obitools4/pkg/obiformats/fastseq_write_fasta.go

// Package obiformats provides functions for formatting and writing biosequences in various formats.
package obiformats

import (
	"bytes"
	"fmt"
	"io"
	"os"
	"strings"
	"sync"
	"time"

	log "github.com/sirupsen/logrus"

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

func min(x, y int) int {
	if x < y {
		return x
	}
	return y
}

// FormatFasta formats a BioSequence as a FASTA-formatted string using the provided format header.
func FormatFasta(seq *obiseq.BioSequence, formater FormatHeader) string {
	var fragments strings.Builder

	if seq == nil {
		log.Panicln("try to format a nil BioSequence")
	}

	s := seq.Sequence()
	l := len(s)

	folded := ""
	if l == 0 {
		log.Println("Writing a BioSequence of length zero")
	} else {
		fragments.Grow(l + int(l/60)*2 + 100)

		for i := 0; i < l; i += 60 {
			to := min(i+60, l)
			fmt.Fprintf(&fragments, "%s\n", string(s[i:to]))
		}

		folded = fragments.String()
		folded = folded[:fragments.Len()-1]
	}

	info := formater(seq)
	return fmt.Sprintf(">%s %s %s\n%s",
		seq.Id(), info,
		seq.Definition(),
		folded)
}

// FormatFastaBatch formats a batch of BioSequences as a single FASTA-formatted byte slice using the provided format header.
func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, skipEmpty bool) []byte {
	var bs bytes.Buffer
	for _, seq := range batch.Slice() {
		if seq.Len() > 0 {
			bs.WriteString(FormatFasta(seq, formater))
			bs.WriteString("\n")	
		} else {
			if skipEmpty {
				log.Warnf("Sequence %s is empty and skiped in output",seq.Id())
			} else {
				log.Fatalf("Sequence %s is empty",seq.Id())
			}
		}
	}
	return bs.Bytes()
}

// The WriteFasta function writes a given iterator of biological sequences to a file in FASTA format.
func WriteFasta(iterator obiiter.IBioSequence,
	file io.WriteCloser,
	options ...WithOption) (obiiter.IBioSequence, error) {
	opt := MakeOptions(options)

	iterator = iterator.Rebatch(1000)
	file, _ = obiutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())

	newIter := obiiter.MakeIBioSequence()

	nwriters := opt.ParallelWorkers()

	obiiter.RegisterAPipe()
	chunkchan := make(chan FileChunck)

	header_format := opt.FormatFastSeqHeader()

	newIter.Add(nwriters)
	var waitWriter sync.WaitGroup

	go func() {
		newIter.WaitAndClose()
		for len(chunkchan) > 0 {
			time.Sleep(time.Millisecond)
		}
		close(chunkchan)
		waitWriter.Wait()
	}()

	ff := func(iterator obiiter.IBioSequence) {
		for iterator.Next() {

			batch := iterator.Get()

			chunkchan <- FileChunck{
				FormatFastaBatch(batch, header_format, opt.SkipEmptySequence()),
				batch.Order(),
			}
			newIter.Push(batch)
		}
		newIter.Done()
	}

	log.Debugln("Start of the fasta file writing")
	go ff(iterator)
	for i := 0; i < nwriters-1; i++ {
		go ff(iterator.Split())
	}

	next_to_send := 0
	received := make(map[int]FileChunck, 100)

	waitWriter.Add(1)
	go func() {
		for chunk := range chunkchan {
			if chunk.order == next_to_send {
				file.Write(chunk.text)
				next_to_send++
				chunk, ok := received[next_to_send]
				for ok {
					file.Write(chunk.text)
					delete(received, next_to_send)
					next_to_send++
					chunk, ok = received[next_to_send]
				}
			} else {
				received[chunk.order] = chunk
			}

		}

		file.Close()

		log.Debugln("End of the fasta file writing")
		obiiter.UnregisterPipe()
		waitWriter.Done()

	}()

	return newIter, nil
}

// The function WriteFastaToStdout writes a FASTA file to standard output.
func WriteFastaToStdout(iterator obiiter.IBioSequence,
	options ...WithOption) (obiiter.IBioSequence, error) {
	options = append(options, OptionDontCloseFile())
	return WriteFasta(iterator, os.Stdout, options...)
}

// The function `WriteFastaToFile` writes a given iterator of biosequences to a file in FASTA format,
// with the option to append to an existing file and save paired sequences to a separate file.
func WriteFastaToFile(iterator obiiter.IBioSequence,
	filename string,
	options ...WithOption) (obiiter.IBioSequence, error) {

	opt := MakeOptions(options)
	flags := os.O_WRONLY | os.O_CREATE

	if opt.AppendFile() {
		flags |= os.O_APPEND
	}
	file, err := os.OpenFile(filename, flags, 0660)

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

	options = append(options, OptionCloseFile())

	iterator, err = WriteFasta(iterator, file, options...)

	if opt.HaveToSavePaired() {
		var revfile *os.File

		revfile, err = os.OpenFile(opt.PairedFileName(), flags, 0660)
		if err != nil {
			log.Fatalf("open file error: %v", err)
			return obiiter.NilIBioSequence, err
		}
		iterator, err = WriteFasta(iterator.PairedWith(), revfile, options...)
	}

	return iterator, err
}