remove stale tests
MODIFY
MANIFEST.in
MANIFEST.in
@@ -4,7 +4,7 @@ include *.py
include *.sh
include LICENSE
include MANIFEST.in
-graft gemini/annotation_provenance
+exclude gemini/annotation_provenance/*
graft gemini/data
graft gemini/scripts
graft gemini/static

MODIFY
gemini/version.py
gemini/version.py
-__version__ = "0.20.2-dev"
+__version__ = "0.30.0-dev"

MODIFY
master-test.sh
master-test.sh
@@ -47,9 +47,6 @@ bash test-query.sh
# Test database dumping
bash test-dump.sh
-# Test burden tests
-bash test-burden.sh
-
# Test basic functionality
bash test-columns.sh
@@ -96,9 +93,6 @@ bash test-comphet.sh
# Test pathway tool
bash test-pathtool.sh
-# Test interaction tool
-bash test-interactions.sh
-
# Test lof sieve tool
bash test-lofsieve.sh

DELETE
test/test-burden.sh
-###################################################################
-# 1. Test high impact burden counts
-###################################################################
-echo " burden.t1...\c"
-echo "gene M10475 M10478 M10500 M128215
-DHODH 1 0 0 0
-WDR37 2 2 2 2
-CTBP2 0 0 0 1" > exp
-gemini burden test.burden.db > obs
-check obs exp
-rm obs exp
-
-###################################################################
-# 2. Test c-alpha test with specified controls and cases
-###################################################################
-echo " burden.t2...\c"
-echo "gene T c Z p_value
-SYCE1 -0.5 0.25 -1.0 0.841344746069
-DHODH 0.0 0.0 nan nan
-WDR37 -1.0 1.5 -0.816496580928 0.792891910879
-ASAH2C -0.5 0.75 -0.57735026919 0.718148569175
-CTBP2 0.0 0.0 nan nan" > exp
-gemini burden --controls M10475 M10478 --cases M10500 M128215 --calpha test.burden.db > obs
-check obs exp
-rm obs exp
-
-####################################################################
-## 3. Test c-alpha test with PED file
-####################################################################
-echo " burden.t3...\c"
-echo "gene T c Z p_value
-SYCE1 -0.5 0.25 -1.0 0.841344746069
-DHODH 0.0 0.0 nan nan
-WDR37 -1.0 1.5 -0.816496580928 0.792891910879
-ASAH2C -0.5 0.75 -0.57735026919 0.718148569175
-CTBP2 0.0 0.0 nan nan" > exp
-gemini burden --calpha test.burden.db > obs
-check obs exp
-rm obs exp

MODIFY
test/test-genotypes.sh
test/test-genotypes.sh
@@ -312,12 +312,12 @@ echo " genotypes.$n x..."
echo "-1.0 -1 -1
0.0 0 2
0.0 0 3
-0.666666666667 2 1
+0.6666666666666666 2 1
-1.0 -1 -1
-1.0 -1 -1
0.0 0 79
-1.0 -1 -1
-0.142857142857 1 6
+0.14285714285714285 1 6
0.0 0 4" > exp
gemini query -q "select gt_alt_freqs.1094PC0009, gt_alt_depths.1094PC0009, gt_ref_depths.1094PC0009 from variants" test.snpeff.vcf.db \
> obs

DELETE
test/test-interactions.sh
-
-check()
-{
- echo $3
- if diff <(sort $1) <(sort $2); then
- echo ok
- else
- echo fail
- fi
-}
-######################################################################
-# 1. Test interaction tool for snpEff (v3.1) annotations
-######################################################################
-echo "sample gene order_of_interaction interacting_gene
-M10475 CTBP2 0_order: none
-M10475 CTBP2 1_order: RAI2
-M10475 CTBP2 2_order: SGTB,UBQLN4
-M10475 CTBP2 3_order: none
-M10475 CTBP2 4_order: WDR37
-M10475 CTBP2 5_order: none
-M128215 CTBP2 0_order: CTBP2
-M128215 CTBP2 1_order: RAI2
-M128215 CTBP2 2_order: RB1
-M128215 CTBP2 3_order: TGM2,NOTCH2NL
-M128215 CTBP2 4_order: WDR37
-M128215 CTBP2 5_order: none
-M10478 CTBP2 0_order: none
-M10478 CTBP2 1_order: RAI2
-M10478 CTBP2 2_order: SGTB,UBQLN4
-M10478 CTBP2 3_order: NOTCH2NL
-M10478 CTBP2 4_order: WDR37
-M10478 CTBP2 5_order: MTG1
-M10500 CTBP2 0_order: none
-M10500 CTBP2 1_order: RAI2
-M10500 CTBP2 2_order: RB1,UBQLN4
-M10500 CTBP2 3_order: NOTCH2NL
-M10500 CTBP2 4_order: WDR37
-M10500 CTBP2 5_order: MTG1" > exp.$$
-gemini interactions -g CTBP2 -r 5 test5.snpeff.db \
- > obs.$$
-check obs.$$ exp.$$ "interact.t01..."
-rm obs.$$ exp.$$
-
-######################################################################
-# 2. Test interaction tool for snpEff (v3.1) annotations (--var mode)
-######################################################################
-echo "sample gene order_of_interaction interacting_gene var_id chrom start end impact biotype
-M10475 CTBP2 1 RAI2 9 chrX 17819376 17819377 missense_variant protein_coding
-M10475 CTBP2 2 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M10475 CTBP2 2 SGTB 8 chr5 64982320 64982321 intron_variant protein_coding
-M10475 CTBP2 4 WDR37 3 chr10 1142207 1142208 stop_lost protein_coding
-M128215 CTBP2 0 CTBP2 4 chr10 126678091 126678092 stop_gained protein_coding
-M128215 CTBP2 1 RAI2 9 chrX 17819376 17819377 missense_variant protein_coding
-M128215 CTBP2 2 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding
-M128215 CTBP2 3 NOTCH2NL 1 chr1 145273344 145273345 missense_variant protein_coding
-M128215 CTBP2 3 TGM2 7 chr20 36779423 36779424 stop_gained protein_coding
-M128215 CTBP2 4 WDR37 3 chr10 1142207 1142208 stop_lost protein_coding
-M10478 CTBP2 1 RAI2 9 chrX 17819376 17819377 missense_variant protein_coding
-M10478 CTBP2 2 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M10478 CTBP2 2 SGTB 8 chr5 64982320 64982321 intron_variant protein_coding
-M10478 CTBP2 3 NOTCH2NL 1 chr1 145273344 145273345 missense_variant protein_coding
-M10478 CTBP2 4 WDR37 3 chr10 1142207 1142208 stop_lost protein_coding
-M10478 CTBP2 5 MTG1 5 chr10 135210790 135210791 intron_variant protein_coding
-M10500 CTBP2 1 RAI2 9 chrX 17819376 17819377 missense_variant protein_coding
-M10500 CTBP2 2 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M10500 CTBP2 2 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding
-M10500 CTBP2 3 NOTCH2NL 1 chr1 145273344 145273345 missense_variant protein_coding
-M10500 CTBP2 4 WDR37 3 chr10 1142207 1142208 stop_lost protein_coding
-M10500 CTBP2 5 MTG1 5 chr10 135210790 135210791 intron_variant protein_coding" > exp.$$
-gemini interactions -g CTBP2 -r 5 --var test5.snpeff.db | cut -f1-10 \
- > obs.$$
-check obs.$$ exp.$$ "interact.t02... "
-rm obs.$$ exp.$$
-
-######################################################################
-# 3. Test lof interaction tool for snpEff (v3.1) annotations
-######################################################################
-echo "sample lof_gene order_of_interaction interacting_gene
-M10475 WDR37 1_order: none
-M10475 WDR37 2_order: none
-M10475 WDR37 3_order: UBQLN4
-M128215 WDR37 1_order: none
-M128215 WDR37 2_order: none
-M128215 WDR37 3_order: RB1
-M128215 TGM2 1_order: RB1
-M128215 TGM2 2_order: none
-M128215 TGM2 3_order: NOTCH2NL,CTBP2
-M128215 CTBP2 1_order: RAI2
-M128215 CTBP2 2_order: RB1
-M128215 CTBP2 3_order: NOTCH2NL,TGM2
-M10478 WDR37 1_order: none
-M10478 WDR37 2_order: none
-M10478 WDR37 3_order: UBQLN4
-M10500 WDR37 1_order: none
-M10500 WDR37 2_order: none
-M10500 WDR37 3_order: RB1,UBQLN4" > exp.$$
-gemini lof_interactions -r 3 test5.snpeff.db \
- > obs.$$
-check obs.$$ exp.$$ "interact.t03... "
-rm obs.$$ exp.$$
-
-######################################################################
-# 4. Test lof_interactions (--var mode) for snpEff (v3.1) annotations
-######################################################################
-echo "sample lof_gene order_of_interaction interacting_gene var_id chrom start end impact biotype
-M10475 WDR37 3 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M128215 WDR37 3 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding
-M128215 TGM2 1 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding
-M128215 TGM2 3 NOTCH2NL 1 chr1 145273344 145273345 missense_variant protein_coding
-M128215 TGM2 3 CTBP2 4 chr10 126678091 126678092 stop_gained protein_coding
-M128215 CTBP2 1 RAI2 9 chrX 17819376 17819377 missense_variant protein_coding
-M128215 CTBP2 2 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding
-M128215 CTBP2 3 NOTCH2NL 1 chr1 145273344 145273345 missense_variant protein_coding
-M128215 CTBP2 3 TGM2 7 chr20 36779423 36779424 stop_gained protein_coding
-M10478 WDR37 3 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M10500 WDR37 3 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M10500 WDR37 3 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding" > exp
-gemini lof_interactions -r 3 --var test5.snpeff.db | cut -f1-10 \
-> obs
-check obs exp "interact.t04... "
-rm obs exp
-
-######################################################################
-# 5. Test interaction tool for VEP (75) annotations
-######################################################################
-echo "sample gene order_of_interaction interacting_gene
-M10475 SGTB 0_order: SGTB
-M10475 SGTB 1_order: RAI2
-M10475 SGTB 2_order: UBQLN4
-M10475 SGTB 3_order: none
-M10475 SGTB 4_order: WDR37
-M128215 SGTB 0_order: none
-M128215 SGTB 1_order: RAI2
-M128215 SGTB 2_order: CTBP2,RB1
-M128215 SGTB 3_order: NOTCH2NL,TGM2
-M128215 SGTB 4_order: WDR37
-M10478 SGTB 0_order: SGTB
-M10478 SGTB 1_order: RAI2
-M10478 SGTB 2_order: UBQLN4
-M10478 SGTB 3_order: NOTCH2NL
-M10478 SGTB 4_order: WDR37
-M10500 SGTB 0_order: none
-M10500 SGTB 1_order: RAI2
-M10500 SGTB 2_order: RB1,UBQLN4
-M10500 SGTB 3_order: NOTCH2NL
-M10500 SGTB 4_order: WDR37" > exp
-gemini interactions -g SGTB -r 4 test5.vep.db \
- > obs
-check obs exp "interact.t05... "
-rm obs exp
-
-####################################################################
-# 6. Test interaction tool (--var mode) for VEP (75) annotations
-######################################################################
-echo "sample gene order_of_interaction interacting_gene var_id chrom start end impact biotype
-M10475 SGTB 0 SGTB 8 chr5 64982320 64982321 intron_variant protein_coding
-M10475 SGTB 1 RAI2 9 chrX 17819376 17819377 missense_variant protein_coding
-M10475 SGTB 2 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M10475 SGTB 4 WDR37 3 chr10 1142207 1142208 stop_lost protein_coding
-M128215 SGTB 1 RAI2 9 chrX 17819376 17819377 missense_variant protein_coding
-M128215 SGTB 2 CTBP2 4 chr10 126678091 126678092 stop_gained protein_coding
-M128215 SGTB 2 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding
-M128215 SGTB 3 NOTCH2NL 1 chr1 145273344 145273345 missense_variant protein_coding
-M128215 SGTB 3 TGM2 7 chr20 36779423 36779424 stop_gained protein_coding
-M128215 SGTB 4 WDR37 3 chr10 1142207 1142208 stop_lost protein_coding
-M10478 SGTB 0 SGTB 8 chr5 64982320 64982321 intron_variant protein_coding
-M10478 SGTB 1 RAI2 9 chrX 17819376 17819377 missense_variant protein_coding
-M10478 SGTB 2 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M10478 SGTB 3 NOTCH2NL 1 chr1 145273344 145273345 missense_variant protein_coding
-M10478 SGTB 4 WDR37 3 chr10 1142207 1142208 stop_lost protein_coding
-M10500 SGTB 1 RAI2 9 chrX 17819376 17819377 missense_variant protein_coding
-M10500 SGTB 2 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M10500 SGTB 2 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding
-M10500 SGTB 3 NOTCH2NL 1 chr1 145273344 145273345 missense_variant protein_coding
-M10500 SGTB 4 WDR37 3 chr10 1142207 1142208 stop_lost protein_coding" > exp
-gemini interactions -g SGTB -r 4 --var test5.vep.db | cut -f1-10 \
- > obs
-check obs exp "interact.t06... "
-rm obs exp
-
-######################################################################
-# 7. Test lof_interactions for VEP (75) annotations
-######################################################################
-echo "sample lof_gene order_of_interaction interacting_gene
-M10475 WDR37 1_order: none
-M10475 WDR37 2_order: none
-M10475 WDR37 3_order: UBQLN4
-M128215 WDR37 1_order: none
-M128215 WDR37 2_order: none
-M128215 WDR37 3_order: RB1
-M128215 TGM2 1_order: RB1
-M128215 TGM2 2_order: none
-M128215 TGM2 3_order: NOTCH2NL,CTBP2
-M128215 CTBP2 1_order: RAI2
-M128215 CTBP2 2_order: RB1
-M128215 CTBP2 3_order: NOTCH2NL,TGM2
-M10478 WDR37 1_order: none
-M10478 WDR37 2_order: none
-M10478 WDR37 3_order: UBQLN4
-M10500 WDR37 1_order: none
-M10500 WDR37 2_order: none
-M10500 WDR37 3_order: RB1,UBQLN4" > exp
-gemini lof_interactions -r 3 test5.vep.db \
- > obs
-check obs exp "interact.t07..."
-rm obs exp
-
-######################################################################
-# 8. Test lof_interactions (--var mode) for VEP (75) annotations
-######################################################################
-echo "sample lof_gene order_of_interaction interacting_gene var_id chrom start end impact biotype
-M10475 WDR37 3 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M128215 WDR37 3 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding
-M128215 TGM2 1 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding
-M128215 TGM2 3 NOTCH2NL 1 chr1 145273344 145273345 missense_variant protein_coding
-M128215 TGM2 3 CTBP2 4 chr10 126678091 126678092 stop_gained protein_coding
-M128215 CTBP2 1 RAI2 9 chrX 17819376 17819377 missense_variant protein_coding
-M128215 CTBP2 2 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding
-M128215 CTBP2 3 NOTCH2NL 1 chr1 145273344 145273345 missense_variant protein_coding
-M128215 CTBP2 3 TGM2 7 chr20 36779423 36779424 stop_gained protein_coding
-M10478 WDR37 3 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M10500 WDR37 3 UBQLN4 2 chr1 156011443 156011444 missense_variant protein_coding
-M10500 WDR37 3 RB1 6 chr13 48873834 48873835 upstream_gene_variant protein_coding" > exp
-gemini lof_interactions -r 3 --var test5.vep.db | cut -f1-10 \
- > obs
-check obs exp "interact.t08... "
-rm obs exp
-
-######################################################################

remove stale tests