." | |
[ ! -x $bwa_s2f ] && error "bwa solid2fastq not exectutable." | |
for i in $o_f3 $o_f3q $o_r3 $o_r3q | |
do | |
[ ! -f $o_f3 ] && error "data file not found: [$i]" | |
done | |
return 0 | |
} | |
log() | |
{ | |
echo "$1" | |
} | |
error() | |
{ | |
echo "$1" | |
exit 1 | |
} | |
diff_this() | |
{ | |
f1=$1 | |
f2=$2 | |
[ ! -f $f1 ] && error "File not found: $f1" | |
[ ! -f $f2 ] && error "File not found: $f2" | |
if [ ".`diff $f1 $f2`" == "." ] | |
then | |
out="OK" | |
else | |
out="ERROR: diff != 0" | |
fi | |
log " diff: [$out] $f1 $f2" | |
} | |
clean() | |
{ | |
rm -rf drd* bf bwa* input* | |
} | |
prep() | |
{ | |
head -$nl $o_f3 > $f3 | |
head -$nl $o_r3 > $r3 | |
head -$nl $o_f3q > $fq3 | |
head -$nl $o_r3q > $rq3 | |
} | |
compile() | |
{ | |
cd $sdir | |
make > /dev/null | |
cd - > /dev/null | |
} | |
run_bf() | |
{ | |
sp="" | |
[ ".$2" != "." ] && sp="$2" | |
mkdir bf | |
cp $1 bf/ | |
cd bf | |
$s2f_bin -b $sp -o prefix $1 | |
cd .. | |
} | |
run_bwa() | |
{ | |
mkdir bwa | |
cp $1 bwa/ | |
cd bwa | |
$bwa_s2f "input_" prefix | |
gzip -d *.gz | |
cd .. | |
} | |
check_split_sizes() | |
{ | |
cd bf | |
for i in *.fastq | |
do | |
[ ! -s $i ] && error " $i: ZERO size!!" | |
done | |
echo " size: [OK] (`ls *.fastq | wc -l | sed 's/ //g'`)" | |
cd .. | |
} | |
# Testing one end | |
test_one() | |
{ | |
log "TEST: No splits. ONE end." | |
run_bf "$f3 $fq3" | |
run_bwa "$f3 $fq3" | |
diff_this bf/prefix.single.fastq bwa/prefix.single.fastq | |
} | |
# Testing two ens | |
test_two() | |
{ | |
log "TEST: No splits. TWO ends." | |
run_bf "$f3 $r3 $fq3 $rq3" | |
run_bwa "$f3 $r3 $fq3 $rq3" | |
diff_this bf/prefix.single.fastq bwa/prefix.single.fastq | |
diff_this bf/prefix.read1.fastq bwa/prefix.read1.fastq | |
diff_this bf/prefix.read2.fastq bwa/prefix.read2.fastq | |
} | |
# Testing one end (split) | |
test_one_split() | |
{ | |
log "TEST: SPLITS, ONE end." | |
run_bf "$f3 $fq3" "-n$n" | |
run_bwa "$f3 $fq3" | |
cat bf/*.fastq > ./bf.merged.fastq | |
diff_this ./bf.merged.fastq bwa/prefix.single.fastq | |
rm -f ./bf.merged.fastq | |
check_split_sizes | |
} | |
test_two_split() | |
{ | |
log "TEST: SPLITS, TWO end." | |
run_bf "$f3 $r3 $fq3 $rq3" "-n$n" | |
run_bwa "$f3 $r3 $fq3 $rq3" | |
cat bf/*read1*fastq > ./bf.r1.fastq | |
cat bf/*read2*fastq > ./bf.r2.fastq | |
cat bf/*single*fastq > ./bf.single.fastq | |
diff_this ./bf.r1.fastq bwa/prefix.read1.fastq | |
diff_this ./bf.r2.fastq bwa/prefix.read2.fastq | |
diff_this ./bf.single.fastq bwa/prefix.single.fastq | |
rm -f ./bf.* | |
check_split_sizes | |
} | |
# main | |
# | |
sdir="/Users/drio/projects/bfast_related/versions/dev/bfast/scripts" | |
s2f_bin="$sdir/solid2fastq" | |
bwa_s2f="/Users/drio/projects/bwa_related/bio-bwa/trunk/bwa/solid2fastq.pl" | |
o_f3="./data/bifxTrainingData_10panels_auto/reads/SHIRAZ_20080320_MP_2_Sample1_F3_10panel.csfasta" | |
o_f3q="./data/bifxTrainingData_10panels_auto/reads/SHIRAZ_20080320_MP_2_Sample1_F3_QV_10panel.qual" | |
o_r3="./data/bifxTrainingData_10panels_auto/reads/SHIRAZ_20080320_MP_2_Sample1_R3_10panel.csfasta" | |
o_r3q="./data/bifxTrainingData_10panels_auto/reads/SHIRAZ_20080320_MP_2_Sample1_R3_QV_10panel.qual" | |
f3="./input_F3.csfasta" | |
r3="./input_R3.csfasta" | |
fq3="./input_F3_QV.qual" | |
rq3="./input_R3_QV.qual" | |
nl="10001" | |
n="1000" | |
check_requirements | |
compile | |
clean; prep; test_one | |
clean; prep; test_two | |
clean; prep; test_one_split | |
clean; prep; test_two_split | |
echo "ALL tests Passed." | |
clean |
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