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Add sorting by average quality to seqkit sort #482

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Add sorting by average quality to seqkit sort #482

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60 changes: 54 additions & 6 deletions seqkit/cmd/sort.go
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Original file line number Diff line number Diff line change
Expand Up @@ -43,8 +43,8 @@ var sortCmd = &cobra.Command{
GroupID: "order",

Use: "sort",
Short: "sort sequences by id/name/sequence/length",
Long: `sort sequences by id/name/sequence/length.
Short: "sort sequences by id/name/sequence/length/quality",
Long: `sort sequences by id/name/sequence/length/quality.

By default, all records will be readed into memory.
For FASTA format, use flag -2 (--two-pass) to reduce memory usage. FASTQ not
Expand Down Expand Up @@ -81,6 +81,8 @@ Attention:
byName := getFlagBool(cmd, "by-name")
byLength := getFlagBool(cmd, "by-length")
byBases := getFlagBool(cmd, "by-bases")
byAvgQual := getFlagBool(cmd, "by-avg-qual")
qBase := getFlagPositiveInt(cmd, "qual-ascii-base")
gapLetters := getFlagString(cmd, "gap-letters")
reverse := getFlagBool(cmd, "reverse")
ignoreCase := getFlagBool(cmd, "ignore-case")
Expand Down Expand Up @@ -113,12 +115,15 @@ Attention:
if byLength {
n++
}
if byAvgQual {
n++
}
if n > 1 {
checkError(fmt.Errorf("only one of the flags -l (--by-length), -n (--by-name) and -s (--by-seq) is allowed"))
}

byID := true
if bySeq || byLength {
if bySeq || byLength || byAvgQual {
byID = false
}
if !quiet {
Expand All @@ -132,6 +137,7 @@ Attention:
name2name0 := make(map[string]string, 1000)
name2sequence := []stringutil.String2ByteSlice{}
name2length := []stringutil.StringCount{}
name2avgQual := []stringutil.StringFloat{}

// for indexing when output and duplicated sequences checking
id2name := make(map[string][]byte)
Expand All @@ -146,9 +152,13 @@ Attention:
}
var name string
var length int
var avgQual float64
for _, file := range files {
fastxReader, err := fastx.NewReader(alphabet, file, idRegexp)
checkError(err)
if byAvgQual && !fastxReader.IsFastq {
checkError(fmt.Errorf("sorting by average quality is not supported for FASTA format"))
}
for {
record, err = fastxReader.Read()
if err != nil {
Expand All @@ -165,7 +175,7 @@ Attention:

if byName {
name = string(record.Name)
} else if byID || bySeq || byLength {
} else if byID || bySeq || byLength || byAvgQual {
name = string(record.ID)
}

Expand All @@ -190,6 +200,9 @@ Attention:
length = len(record2.Seq.Seq)
}
name2length = append(name2length, stringutil.StringCount{Key: name, Count: length})
} else if byAvgQual {
avgQual = record2.Seq.AvgQual(qBase)
name2avgQual = append(name2avgQual, stringutil.StringFloat{Key: name, Value: avgQual})
} else if byID || byName || bySeq {
if ignoreCase {
name2sequence = append(name2sequence, stringutil.String2ByteSlice{Key: name, Value: bytes.ToLower(record2.Seq.Seq)})
Expand Down Expand Up @@ -218,6 +231,12 @@ Attention:
} else {
sort.Sort(stringutil.StringCountList(name2length))
}
} else if byAvgQual {
if reverse {
sort.Sort(stringutil.ReversedByValue{stringutil.StringFloatList(name2avgQual)})
} else {
sort.Sort(stringutil.ByValue{stringutil.StringFloatList(name2avgQual)})
}
} else if byName || byID { // by name/id
stringutil.NaturalOrder = inNaturalOrder
if reverse {
Expand All @@ -244,6 +263,11 @@ Attention:
record = sequences[kv.Key]
record.FormatToWriter(outfh, config.LineWidth)
}
} else if byAvgQual {
for _, kv := range name2avgQual {
record = sequences[kv.Key]
record.FormatToWriter(outfh, config.LineWidth)
}
}

return
Expand Down Expand Up @@ -328,7 +352,7 @@ Attention:
for i, head := range ids {
if byName {
name = head
} else if byID || bySeq || byLength {
} else if byID || bySeq || byLength || byAvgQual {
name = string(fastx.ParseHeadID(idRe, []byte(head)))
}

Expand Down Expand Up @@ -370,7 +394,7 @@ Attention:

if byName {
name = string(record.Name)
} else if byID || bySeq || byLength {
} else if byID || bySeq || byLength || byAvgQual {
name = string(record.ID)
}

Expand Down Expand Up @@ -421,6 +445,12 @@ Attention:
} else {
sort.Sort(stringutil.StringCountList(name2length))
}
} else if byAvgQual {
if reverse {
sort.Sort(stringutil.ReversedByValue{stringutil.StringFloatList(name2avgQual)})
} else {
sort.Sort(stringutil.ByValue{stringutil.StringFloatList(name2avgQual)})
}
} else if byName || byID { // by name/id
stringutil.NaturalOrder = inNaturalOrder
if reverse {
Expand Down Expand Up @@ -464,6 +494,22 @@ Attention:
continue
}

sequence := subseqByFaixNotCleaned(faidx, chr, r, 1, -1)
outfh.Write([]byte(fmt.Sprintf(">%s\n", chr)))
outfh.Write(sequence)
if len(sequence) > 0 && sequence[len(sequence)-1] != '\n' {
outfh.WriteString("\n")
}
}
} else if byAvgQual {
for _, kv := range name2avgQual {
chr = string(id2name[name2name0[kv.Key]])
r, ok := faidx.Index[chr]
if !ok {
checkError(fmt.Errorf(`sequence (%s) not found in file: %s`, chr, newFile))
continue
}

sequence := subseqByFaixNotCleaned(faidx, chr, r, 1, -1)
outfh.Write([]byte(fmt.Sprintf(">%s\n", chr)))
outfh.Write(sequence)
Expand All @@ -487,6 +533,8 @@ func init() {
sortCmd.Flags().BoolP("by-seq", "s", false, "by sequence")
sortCmd.Flags().BoolP("by-length", "l", false, "by sequence length")
sortCmd.Flags().BoolP("by-bases", "b", false, "by non-gap bases")
sortCmd.Flags().BoolP("by-avg-qual", "q", false, "by average quality of sequences")
sortCmd.Flags().IntP("qual-ascii-base", "Q", 33, "ASCII base for quality scores")
sortCmd.Flags().StringP("gap-letters", "G", "- .", "gap letters")
sortCmd.Flags().BoolP("reverse", "r", false, "reverse the result")
sortCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")
Expand Down