// Copyright (C) The Lightning Authors. All rights reserved. // // SPDX-License-Identifier: AGPL-3.0 package lightning import ( "bytes" "io/ioutil" "os" "github.com/kshedden/gonpy" "gopkg.in/check.v1" ) type exportNumpySuite struct{} var _ = check.Suite(&exportNumpySuite{}) func (s *exportNumpySuite) TestFastaToNumpy(c *check.C) { tmpdir := c.MkDir() err := ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644) c.Check(err, check.IsNil) var buffer bytes.Buffer exited := (&importer{}).RunCommand("import", []string{"-local=true", "-o", tmpdir + "/library.gob.gz", "-tag-library", "testdata/tags", "-output-tiles", "-save-incomplete-tiles", "testdata/a.1.fasta", "testdata/tinyref.fasta"}, &bytes.Buffer{}, os.Stderr, os.Stderr) c.Assert(exited, check.Equals, 0) exited = (&exportNumpy{}).RunCommand("export-numpy", []string{"-local=true", "-input-dir", tmpdir, "-output-dir", tmpdir, "-output-annotations", tmpdir + "/annotations.csv", "-regions", tmpdir + "/chr1-12-100.bed"}, &buffer, os.Stderr, os.Stderr) c.Check(exited, check.Equals, 0) f, err := os.Open(tmpdir + "/matrix.npy") c.Assert(err, check.IsNil) defer f.Close() npy, err := gonpy.NewReader(f) c.Assert(err, check.IsNil) variants, err := npy.GetInt16() c.Assert(err, check.IsNil) c.Check(variants, check.HasLen, 6) for i := 0; i < 4 && i < len(variants); i += 2 { if variants[i] == 1 { c.Check(variants[i+1], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants)) } else { c.Check(variants[i], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants)) } } for i := 4; i < 6 && i < len(variants); i += 2 { c.Check(variants[i], check.Equals, int16(1), check.Commentf("i=%d, v=%v", i, variants)) } annotations, err := ioutil.ReadFile(tmpdir + "/annotations.csv") c.Check(err, check.IsNil) c.Logf("%s", string(annotations)) c.Check(string(annotations), check.Matches, `(?ms)(.*\n)?1,1,2,chr1:g.84_85insACTGCGATCTGA\n.*`) c.Check(string(annotations), check.Matches, `(?ms)(.*\n)?1,1,1,chr1:g.87_96delinsGCATCTGCA\n.*`) } func sortUints(variants []int16) { for i := 0; i < len(variants); i += 2 { if variants[i] > variants[i+1] { for j := 0; j < len(variants); j++ { variants[j], variants[j+1] = variants[j+1], variants[j] } return } } } func (s *exportNumpySuite) TestOnehot(c *check.C) { for _, trial := range []struct { incols int in []int16 outcols int out []int16 }{ {2, []int16{1, 1, 1, 1}, 2, []int16{1, 1, 1, 1}}, {2, []int16{1, 1, 1, 2}, 3, []int16{1, 1, 0, 1, 0, 1}}, { // 2nd column => 3 one-hot columns // 4th column => 0 one-hot columns 4, []int16{ 1, 1, 0, 0, 1, 2, 1, 0, 1, 3, 0, 0, }, 5, []int16{ 1, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 0, }, }, } { out, _, outcols := recodeOnehot(trial.in, trial.incols) c.Check(out, check.DeepEquals, trial.out) c.Check(outcols, check.Equals, trial.outcols) } }