obitools4/pkg/obiformats/ecopcr_read.go

package obiformats

import (
	"encoding/csv"
	"fmt"
	"io"
	"path"
	"strconv"
	"strings"

	log "github.com/sirupsen/logrus"

	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)

type __ecopcr_file__ struct {
	file           io.Reader
	csv            *csv.Reader
	names          map[string]int
	version        int
	mode           string
	forward_primer string
	reverse_primer string
}

func __readline__(stream io.Reader) string {
	line := make([]byte, 1024)
	char := make([]byte, 1)

	i := 0
	for n, err := stream.Read(char); err == nil && n == 1 && char[0] != '\n'; n, err = stream.Read(char) {
		line[i] = char[0]
		i++
	}
	return string(line[0:i])
}

func __read_ecopcr_bioseq__(file *__ecopcr_file__) (*obiseq.BioSequence, error) {

	record, err := file.csv.Read()

	if err != nil {
		return nil, err
	}

	name := strings.TrimSpace(record[0])

	// Ensure that sequence name is unique accross a file.
	if val, ok := file.names[name]; ok {
		file.names[name]++
		name = fmt.Sprintf("%s_%d", name, val)
	} else {
		file.names[name] = 1
	}

	var sequence []byte
	var comment string

	if file.version == 2 {
		sequence = []byte(strings.TrimSpace(record[20]))
		comment = strings.TrimSpace(record[21])

	} else {
		sequence = []byte(strings.TrimSpace(record[18]))
		comment = strings.TrimSpace(record[19])
	}

	bseq := obiseq.NewBioSequence(name, sequence, comment)
	annotation := bseq.Annotations()

	annotation["ac"] = name
	annotation["seq_length"], _ = strconv.Atoi(strings.TrimSpace(record[1]))
	annotation["taxid"], _ = strconv.Atoi(strings.TrimSpace(record[2]))
	annotation["rank"] = strings.TrimSpace(record[3])
	annotation["species_taxid"], _ = strconv.Atoi(strings.TrimSpace(record[4]))
	annotation["species_name"] = strings.TrimSpace(record[5])
	annotation["genus_taxid"], _ = strconv.Atoi(strings.TrimSpace(record[6]))
	annotation["genus_name"] = strings.TrimSpace(record[7])
	annotation["family_taxid"], _ = strconv.Atoi(strings.TrimSpace(record[8]))
	annotation["family_name"] = strings.TrimSpace(record[9])
	k_m_taxid := file.mode + "_taxid"
	k_m_name := file.mode + "_name"
	annotation[k_m_taxid], _ = strconv.Atoi(strings.TrimSpace(record[10]))
	annotation[k_m_name] = strings.TrimSpace(record[11])
	annotation["strand"] = strings.TrimSpace(record[12])
	annotation["forward_primer"] = file.forward_primer
	annotation["forward_match"] = strings.TrimSpace(record[13])
	annotation["forward_mismatch"], _ = strconv.Atoi(strings.TrimSpace(record[14]))

	delta := 0
	if file.version == 2 {
		value, err := strconv.ParseFloat(strings.TrimSpace(record[15]), 64)
		if err != nil {
			annotation["forward_tm"] = value
		} else {
			annotation["forward_tm"] = -1
		}
		delta++
	}

	annotation["reverse_primer"] = file.reverse_primer
	annotation["reverse_match"] = strings.TrimSpace(record[15+delta])
	annotation["reverse_mismatch"], _ = strconv.Atoi(strings.TrimSpace(record[16+delta]))

	if file.version == 2 {
		value, err := strconv.ParseFloat(strings.TrimSpace(record[17+delta]), 64)
		if err != nil {
			annotation["reverse_tm"] = value
		} else {
			annotation["reverse_tm"] = -1
		}
		delta++
	}

	annotation["amplicon_length"], _ = strconv.Atoi(strings.TrimSpace(record[17+delta]))

	return bseq, nil
}

func ReadEcoPCR(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, error) {
	tag := make([]byte, 11)
	n, _ := reader.Read(tag)

	version := 1
	if n == 11 && string(tag) == "#@ecopcr-v2" {
		version = 2
	}

	line := __readline__(reader)
	for !strings.HasPrefix(line, "# direct  strand oligo1") {
		line = __readline__(reader)
	}
	forward_primer := (strings.Split(line, " "))[6]

	line = __readline__(reader)
	for !strings.HasPrefix(line, "# reverse strand oligo2") {
		line = __readline__(reader)
	}
	reverse_primer := (strings.Split(line, " "))[5]

	line = __readline__(reader)
	for !strings.HasPrefix(line, "# output in") {
		line = __readline__(reader)
	}
	mode := (strings.Split(line, " "))[3]

	file := csv.NewReader(reader)
	file.Comma = '|'
	file.Comment = '#'
	file.TrimLeadingSpace = true
	file.ReuseRecord = true

	log.Printf("EcoPCR file version : %d  Mode : %s\n", version, mode)

	ecopcr := __ecopcr_file__{
		file:           reader,
		csv:            file,
		names:          make(map[string]int),
		version:        version,
		mode:           mode,
		forward_primer: forward_primer,
		reverse_primer: reverse_primer}

	opt := MakeOptions(options)

	newIter := obiiter.MakeIBioSequence()
	newIter.Add(1)

	go func() {
		newIter.Wait()
		newIter.Close()
	}()

	go func() {
		var err error = nil
		var seq *obiseq.BioSequence

		seq, err = __read_ecopcr_bioseq__(&ecopcr)
		seq.SetSource(opt.Source())
		slice := make(obiseq.BioSequenceSlice, 0, opt.BatchSize())
		i := 0
		ii := 0
		for err == nil {
			slice = append(slice, seq)
			ii++
			if ii >= opt.BatchSize() {
				newIter.Push(obiiter.MakeBioSequenceBatch(opt.Source(), i, slice))
				slice = obiseq.MakeBioSequenceSlice()
				i++
				ii = 0
			}

			seq, err = __read_ecopcr_bioseq__(&ecopcr)

			if err == nil {
				seq.SetSource(opt.Source())
			} else if err != io.EOF {
				log.Panicf("%+v", err)
			}
		}

		if len(slice) > 0 {
			newIter.Push(obiiter.MakeBioSequenceBatch(opt.Source(), i, slice))
		}

		newIter.Done()

		if err != nil && err != io.EOF {
			log.Panicf("%+v", err)
		}

	}()

	if opt.pointer.full_file_batch {
		newIter = newIter.CompleteFileIterator()
	}

	return newIter, nil
}

func ReadEcoPCRFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
	var reader io.Reader
	var err error

	options = append(options, OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))))

	reader, err = obiutils.Ropen(filename)

	if err == obiutils.ErrNoContent {
		log.Infof("file %s is empty", filename)
		return ReadEmptyFile(options...)
	}

	if err != nil {
		log.Printf("open file error: %+v", err)
		return obiiter.NilIBioSequence, err
	}

	return ReadEcoPCR(reader, options...)
}