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Patch sequence writers to remove definition from header when json format is used.

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Former-commit-id: a8a74cccb52d577d4ea1c0ad88b121a8e511149d
This commit is contained in:
Eric Coissac
2023-10-05 07:31:31 +02:00
parent d23a911080
commit 0a8f7afb2a
5 changed files with 27 additions and 27 deletions
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36
pkg/obiformats/fastseq_obi_header.go
View File

@ -298,27 +298,29 @@ func FormatFastSeqOBIHeader(sequence *obiseq.BioSequence) string {
var text strings.Builder var text strings.Builder
for key, value := range annotations { for key, value := range annotations {
switch t := value.(type) { if key != "definition" {
case string: switch t := value.(type) {
text.WriteString(fmt.Sprintf("%s=%s; ", key, t)) case string:
case map[string]int, text.WriteString(fmt.Sprintf("%s=%s; ", key, t))
map[string]string, case map[string]int,
map[string]interface{}, map[string]string,
obiseq.StatsOnValues: map[string]interface{},
tv, err := obiutils.JsonMarshal(t) obiseq.StatsOnValues:
if err != nil { tv, err := obiutils.JsonMarshal(t)
log.Fatalf("Cannot convert %v value", value) if err != nil {
log.Fatalf("Cannot convert %v value", value)
}
tv = bytes.ReplaceAll(tv, []byte(`"`), []byte("'"))
text.WriteString(fmt.Sprintf("%s=", key))
text.Write(tv)
text.WriteString("; ")
default:
text.WriteString(fmt.Sprintf("%s=%v; ", key, value))
} }
tv = bytes.ReplaceAll(tv, []byte(`"`), []byte("'"))
text.WriteString(fmt.Sprintf("%s=", key))
text.Write(tv)
text.WriteString("; ")
default:
text.WriteString(fmt.Sprintf("%s=%v; ", key, value))
} }
} }
return text.String() return text.String() + " " + sequence.Definition()
} }
return "" return ""

5
pkg/obiformats/fastseq_write_fasta.go
View File

@ -63,9 +63,8 @@ func FormatFasta(seq *obiseq.BioSequence, formater FormatHeader) string {
} }
info := formater(seq) info := formater(seq)
return fmt.Sprintf(">%s %s %s\n%s", return fmt.Sprintf(">%s %s\n%s",
seq.Id(), info, seq.Id(), info,
seq.Definition(),
folded) folded)
} }
@ -199,7 +198,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
// configuration options as variadic arguments. It appends the option to not close the file // configuration options as variadic arguments. It appends the option to not close the file
// to the options slice and then calls the WriteFasta function passing the iterator, // to the options slice and then calls the WriteFasta function passing the iterator,
// os.Stdout as the output file, and the options slice. // os.Stdout as the output file, and the options slice.
// //
// The function returns the same bio sequence iterator and an error if any occurred. // The function returns the same bio sequence iterator and an error if any occurred.
func WriteFastaToStdout(iterator obiiter.IBioSequence, func WriteFastaToStdout(iterator obiiter.IBioSequence,
options ...WithOption) (obiiter.IBioSequence, error) { options ...WithOption) (obiiter.IBioSequence, error) {

3
pkg/obiformats/fastseq_write_fastq.go
View File

@ -32,9 +32,8 @@ func FormatFastq(seq *obiseq.BioSequence, quality_shift int, formater FormatHead
info = formater(seq) info = formater(seq)
} }
return fmt.Sprintf("@%s %s %s\n%s\n+\n%s", return fmt.Sprintf("@%s %s\n%s\n+\n%s",
seq.Id(), info, seq.Id(), info,
seq.Definition(),
string(seq.Sequence()), string(seq.Sequence()),
string(ascii), string(ascii),
) )

6
pkg/obiformats/xopen.go
View File

@ -403,7 +403,7 @@ func WopenFile(f string, flag int, perm os.FileMode) (*Writer, error) {
if strings.HasSuffix(f2, ".gz") { if strings.HasSuffix(f2, ".gz") {
gz, err := gzip.NewWriterLevel(wtr, Level) gz, err := gzip.NewWriterLevel(wtr, Level)
if err != nil { if err != nil {
err = errors.New(fmt.Sprintf("xopen: %s", err)) err = fmt.Errorf("xopen: %s", err)
} }
return &Writer{bufio.NewWriterSize(gz, bufSize), wtr, gz, nil, nil, nil}, err return &Writer{bufio.NewWriterSize(gz, bufSize), wtr, gz, nil, nil, nil}, err
} }
@ -418,7 +418,7 @@ func WopenFile(f string, flag int, perm os.FileMode) (*Writer, error) {
} }
zw, err := zstd.NewWriter(wtr, zstd.WithEncoderLevel(zstd.EncoderLevel(level))) zw, err := zstd.NewWriter(wtr, zstd.WithEncoderLevel(zstd.EncoderLevel(level)))
if err != nil { if err != nil {
err = errors.New(fmt.Sprintf("xopen: zstd: %s", err)) err = fmt.Errorf("xopen: zstd: %s", err)
} }
return &Writer{bufio.NewWriterSize(zw, bufSize), wtr, nil, nil, zw, nil}, err return &Writer{bufio.NewWriterSize(zw, bufSize), wtr, nil, nil, zw, nil}, err
} }
@ -429,7 +429,7 @@ func WopenFile(f string, flag int, perm os.FileMode) (*Writer, error) {
} }
bz2, err := bzip2.NewWriter(wtr, &bzip2.WriterConfig{Level: level}) bz2, err := bzip2.NewWriter(wtr, &bzip2.WriterConfig{Level: level})
if err != nil { if err != nil {
err = errors.New(fmt.Sprintf("xopen: %s", err)) err = fmt.Errorf("xopen: %s", err)
} }
return &Writer{bufio.NewWriterSize(bz2, bufSize), wtr, nil, nil, nil, bz2}, err return &Writer{bufio.NewWriterSize(bz2, bufSize), wtr, nil, nil, nil, bz2}, err
} }

4
pkg/obiformats/xopen_test.go
View File

@ -61,7 +61,7 @@ func (s *XopenTest) TestWopen(c *C) {
_, err = os.Stat(f) _, err = os.Stat(f)
c.Assert(err, IsNil) c.Assert(err, IsNil)
c.Assert(wtr.wtr, NotNil) c.Assert(wtr.wtr, NotNil)
fmt.Fprintf(wtr, testString) fmt.Fprint(wtr, testString)
wtr.Close() wtr.Close()
rdr, err := Ropen(f) rdr, err := Ropen(f)
@ -70,7 +70,7 @@ func (s *XopenTest) TestWopen(c *C) {
str, err := rdr.ReadString(99) str, err := rdr.ReadString(99)
c.Assert(str, Equals, testString) c.Assert(str, Equals, testString)
c.Assert(err, Equals, io.EOF) c.Assert(err, Equals, io.EOF)
str, err = rdr.ReadString(99) str, _ = rdr.ReadString(99)
c.Assert(str, Equals, "") c.Assert(str, Equals, "")
rdr.Close() rdr.Close()