#! /bin/sh # Exercise LAST programs, and compare the output to a reference # output. More tests should be added! try () { echo TEST "$@" eval "$@" echo } cd $(dirname $0) # Make sure we use this version of LAST: PATH=../bin:$PATH dnaSeq=galGal3-M-32.fa protSeq=Q2LCP8.fa fastq=SRR001981-1k.fastq gc=../examples/vertebrateMito.gc db=/tmp/last-test trap 'rm -f $db*' EXIT { lastdb -uMURPHY10 $db /dev/null # this triggered a getopt reset bug lastdb $db /dev/null lastdb -D $db lastal $db /dev/null # spaced seeds, soft-masking, centroid alignment, matrix file lastdb -c -m110 -C3 -R10 $db $dnaSeq try lastal -fMAF -u1 -j5 -p ../data/HOXD70.mat -z3400 -e2500 $db $dnaSeq # multiple volumes & query batches lastdb --bits=4 -m1 -s1 -C2 -R10 $db $dnaSeq lastdb -D $db try lastal -fTAB -i1 -w0 -e40 $db $dnaSeq # match-counting, with multiple query batches try lastal -j0 -i1 -s0 $db $dnaSeq # FASTQ quality scores try lastal -Q1 -e90 -a9 $db $fastq # gapless translated alignment & genetic code file lastdb -p -R10 $db $protSeq try lastal -F12 -pBL62 -e40 -G $gc -j1 $db $dnaSeq try lastal -F12 -pBL62 -e40 -G2 -j1 $db $dnaSeq # subset seed file, soft-masking lastdb -c -R10 -u ../data/YASS.seed $db $dnaSeq try lastal -s0 -f0 -e18 $db $dnaSeq # asymmetric scoring matrix try lastal -s0 -f0 -p asymmetric.mat -e2000 $db $dnaSeq # FASTQ-Illumina quality scores lastdb -m1111110 -R10 $db $dnaSeq try lastal -Q3 -e110 $db illumina100.txt # PRB-format quality data try lastal -Q4 -e90 $db mouse_tss_prb.txt # probabilistic alignment with quality scores try lastal -Q1 -j6 -e90 -a9 $db $fastq # sparse index, generalized affine gap costs, self-alignment lastdb -w2 -c -R10 $db $dnaSeq try lastal -r3 -q3 -a21 -c2 -e60 -f0 $db $dnaSeq # generalized affine gaps, frameshifts, tabular output lastdb -p -c -R10 $db $protSeq try lastal -F12 -pBL62 -c2 -e40 -f0 $db $dnaSeq # gapless alignment, protein-protein alignment, seed freq try lastal -j1 -f0 -e37 -m100 $db $protSeq # fastq-versus-fastq, seed freq lastdb -Q1 -R10 $db sd-ccs-100.fq try lastal -Q1 -r1 -q2 -a1 -b1 -e44 -m100 -s0 $db sd-ccs-100.fq # incomplete sorting, lastal on one volume lastdb -i10 -s1 $db $dnaSeq try lastal -Q1 -e90 -a9 -f0 ${db}0 $fastq # multiple seeds, transition constraints lastdb -c -R10 -m 11101T011T11,111001010010111 $db $dnaSeq try lastal -s0 -f0 -e18 $db $dnaSeq # Iedera notation lastdb -c -R10 -m '#@#--##--#-#' $db $dnaSeq try lastal -s0 -f0 -e18 $db $dnaSeq # overlap alignment, tabular output ending in gaps lastdb -m1111110 -R10 $db $dnaSeq try lastal -T1 -Q1 -e60 -a9 -f0 $db $fastq # probabilistic overlap alignment try lastal -T1 -Q1 -e60 -a9 -j4 $db $fastq # fastq-versus-fasta gapless overlap alignment try lastal -T1 -Q1 -e60 -j1 -fTAB $db $fastq # expected counts try lastal -s0 -e18 -j7 $db $dnaSeq # overlap alignment, hitting edge of ref seq, fastq head -n21 $dnaSeq | cut -c-35 | lastdb -m1111110 $db try lastal -T1 -Q1 -e60 -a9 -f0 $db $fastq # named multi-seed, sparse query seeding lastdb -c -R10 -uMAM8 $db hg19-M.fa try lastal -e34 -k128 -f0 $db galGal3-M-32.fa # named score matrix, sparse query seeding try lastal -pHOXD70 -e4500 -k128 -f0 $db galGal3-M-32.fa # MAM4, gapless alignment culling lastdb -uMAM4 $db hg19-M.fa try lastal -e34 -C2 -f0 $db galGal3-M-32.fa # minimum seed length try lastal -e34 -f0 -l30 $db galGal3-M-32.fa # match-counting with min & max lengths lastdb -m1 $db $dnaSeq try lastal -j0 -l4 -L11 -s0 $db $dnaSeq lastdb -i10 $db tttttccccc.fa try lastal -e5 -f0 $db ttttt.fa | grep -v '^#' # tantan masking on DNA lastdb -cR01 $db galGal3-M-32.fa try lastal -e40 $db hg19-M.fa # hard-masking try lastal -e40 -u3 -fTAB $db hg19-M.fa # -J1 lastal -J1 -fTAB -p hufu.train $db hg19-M.fa lastal -J1 -Q1 -D1000 -p hufu.train $db $fastq # tantan masking on protein lastdb -pcR01 $db Q2LCP8.fa try lastal -e100 $db Q5GS15.fa # tantan masking for translated alignment try lastal -F15 -pBLOSUM62 -e100 $db galGal3-M-32.fa # AT-rich DNA, tantan lastdb -cR02 $db at-rich.fa try lastal -pAT77 -e100 -s0 $db at-rich.fa # fastq + tantan lastdb -R01 $db $dnaSeq try lastal -Q1 -a15 -b3 -e80 $db nano.fq # fasta query versus fastq reference lastdb -Q1 -R10 $db sd-ccs-100.fq lastdb -D $db try lastal -a1 -D1000 $db galGal3-M-32.fa # prb query versus fastq reference try lastal -Q4 -a1 -D100 $db mouse_tss_prb.txt # fastq DNA versus protein lastdb -pcR00 $db Q2LCP8.fa try lastal -Q1 -pBL62 -F12 -D1000 $db sd-ccs-100.fq # protein-codon alignment lastdb -qR01 $db Q2LCP8.fa try lastal -Q1 -pBL62codon.mat -F12 -t3.08611 -e36 -d29 $db sd-ccs-100.fq try lastal -Q1 -pbadcodon.mat -a17 -F0 -j4 -X1 -D1000 $db sd-ccs-100.fq try lastal -Q1 -pbadcodon.mat -a17 -b1 -F9,9,9,9 -X1 -D1e3 -j4 $db sd-ccs-100.fq try lastal -Q1 -pBL62 -b1 -F3,3,3,3 -X1 -j4 -e56 $db sd-ccs-100.fq lastdb -qcR01 -B1 $db Q2LCP8.fa lastdb -D $db try lastal -Q1 -pbadcodon.mat -a17 -b1 -F9,9,9,9 -X1 -D1e3 $db sd-ccs-100.fq # BlastTab format lastdb -pR01 $db Q2LCP8.fa try lastal -fBlastTab -pBL62 -b1 -F15 -D1e3 $db galGal3-M-32.fa # BlastTab+ format try lastal -fBlastTab+ -pBL62 -b1 -F15 -D1e3 $db galGal3-M-32.fa # DNA-versus-protein alignment without frameshifts try lastal -j4 -pBL62 -b1 -F0 -D1e3 $db galGal3-M-32.fa # strand asymmetry lastdb $db hg19-M.fa try lastal -S1 -pBISF -Q1 -e120 -f0 -j4 $db bs100.fastq # culling try lastal -D1000 -fTAB -K2 $db galGal3-M-32.fa try lastal -D1000 -fTAB -K0 $db galGal3-M-32.fa # minimizers lastdb -W3 -R10 $db galGal3-M-32.fa try lastal -W19 -fTAB $db hg19-M.fa # minimum-difference alignment try lastal -W1 -M -fTAB $db hg19-M.fa # asymmetric gap costs try lastal -fTAB -j4 -A2 -B2 $db hg19-M.fa try lastal -fTAB -j4 -Q1 -e90 -a7 -A12 -B4 $db $fastq # fastq-ignore try lastal -fTAB -j4 -Q0 -e90 -a7 -A12 -B4 -b9 -r6 -q18 $db $fastq try lastal -j4 -Qkeep -e90 -a7 -A12 -B4 -b9 -r6 -q18 $db $fastq # first alignments only try lastal -N2 $db hg19-M.fa # "U" nucleotide try "tr Tt Uu < hg19-M.fa | lastal -N2 $db" # -z % try lastal -W19 -z50% -fTAB $db hg19-M.fa # -x g try lastal -W19 -x1g -fTAB $db hg19-M.fa # non-negative score matrix try lastal -L9 -m0 -j1 -q0 -d5 -n6 -fTAB $db tttttccccc.fa # fastq-versus-fastq gapless overlap alignment lastdb -Q1 -uNEAR -cR01 $db $fastq try lastal -Q1 -T1 -j1 -s0 $db $fastq lastdb $db dfam3-LTR22B1.fa lastal -r2 -q2 -a10 -X1 $db dfam3-LTR22C.fa lastal -r2 -q2 -a10 -X2 $db dfam3-LTR22C.fa lastal -r2 -q2 -a10 -X3 $db dfam3-LTR22C.fa # gap cost > SCHAR_MAX lastal -r12 -q12 -a128 $db dfam3-LTR22C.fa # word-restricted seeds, lastdb -B lastdb -uRY8-8 -B1 $db hg19-M.fa lastdb -uRY8 -B1 $db hg19-M.fa lastal -fTAB -q8 -b4 $db galGal3-M-32.fa # tricky Forward-Backward bug that happened once lastdb $db alli.fa lastal -j7 -r5 -q5 -a15 -b3 $db huma.fa lastdb --bits=4 -uNEAR $db od-xsr-100k.fa lastal -D10 --split-d=2 -p od.mat $db od-rna.fq # lastdb strands & volumes lastdb --bits=4 -S2 -s1 -m1 $db galGal3-M-32.fa lastal -s0 -fTAB -p hufu.train $db hg19-M.fa lastal -fTAB -p hufu.train $db hg19-M.fa } 2>&1 | grep -v version | diff -u last-test.out - # Test: last-bisulfite, last-merge-batches, last-split, named seeds lastdb -uBISF -R10 f hg19-M.fa lastdb -uBISR -R10 r hg19-M.fa ../examples/last-bisulfite.sh f r bs100.fastq | grep -v '^#' | diff bs100.maf - rm f.* r.* ./last-map-probs-test.sh ./last-pair-test.sh ./last-postmask-test.sh ./last-split-test.sh ./last-train-test.sh ./maf-convert-test.sh ./maf-cut-test.sh ./maf-swap-test.sh # Test: lastdb, lastal, last-split, maf-sort, maf-join cd ../examples ./multiMito.sh | diff multiMito.maf -