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|
#---------
# testing
#
# Small tests to give some comfort level that the program has built properly,
# or that changes you've made to the source code haven't broken it. The
# results of lav_compare should be of this form:
# SUCCESS: ../test_data/xxx and ../test_results/yyy are equivalent
#
# Note that a simple diff could be used in most cases, except that there will
# be some mismatches due to version number differences. For the overweight
# seed test, diff is useless since the files being compared will have seed hits
# in different orders.
#
# The tests:
# test Same as base_test_default, but success is silent
# (this is included for backward compatibility)
# base_test_hits Seed hits only
# base_test_hsp HSP alignments only
# base_test_adaptive_k HSP alignments only, adaptive-K
# base_test_default Default alignment (gapped without chaining)
# base_test_axt AXT output format
# base_test_chained chained HSPs
# base_test_extended gapped alignments
# base_test_interpolated interpolated alignments
# base_test_segments reading and writing anchor segments
# base_test_stdin2 sequence2 comes from stdin
# base_test_2bit1 sequence1 comes from .2bit file
# base_test_2bit2 sequence2 comes from .2bit file
# base_test_float floating point scoring
# base_test_seeded non-standard seed pattern
# base_test_hw_seeded half weight seed pattern
# base_test_ow_seeded overweight seed pattern
# base_test_masking dynamic masking
# base_test_anchors external anchors
# base_test_anchors_multi external anchors with multi-sequence file
# base_test_subrange sequence subranges
# base_test_mask sequence masking
# base_test_coi contigs-of-interest file
# base_test_multi multi-sequence file
# base_test_multi_subrange multi-sequence file with subranges
#---------
lavCompare = ../tools/lav_compare.py
gfaCompare = ../tools/gfa_compare.py
axtCompare = ../tools/axt_compare.py
mafSort = ../tools/maf_sort.py
clean_test: clean_tests
clean_tests:
rm -f ../test_results/base_test*.*
test:
@rm -f ../test_results/base_test.default.lav
@./lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
| sed "s/\"lastz\.[^ ]* //g" \
> ../test_results/base_test.default.lav
@diff \
../test_data/base_test.default.lav \
../test_results/base_test.default.lav
base_tests: \
base_test_hits \
base_test_hsp \
base_test_adaptive_k \
base_test_default \
base_test_axt \
base_test_chained \
base_test_extended \
base_test_interpolated \
base_test_segments \
base_test_stdin2 \
base_test_2bit1 \
base_test_2bit2 \
base_test_float \
base_test_seeded \
base_test_hw_seeded \
base_test_ow_seeded \
base_test_masking \
base_test_anchors \
base_test_anchors_multi \
base_test_subrange \
base_test_mask \
base_test_coi \
base_test_multi \
base_test_multi_subrange
base_tests_non_float: \
base_test_hits \
base_test_hsp \
base_test_adaptive_k \
base_test_default \
base_test_axt \
base_test_chained \
base_test_extended \
base_test_interpolated \
base_test_segments \
base_test_stdin2 \
base_test_2bit1 \
base_test_2bit2 \
base_test_seeded \
base_test_hw_seeded \
base_test_ow_seeded \
base_test_masking \
base_test_anchors \
base_test_anchors_multi \
base_test_subrange \
base_test_mask \
base_test_coi \
base_test_multi \
base_test_multi_subrange
base_tests_no_stdin2: \
base_test_hits \
base_test_hsp \
base_test_adaptive_k \
base_test_default \
base_test_axt \
base_test_chained \
base_test_extended \
base_test_interpolated \
base_test_segments \
base_test_2bit1 \
base_test_2bit2 \
base_test_float \
base_test_seeded \
base_test_hw_seeded \
base_test_ow_seeded \
base_test_masking \
base_test_anchors \
base_test_anchors_multi \
base_test_subrange \
base_test_mask \
base_test_coi \
base_test_multi \
base_test_multi_subrange
base_test_hits:
@rm -f ../test_results/base_test.hits.lav
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
W=8 T=0 --plus --nogfextend --nogapped \
> ../test_results/base_test.hits.lav
@${lavCompare} \
../test_data/base_test.hits.lav \
../test_results/base_test.hits.lav
base_test_hsp:
@rm -f ../test_results/base_test.hsp.lav
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
C=3 W=8 T=0 \
> ../test_results/base_test.hsp.lav
@${lavCompare} \
../test_data/base_test.hsp.lav \
../test_results/base_test.hsp.lav
base_test_adaptive_k:
@rm -f ../test_results/base_test.adaptive_k.gfa
@/usr/bin/lastz \
../test_data/aglobin.2bit/human \
../test_data/aglobin.2bit/cow \
C=3 W=8 T=0 --noentropy K=top50% --gfa \
| grep "^a" | sort -rn -k 4 \
> ../test_results/base_test.adaptive_k.gfa
@${gfaCompare} \
../test_data/base_test.adaptive_k.gfa \
../test_results/base_test.adaptive_k.gfa
base_test_default:
@rm -f ../test_results/base_test.default.lav
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
| sed "s/\"lastz\.[^ ]* //g" \
> ../test_results/base_test.default.lav
@${lavCompare} \
../test_data/base_test.default.lav \
../test_results/base_test.default.lav
base_test_axt:
@rm -f ../test_results/base_test.default.axt
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
--format=axt \
> ../test_results/base_test.default.axt
@${axtCompare} \
../test_data/base_test.default.axt \
../test_results/base_test.default.axt
base_test_chained:
@rm -f ../test_results/base_test.chained.lav
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
C=1 W=8 T=0 \
> ../test_results/base_test.chained.lav
@${lavCompare} \
../test_data/base_test.chained.lav \
../test_results/base_test.chained.lav
base_test_extended:
@rm -f ../test_results/base_test.extended.lav
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
C=2 W=8 T=0 \
> ../test_results/base_test.extended.lav
@${lavCompare} \
../test_data/base_test.extended.lav \
../test_results/base_test.extended.lav
base_test_interpolated:
@rm -f ../test_results/base_test.interpolated.lav
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
C=2 W=8 T=0 H=2200 \
> ../test_results/base_test.interpolated.lav
@${lavCompare} \
../test_data/base_test.interpolated.lav \
../test_results/base_test.interpolated.lav
base_test_segments:
@rm -f ../test_results/base_test.segments.hsps
@rm -f ../test_results/base_test.segments.lav
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
--nogapped --format=segments \
> ../test_results/base_test.segments.hsps
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
--segments=../test_results/base_test.segments.hsps \
| sed "s/\"lastz\.[^ ]* //g" \
> ../test_results/base_test.segments.lav
@${lavCompare} \
../test_data/base_test.default.lav \
../test_results/base_test.segments.lav
base_test_stdin2:
@rm -f ../test_results/base_test.stdin2.lav
@cat ../test_data/pseudopig.fa \
| /usr/bin/lastz \
../test_data/pseudocat.fa \
C=3 W=8 T=0 \
| sed "s/(stdin)/..\/test_data\/pseudopig.fa/g" \
> ../test_results/base_test.stdin2.lav
@${lavCompare} \
../test_data/base_test.hsp.lav \
../test_results/base_test.stdin2.lav
base_test_nib1:
@rm -f ../test_results/base_test.nib1.lav
@/usr/bin/lastz \
../test_data/pseudopig2.nib \
../test_data/pseudocat.fa \
C=2 W=8 T=0 \
| sed "s/\.\..*\.nib:.*\"/> pig2\"/g" \
| sed "s/\.nib/.fa/g" \
> ../test_results/base_test.nib1.lav
@${lavCompare} \
../test_data/base_test.pig_cat.lav \
../test_results/base_test.nib1.lav
base_test_2bit1:
@rm -f ../test_results/base_test.2bit1.lav
@/usr/bin/lastz \
../test_data/pseudopig.2bit/pig2 \
../test_data/pseudocat.fa \
C=2 W=8 T=0 \
| sed "s/pig/> pig/g" \
| sed "s/do> pig.2bit/dopig2.fa/g" \
| sed "s/\(dopig2.*\) 0 2/\1 0 1/g" \
> ../test_results/base_test.2bit1.lav
@${lavCompare} \
../test_data/base_test.pig_cat.lav \
../test_results/base_test.2bit1.lav
base_test_2bit2:
@rm -f ../test_results/base_test.2bit2.lav
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.2bit \
C=2 W=8 T=0 \
| sed "s/pig/> pig/g" \
| sed "s/do> pig.2bit/dopig.fa/g" \
> ../test_results/base_test.2bit2.lav
@${lavCompare} \
../test_data/base_test.extended.lav \
../test_results/base_test.2bit2.lav
base_test_float:
@rm -f ../test_results/base_test.float.lav
@/usr/bin/lastz_D \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
C=2 W=8 T=0 \
> ../test_results/base_test.float.lav
@${lavCompare} \
../test_data/base_test.float.lav \
../test_results/base_test.float.lav
base_test_seeded:
@rm -f ../test_results/base_test.seeded.lav
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
C=3 --seed=111010011101 \
> ../test_results/base_test.seeded.lav
@${lavCompare} \
../test_data/base_test.seeded.lav \
../test_results/base_test.seeded.lav
base_test_hw_seeded:
@rm -f ../test_results/base_test.hwseeded.lav
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
C=3 --seed=TTT0T0T0TTT00T0T \
> ../test_results/base_test.hwseeded.lav
@${lavCompare} \
../test_data/base_test.hwseeded.lav \
../test_results/base_test.hwseeded.lav
base_test_ow_seeded:
@rm -f ../test_results/base_test.owseeded.gfa
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa \
--justhits --seed=111010011101 --word=12 \
--gfa \
> ../test_results/base_test.owseeded.gfa
@${gfaCompare} --sort \
../test_data/base_test.owseeded.gfa \
../test_results/base_test.owseeded.gfa
base_test_masking:
@rm -f ../test_results/base_test.masking.lav
@/usr/bin/lastz \
../test_data/fake_apple.fa \
../test_data/fake_orange_reads.fa \
--masking=3 \
> ../test_results/base_test.masking.lav
@${lavCompare} \
../test_data/base_test.masking.lav \
../test_results/base_test.masking.lav
base_test_anchors:
@rm -f ../test_results/base_test.anchors.maf
@/usr/bin/lastz \
../test_data/aglobin.2bit/human \
../test_data/aglobin.2bit/cow \
C=0 --format=maf- \
--anchors=../test_data/base_test.anchors.anchors \
> ../test_results/base_test.anchors.maf
@diff \
../test_data/base_test.anchors.maf \
../test_results/base_test.anchors.maf
base_test_anchors_multi:
@rm -f ../test_results/base_test.anchors_multi.maf
@/usr/bin/lastz \
../test_data/aglobin.2bit/human \
../test_data/shorties.fa[subset=../test_data/shorties.names] \
C=0 --format=maf- \
--anchors=../test_data/base_test.anchors_multi.anchors \
> ../test_results/base_test.anchors_multi.maf
@diff \
../test_data/base_test.anchors_multi.maf \
../test_results/base_test.anchors_multi.maf
base_test_subrange:
@/usr/bin/lastz \
../test_data/aglobin.2bit/human[10000,60000] \
../test_data/aglobin.2bit/cow[15000#40000] \
> ../test_results/base_test.subrange.lav
@${lavCompare} \
../test_data/base_test.subrange.lav \
../test_results/base_test.subrange.lav
base_test_mask:
@/usr/bin/lastz \
../test_data/pseudocat.fa \
../test_data/pseudopig.fa[nmask=../test_data/pseudopig.n.mask] \
--ambiguous=n,60 \
> ../test_results/base_test.mask.lav
@${lavCompare} \
../test_data/base_test.mask.lav \
../test_results/base_test.mask.lav
base_test_coi:
@/usr/bin/lastz \
../test_data/aglobin.2bit/human \
../test_data/shorties.fa[subset=../test_data/shorties.names] \
K=3000 --maf- \
> ../test_results/base_test.coi_fa.maf
@diff \
../test_data/base_test.coi.maf \
../test_results/base_test.coi_fa.maf
@/usr/bin/lastz \
../test_data/aglobin.2bit/human \
../test_data/shorties.2bit[subset=../test_data/shorties.names] \
K=3000 --maf- \
> ../test_results/base_test.coi_2bit.maf
@diff \
../test_data/base_test.coi.maf \
../test_results/base_test.coi_2bit.maf
base_test_multi:
@/usr/bin/lastz \
../test_data/aglobin.2bit/human \
../test_data/shorties.2bit[multi,@../test_data/shorties.names] \
K=3000 --maf- \
| ${mafSort} --key=pos1 \
> ../test_results/base_test.multi.maf
@diff \
../test_data/base_test.multi.maf \
../test_results/base_test.multi.maf
base_test_multi_subrange:
@/usr/bin/lastz \
../test_data/aglobin.2bit/human \
../test_data/shorties.2bit[multi,51..200] \
K=3000 --maf- \
> ../test_results/base_test.multi_subrange.maf
@diff \
../test_data/base_test.multi_subrange.maf \
../test_results/base_test.multi_subrange.maf
|
