diff_test.go

   1 package lightning
   2
   3 import (
   4         "bytes"
   5         "io/ioutil"
   6         "os"
   7
   8         "gopkg.in/check.v1"
   9 )
  10
  11 type diffSuite struct{}
  12
  13 var _ = check.Suite(&diffSuite{})
  14
  15 func (s *diffSuite) TestDiff(c *check.C) {
  16         tempdir, err := ioutil.TempDir("", "")
  17         c.Assert(err, check.IsNil)
  18         defer os.RemoveAll(tempdir)
  19
  20         err = ioutil.WriteFile(tempdir+"/f1.fa", []byte(">f1\nactgactCacgtacgt\nactgactgacgAAcgt\n"), 0700)
  21         c.Assert(err, check.IsNil)
  22         err = ioutil.WriteFile(tempdir+"/f2.fa", []byte(">f2\nactgactGacgtacgt\nactgactgacgTTcgtA\n"), 0700)
  23         c.Assert(err, check.IsNil)
  24
  25         var output bytes.Buffer
  26         exited := (&diffFasta{}).RunCommand("diff-fasta", []string{"-sequence", "chr2", "-offset", "1000", tempdir + "/f1.fa", tempdir + "/f2.fa"}, nil, &output, os.Stderr)
  27         c.Check(exited, check.Equals, 0)
  28         c.Check("\n"+output.String(), check.Equals, `
  29 chr2:g.1008C>G  chr2    1008    C       G       false
  30 chr2:g.1028_1029delinsTT        chr2    1028    AA      TT      false
  31 chr2:g.1032_1033insA    chr2    1033            A       false
  32 `)
  33 }