Author: Andreas Tille Last-Update: Thu, 18 Oct 2018 18:16:40 +0200 Description: Test suite makefile has syntax errors and there was at least one buggy data file which was fixed. . With these changes `make msa_view` works but other targets are throwing errors. This needs to be investigated --- a/test/Makefile +++ b/test/Makefile @@ -7,30 +7,30 @@ all: msa_view phyloFit phastCons msa_view: @echo "*** Testing msa_view ***" msa_view hmrc.ss -i SS --end 10000 > hmrc.fa - @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o PHYLIP > hmrc.ph msa_view hmrc.ph -i PHYLIP > hmrc.fa - @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm msa_view hmrc.mpm --in-format MPM > hmrc.fa - @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o SS > hmrc_short_a.ss msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss - @if [[ -n `diff --brief hmrc_short_[ab].ss` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa msa_view --seqs human,cow hmrc.fa > hm_b.fa - @if [[ -n `diff --brief hm_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa - @if [[ -n `diff --brief hmrc_nogaps_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa - @if [[ -n `diff --brief hm_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa - @if [[ -n `diff --brief hmrc_sub_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --summary -i SS > hmrc_summary - @if [[ -n `diff --brief hmrc_summary hmrc_summary_correct` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi @echo -e "Passed all tests.\n" @rm -f hmrc.ph hmrc.fa hmrc.mpm hmrc_short_[ab].ss hm_[ab].fa hmrc_nogaps_[ab].fa hmrc_sub_[ab].fa hmrc_summary @@ -43,40 +43,40 @@ msa_view: phyloFit: @echo "*** Testing phyloFit ***" phyloFit hmrc.ss --subst-mod JC69 --tree "(human, (mouse,rat), cow)" -i SS --quiet - @if [[ -n `diff --brief phyloFit.mod jc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod jc.mod ; then echo "Rounding errors found" ; diff -u phyloFit.mod jc.mod ; fi phyloFit hmrc.ss --subst-mod JC69 --tree "((((human,chimp), (mouse,rat)), cow), chicken)" -i SS --quiet - @if [[ -n `diff --brief phyloFit.mod jc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod jc.mod ; then echo "ERROR" ; exit 1 ; fi phyloFit hmrc.ss --subst-mod F81 --tree "(human, (mouse,rat), cow)" -i SS --quiet - @if [[ -n `diff --brief phyloFit.mod f81.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod f81.mod ; then echo "ERROR" ; exit 1 ; fi phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS --quiet - @if [[ -n `diff --brief phyloFit.mod hky.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod hky.mod ; then echo "ERROR" ; exit 1 ; fi phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS --quiet - @if [[ -n `diff --brief phyloFit.mod rev.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod rev.mod ; then echo "ERROR" ; exit 1 ; fi phyloFit hmrc.ss --subst-mod UNREST --tree "(human, (mouse,rat), cow)" -i SS --quiet - @if [[ -n `diff --brief phyloFit.mod unrest.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod unrest.mod ; then echo "ERROR" ; exit 1 ; fi phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS -k 4 --quiet - @if [[ -n `diff --brief phyloFit.mod hky-dg.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod hky-dg.mod ; then echo "ERROR" ; exit 1 ; fi phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS -k 4 --quiet - @if [[ -n `diff --brief phyloFit.mod rev-dg.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod rev-dg.mod ; then echo "ERROR" ; exit 1 ; fi phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS --EM --quiet - @if [[ -n `diff --brief phyloFit.mod hky-em.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod hky-em.mod ; then echo "ERROR" ; exit 1 ; fi phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS --EM --quiet - @if [[ -n `diff --brief phyloFit.mod rev-em.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod rev-em.mod ; then echo "ERROR" ; exit 1 ; fi phyloFit hpmrc.ss --subst-mod REV --tree "(hg16, (mm3,rn3), galGal2)" -i SS --gaps-as-bases --quiet - @if [[ -n `diff --brief phyloFit.mod rev-gaps.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod rev-gaps.mod ; then echo "ERROR" ; exit 1 ; fi phyloFit hmrc.ss --subst-mod REV -i SS --init-model rev.mod --post-probs --lnl --quiet - @if [[ -n `diff --brief phyloFit.mod rev-lnl.mod` ]] ; then echo "ERROR" ; exit 1 ; fi - @if [[ -n `diff --brief phyloFit.postprob rev.postprob` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod rev-lnl.mod ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.postprob rev.postprob ; then echo "ERROR" ; exit 1 ; fi phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat))" -i SS --quiet - @if [[ -n `diff --brief phyloFit.mod rev-hmr.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod rev-hmr.mod ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss -i SS --seqs human,mouse,rat --unordered -o SS > hmr.ss phyloFit hmr.ss -i SS --quiet - @if [[ -n `diff --brief phyloFit.mod rev-hmr2.mod` ]] ; then echo "ERROR" ; exit 1 ; fi # FIXME: rev-hmr.mod and rev-hmr2.mod should be equal (eq freqs being obtained from all seqs) + if ! diff --brief phyloFit.mod rev-hmr2.mod ; then echo "ERROR" ; exit 1 ; fi # FIXME: rev-hmr.mod and rev-hmr2.mod should be equal (eq freqs being obtained from all seqs) msa_view hmrc.ss -i SS --seqs human,mouse --unordered -o SS > hm.ss phyloFit hm.ss -i SS --quiet - @if [[ -n `diff --brief phyloFit.mod rev-hm.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod rev-hm.mod ; then echo "ERROR" ; exit 1 ; fi phyloFit hmrc.ss --subst-mod UNREST --tree "((human, mouse), cow)" -i SS --ancestor cow --quiet - @if [[ -n `diff --brief phyloFit.mod unrest-cow-anc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief phyloFit.mod unrest-cow-anc.mod ; then echo "ERROR" ; exit 1 ; fi @echo -e "Passed all tests.\n" @rm -f phyloFit.mod phyloFit.postprob hmr.ss hm.ss @@ -87,12 +87,12 @@ phyloFit: phastCons: @echo "*** Testing phastCons ***" phastCons hpmrc.ss hpmrc-rev-dg-global.mod --nrates 20 --transitions .08,.008 --quiet --viterbi elements.bed --seqname chr22 > cons.dat - @if [[ -n `diff --brief cons.dat cons_correct.dat` ]] ; then echo "ERROR" ; exit 1 ; fi - @if [[ -n `diff --brief elements.bed elements_correct.bed` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief cons.dat cons_correct.dat ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief elements.bed elements_correct.bed ; then echo "ERROR" ; exit 1 ; fi tree_doctor hpmrc-rev-dg-global.mod --prune galGal2 > hpmr.mod phastCons hpmrc.ss hpmr.mod --nrates 20 --transitions .08,.008 --quiet --viterbi elements-4way.bed --seqname chr22 > cons-4way.dat - @if [[ -n `diff --brief cons-4way.dat cons-4way_correct.dat` ]] ; then echo "ERROR" ; exit 1 ; fi - @if [[ -n `diff --brief elements-4way.bed elements-4way_correct.bed` ]] ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief cons-4way.dat cons-4way_correct.dat ; then echo "ERROR" ; exit 1 ; fi + if ! diff --brief elements-4way.bed elements-4way_correct.bed ; then echo "ERROR" ; exit 1 ; fi @echo -e "Passed all tests.\n" @rm -f cons.dat cons-4way.dat elements.bed elements-4way.bed hpmr.mod @@ -110,7 +110,7 @@ phyloP: phyloP --null 10 phyloFit.mod > phyloP_null_test.txt phyloP -i SS phyloFit.mod hmrc.ss > phyloP_sph_test.txt phyloP -i SS --method LRT phyloFit.mod hmrc.ss > phyloP_lrt_test.txt - phyloP -i SS --method LRT --mode CONACC phyloFit.mod hmrc.ss > phyloP_lrt_conacc_test.txt + phyloP -i SS --method LRT --mode CONACC phyloFit.mod hmrc.ss > phyloP_lrt_conacc_test.txt phyloP -i SS --method GERP phyloFit.mod hmrc.ss > phyloP_gerp_test.txt phyloP -i SS --method SCORE phyloFit.mod hmrc.ss > phyloP_score_test.txt phyloP -i SS --method LRT --wig-scores phyloFit.mod hmrc.ss > phyloP_wig_test.wig --- a/test/hmrc_summary_correct +++ b/test/hmrc_summary_correct @@ -1,5 +1,2 @@ -descrip. A C G T G+C length all_gaps some_gaps descrip. A C G T G+C length all_gaps some_gaps - -hmrc.ss 0.3258 0.1913 0.1827 0.3001 0.3740 95927 0 82185 hmrc.ss 0.3258 0.1913 0.1827 0.3001 0.3740 95927 0 82185