From 2a8986eef484d641f89a09622dd5f93cedc05e89 Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Thu, 11 Apr 2024 13:52:27 -0400 Subject: [PATCH] Fix some tests. No issue # Arvados-DCO-1.1-Signed-off-by: Tom Clegg --- export_test.go | 8 ++--- pipeline_test.go | 6 ++-- slice_test.go | 90 ++++++++++++++++++++++++++++++++++++++---------- 3 files changed, 79 insertions(+), 25 deletions(-) diff --git a/export_test.go b/export_test.go index f904e76f4a..15278bea29 100644 --- a/export_test.go +++ b/export_test.go @@ -82,7 +82,7 @@ chr2.125_127delinsAAA 0 1 chr2.241_254del 1 0 chr2.258_269delinsAA 1 0 chr2.315C>A 1 0 -chr2.470_472del 1 0 +chr2.469_471del 1 0 chr2.471G>A 1 0 chr2.472G>A 1 0 `)) @@ -123,7 +123,7 @@ chr2 125 . CTT AAA . . . GT 0/0 1/1 chr2 240 . ATTTTTCTTGCTCTC A . . . GT 1/0 0/0 chr2 258 . CCTTGTATTTTT AA . . . GT 1/0 0/0 chr2 315 . C A . . . GT 1/0 0/0 -chr2 469 . GTGG G . . . GT 1/0 0/0 +chr2 468 . CGTG C . . . GT 1/0 0/0 chr2 471 . G A . . . GT 0/1 0/0 chr2 472 . G A . . . GT 0/1 0/0 `)) @@ -157,7 +157,7 @@ chr2 125 . CTT AAA . . AC=2 chr2 240 . ATTTTTCTTGCTCTC A . . AC=1 chr2 258 . CCTTGTATTTTT AA . . AC=1 chr2 315 . C A . . AC=1 -chr2 469 . GTGG G . . AC=1 +chr2 468 . CGTG C . . AC=1 chr2 471 . G A . . AC=1 chr2 472 . G A . . AC=1 `)) @@ -218,7 +218,7 @@ chr2 472 . G A . . AC=1 2,"chr2.241_254del" 3,"chr2.258_269delinsAA" 4,"chr2.315C>A" -5,"chr2.470_472del" +5,"chr2.469_471del" 6,"chr2.471G>A" 7,"chr2.472G>A" `) diff --git a/pipeline_test.go b/pipeline_test.go index 391312e507..606cac243d 100644 --- a/pipeline_test.go +++ b/pipeline_test.go @@ -107,7 +107,7 @@ chr1:g.[302=];[302_305delinsAAAA] . chr2:g.[241_254del];[241=] . chr2:g.[258_269delinsAA];[258=] . chr2:g.[315C>A];[315=] . -chr2:g.[470_472del];[470=] . +chr2:g.[469_471del];[469=] . chr2:g.[471=];[471G>A] . chr2:g.[472=];[472G>A] . `)) @@ -130,7 +130,7 @@ chr2 125 . CTT AAA . . . GT 0/0 1/1 chr2 240 . ATTTTTCTTGCTCTC A . . . GT 1/0 0/0 chr2 258 . CCTTGTATTTTT AA . . . GT 1/0 0/0 chr2 315 . C A . . . GT 1/0 0/0 -chr2 469 . GTGG G . . . GT 1/0 0/0 +chr2 468 . CGTG C . . . GT 1/0 0/0 chr2 471 . G A . . . GT 0/1 0/0 chr2 472 . G A . . . GT 0/1 0/0 `)) @@ -169,7 +169,7 @@ chr2 472 572 7 1000 . 496 572 4,4,fe9a71a42adb4,chr2:g.125_127delinsAAA 6,6,e36dce85efbef,chr2:g.471G>A 6,6,e36dce85efbef,chr2:g.472G>A -6,6,f81388b184f4a,chr2:g.470_472del +6,6,f81388b184f4a,chr2:g.469_471del `)) } diff --git a/slice_test.go b/slice_test.go index ec87958995..7b81e0ec66 100644 --- a/slice_test.go +++ b/slice_test.go @@ -244,12 +244,21 @@ pipeline1dup/input1 1 pipeline1dup/input2 0 `), 0600) c.Assert(err, check.IsNil) + + exited := (&chooseSamples{}).RunCommand("choose-samples", []string{ + "-local=true", + "-case-control-file=" + tmpdir + "/casecontrol.tsv", + "-case-control-column=CC", + "-input-dir=" + slicedir, + "-output-dir=" + tmpdir, + }, nil, os.Stderr, os.Stderr) + c.Check(exited, check.Equals, 0) + npydir := c.MkDir() - exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{ + exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{ "-local=true", "-chunked-hgvs-matrix=true", - "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv", - "-chi2-case-control-column=CC", + "-samples=" + tmpdir + "/samples.csv", "-chi2-p-value=0.5", "-min-coverage=0.75", "-input-dir=" + slicedir, @@ -280,12 +289,21 @@ pipeline1dup/input1 1 pipeline1dup/input2 0 `), 0600) c.Assert(err, check.IsNil) + + exited := (&chooseSamples{}).RunCommand("choose-samples", []string{ + "-local=true", + "-case-control-file=" + tmpdir + "/casecontrol.tsv", + "-case-control-column=CC", + "-input-dir=" + slicedir, + "-output-dir=" + tmpdir, + }, nil, os.Stderr, os.Stderr) + c.Check(exited, check.Equals, 0) + npydir := c.MkDir() - exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{ + exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{ "-local=true", "-chunked-onehot=true", - "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv", - "-chi2-case-control-column=CC", + "-samples=" + tmpdir + "/samples.csv", "-chi2-p-value=0.5", "-min-coverage=0.75", "-input-dir=" + slicedir, @@ -324,12 +342,21 @@ pipeline1dup/input1 1 pipeline1dup/input2 0 `), 0600) c.Assert(err, check.IsNil) + + exited := (&chooseSamples{}).RunCommand("choose-samples", []string{ + "-local=true", + "-case-control-file=" + tmpdir + "/casecontrol.tsv", + "-case-control-column=CC", + "-input-dir=" + slicedir, + "-output-dir=" + tmpdir, + }, nil, os.Stderr, os.Stderr) + c.Check(exited, check.Equals, 0) + npydir := c.MkDir() - exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{ + exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{ "-local=true", "-single-onehot=true", - "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv", - "-chi2-case-control-column=CC", + "-samples=" + tmpdir + "/samples.csv", "-chi2-p-value=0.5", "-min-coverage=0.75", "-input-dir=" + slicedir, @@ -580,12 +607,21 @@ func (s *sliceSuite) TestSpanningTile(c *check.C) { spanningtile/input1 1 `), 0600) c.Assert(err, check.IsNil) + + exited := (&chooseSamples{}).RunCommand("choose-samples", []string{ + "-local=true", + "-case-control-file=" + tmpdir + "/casecontrol.tsv", + "-case-control-column=CC", + "-input-dir=" + slicedir, + "-output-dir=" + tmpdir, + }, nil, os.Stderr, os.Stderr) + c.Check(exited, check.Equals, 0) + npydir := c.MkDir() - exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{ + exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{ "-local=true", "-chunked-hgvs-matrix=true", - "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv", - "-chi2-case-control-column=CC", + "-samples=" + tmpdir + "/samples.csv", "-chi2-p-value=1", "-min-coverage=0.75", "-input-dir=" + slicedir, @@ -607,12 +643,21 @@ spanningtile/input1 1 spanningtile/input1 1 `), 0600) c.Assert(err, check.IsNil) + + exited := (&chooseSamples{}).RunCommand("choose-samples", []string{ + "-local=true", + "-case-control-file=" + tmpdir + "/casecontrol.tsv", + "-case-control-column=CC", + "-input-dir=" + slicedir, + "-output-dir=" + tmpdir, + }, nil, os.Stderr, os.Stderr) + c.Check(exited, check.Equals, 0) + npydir := c.MkDir() - exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{ + exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{ "-local=true", "-chunked-onehot=true", - "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv", - "-chi2-case-control-column=CC", + "-samples=" + tmpdir + "/samples.csv", "-chi2-p-value=1", "-min-coverage=0.75", "-input-dir=" + slicedir, @@ -645,12 +690,21 @@ spanningtile/input1 1 spanningtile/input1 1 `), 0600) c.Assert(err, check.IsNil) + + exited := (&chooseSamples{}).RunCommand("choose-samples", []string{ + "-local=true", + "-case-control-file=" + tmpdir + "/casecontrol.tsv", + "-case-control-column=CC", + "-input-dir=" + slicedir, + "-output-dir=" + tmpdir, + }, nil, os.Stderr, os.Stderr) + c.Check(exited, check.Equals, 0) + npydir := c.MkDir() - exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{ + exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{ "-local=true", "-single-onehot=true", - "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv", - "-chi2-case-control-column=CC", + "-samples=" + tmpdir + "/samples.csv", "-chi2-p-value=1", "-min-coverage=0.75", "-input-dir=" + slicedir, -- 2.30.2