First commit

pkg/obiformats/universal_read.go

@@ -0,0 +1,93 @@
+package obiformats
+
+import (
+	"bufio"
+	"compress/gzip"
+	"io"
+	"log"
+	"os"
+	"strings"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func GuessSeqFileType(firstline string) string {
+	switch {
+	case strings.HasPrefix(firstline, "#@ecopcr-v2"):
+		return "ecopcr"
+
+	case strings.HasPrefix(firstline, "#"):
+		return "ecopcr"
+
+	case strings.HasPrefix(firstline, ">"):
+		return "fasta"
+
+	case strings.HasPrefix(firstline, "@"):
+		return "fastq"
+
+	case strings.HasPrefix(firstline, "ID   "):
+		return "embl"
+
+	case strings.HasPrefix(firstline, "LOCUS       "):
+		return "genebank"
+
+	default:
+		return "unknown"
+	}
+}
+
+func ReadSequencesBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	var file *os.File
+	var reader io.Reader
+	var greader io.Reader
+	var err error
+
+	file, err = os.Open(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return obiseq.NilIBioSequenceBatch, err
+	}
+
+	reader = file
+
+	// Test if the flux is compressed by gzip
+	greader, err = gzip.NewReader(reader)
+	if err != nil {
+		file.Seek(0, 0)
+	} else {
+		log.Printf("File %s is gz compressed ", filename)
+		reader = greader
+	}
+
+	breader := bufio.NewReader(reader)
+
+	tag, _ := breader.Peek(30)
+
+	filetype := GuessSeqFileType(string(tag))
+	log.Printf("File guessed format : %s (tag: %s)",
+		filetype, (strings.Split(string(tag), "\n"))[0])
+	reader = breader
+
+	switch filetype {
+	case "fastq", "fasta":
+		file.Close()
+		is, _ := ReadFastSeqBatchFromFile(filename, options...)
+		return is, nil
+	case "ecopcr":
+		return ReadEcoPCRBatch(reader, options...), nil
+	case "embl":
+		return ReadEMBLBatch(reader, options...), nil
+	default:
+		log.Fatalf("File %s has guessed format %s which is not yet implemented",
+			filename, filetype)
+	}
+
+	return obiseq.NilIBioSequenceBatch, nil
+}
+
+func ReadSequencesFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
+	ib, err := ReadSequencesBatchFromFile(filename, options...)
+	return ib.SortBatches().IBioSequence(), err
+
+}