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238
pkg/obiformats/ecopcr_read.go
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238
pkg/obiformats/ecopcr_read.go
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@ -0,0 +1,238 @@
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package obiformats
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import (
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"compress/gzip"
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"encoding/csv"
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"fmt"
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"io"
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"log"
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"os"
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"strconv"
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"strings"
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"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
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)
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type __ecopcr_file__ struct {
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file io.Reader
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csv *csv.Reader
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names map[string]int
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version int
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mode string
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forward_primer string
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reverse_primer string
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}
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func __readline__(stream io.Reader) string {
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line := make([]byte, 1024)
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char := make([]byte, 1)
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i := 0
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for n, err := stream.Read(char); err == nil && n == 1 && char[0] != '\n'; n, err = stream.Read(char) {
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line[i] = char[0]
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i++
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}
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return string(line[0:i])
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}
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func __read_ecopcr_bioseq__(file *__ecopcr_file__) (obiseq.BioSequence, error) {
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record, err := file.csv.Read()
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if err != nil {
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return obiseq.NilBioSequence, err
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}
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name := strings.TrimSpace(record[0])
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// Ensure that sequence name is unique accross a file.
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if val, ok := file.names[name]; ok {
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file.names[name]++
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name = fmt.Sprintf("%s_%d", name, val)
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} else {
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file.names[name] = 1
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}
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var sequence []byte
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var comment string
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if file.version == 2 {
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sequence = []byte(strings.TrimSpace(record[20]))
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comment = strings.TrimSpace(record[21])
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} else {
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sequence = []byte(strings.TrimSpace(record[18]))
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comment = strings.TrimSpace(record[19])
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}
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bseq := obiseq.MakeBioSequence(name, sequence, comment)
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annotation := bseq.Annotations()
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annotation["ac"] = name
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annotation["seq_length"], _ = strconv.Atoi(strings.TrimSpace(record[1]))
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annotation["taxid"], _ = strconv.Atoi(strings.TrimSpace(record[2]))
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annotation["rank"] = strings.TrimSpace(record[3])
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annotation["species_taxid"], _ = strconv.Atoi(strings.TrimSpace(record[4]))
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annotation["species_name"] = strings.TrimSpace(record[5])
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annotation["genus_taxid"], _ = strconv.Atoi(strings.TrimSpace(record[6]))
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annotation["genus_name"] = strings.TrimSpace(record[7])
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annotation["family_taxid"], _ = strconv.Atoi(strings.TrimSpace(record[8]))
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annotation["family_name"] = strings.TrimSpace(record[9])
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k_m_taxid := file.mode + "_taxid"
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k_m_name := file.mode + "_name"
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annotation[k_m_taxid], _ = strconv.Atoi(strings.TrimSpace(record[10]))
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annotation[k_m_name] = strings.TrimSpace(record[11])
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annotation["strand"] = strings.TrimSpace(record[12])
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annotation["forward_primer"] = file.forward_primer
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annotation["forward_match"] = strings.TrimSpace(record[13])
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annotation["forward_mismatch"], _ = strconv.Atoi(strings.TrimSpace(record[14]))
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delta := 0
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if file.version == 2 {
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value, err := strconv.ParseFloat(strings.TrimSpace(record[15]), 64)
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if err != nil {
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annotation["forward_tm"] = value
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} else {
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annotation["forward_tm"] = -1
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}
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delta++
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}
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annotation["reverse_primer"] = file.reverse_primer
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annotation["reverse_match"] = strings.TrimSpace(record[15+delta])
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annotation["reverse_mismatch"], _ = strconv.Atoi(strings.TrimSpace(record[16+delta]))
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if file.version == 2 {
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value, err := strconv.ParseFloat(strings.TrimSpace(record[17+delta]), 64)
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if err != nil {
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annotation["reverse_tm"] = value
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} else {
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annotation["reverse_tm"] = -1
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}
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delta++
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}
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annotation["amplicon_length"], _ = strconv.Atoi(strings.TrimSpace(record[17+delta]))
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return bseq, nil
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}
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func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenceBatch {
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tag := make([]byte, 11)
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n, _ := reader.Read(tag)
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version := 1
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if n == 11 && string(tag) == "#@ecopcr-v2" {
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version = 2
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}
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line := __readline__(reader)
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for !strings.HasPrefix(line, "# direct strand oligo1") {
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line = __readline__(reader)
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}
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forward_primer := (strings.Split(line, " "))[6]
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line = __readline__(reader)
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for !strings.HasPrefix(line, "# reverse strand oligo2") {
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line = __readline__(reader)
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}
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reverse_primer := (strings.Split(line, " "))[5]
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line = __readline__(reader)
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for !strings.HasPrefix(line, "# output in") {
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line = __readline__(reader)
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}
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mode := (strings.Split(line, " "))[3]
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file := csv.NewReader(reader)
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file.Comma = '|'
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file.Comment = '#'
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file.TrimLeadingSpace = true
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file.ReuseRecord = true
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log.Printf("EcoPCR file version : %d Mode : %s\n", version, mode)
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ecopcr := __ecopcr_file__{
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file: reader,
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csv: file,
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names: make(map[string]int),
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version: version,
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mode: mode,
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forward_primer: forward_primer,
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reverse_primer: reverse_primer}
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opt := MakeOptions(options)
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new_iter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
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new_iter.Add(1)
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go func() {
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new_iter.Wait()
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close(new_iter.Channel())
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}()
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go func() {
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seq, err := __read_ecopcr_bioseq__(&ecopcr)
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slice := make(obiseq.BioSequenceSlice, 0, opt.BatchSize())
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i := 0
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ii := 0
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for err == nil {
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slice = append(slice, seq)
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ii++
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if ii >= opt.BatchSize() {
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new_iter.Channel() <- obiseq.MakeBioSequenceBatch(i, slice...)
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slice = make(obiseq.BioSequenceSlice, 0, opt.BatchSize())
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i++
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ii = 0
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}
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seq, err = __read_ecopcr_bioseq__(&ecopcr)
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}
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if len(slice) > 0 {
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new_iter.Channel() <- obiseq.MakeBioSequenceBatch(i, slice...)
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}
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new_iter.Done()
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if err != nil && err != io.EOF {
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log.Panicf("%+v", err)
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}
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}()
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return new_iter
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}
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func ReadEcoPCR(reader io.Reader, options ...WithOption) obiseq.IBioSequence {
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ib := ReadEcoPCRBatch(reader, options...)
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return ib.SortBatches().IBioSequence()
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}
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func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
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var reader io.Reader
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var greader io.Reader
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var err error
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reader, err = os.Open(filename)
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if err != nil {
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log.Printf("open file error: %+v", err)
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return obiseq.NilIBioSequenceBatch, err
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}
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// Test if the flux is compressed by gzip
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greader, err = gzip.NewReader(reader)
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if err == nil {
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reader = greader
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}
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return ReadEcoPCRBatch(reader, options...), nil
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}
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func ReadEcoPCRFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
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ib, err := ReadEcoPCRBatchFromFile(filename, options...)
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return ib.SortBatches().IBioSequence(), err
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}
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