mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
107 lines
2.2 KiB
Go
107 lines
2.2 KiB
Go
package obiformats
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import (
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"bufio"
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gzip "github.com/klauspost/pgzip"
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"io"
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"os"
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"path"
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"strings"
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
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)
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func GuessSeqFileType(firstline string) string {
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switch {
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case strings.HasPrefix(firstline, "#@ecopcr-v2"):
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return "ecopcr"
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case strings.HasPrefix(firstline, "#"):
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return "ecopcr"
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case strings.HasPrefix(firstline, ">"):
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return "fasta"
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case strings.HasPrefix(firstline, "@"):
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return "fastq"
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case strings.HasPrefix(firstline, "ID "):
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return "embl"
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case strings.HasPrefix(firstline, "LOCUS "):
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return "genbank"
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// Special case for genbank release files
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// I hope it is enougth stringeant
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case strings.HasSuffix(firstline, " Genetic Se"):
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return "genbank"
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default:
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return "unknown"
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}
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}
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func ReadSequencesFromFile(filename string,
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options ...WithOption) (obiiter.IBioSequence, error) {
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var file *os.File
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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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options = append(options, OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))))
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file, err = os.Open(filename)
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if err != nil {
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log.Fatalf("open file error: %v", err)
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return obiiter.NilIBioSequence, err
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}
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reader = file
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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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file.Seek(0, 0)
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} else {
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log.Debugf("File %s is gz compressed ", filename)
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reader = greader
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}
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breader := bufio.NewReader(reader)
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tag, _ := breader.Peek(30)
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if len(tag) < 30 {
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newIter := obiiter.MakeIBioSequence()
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newIter.Close()
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return newIter, nil
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}
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filetype := GuessSeqFileType(string(tag))
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log.Debugf("File guessed format : %s (tag: %s)",
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filetype, (strings.Split(string(tag), "\n"))[0])
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reader = breader
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switch filetype {
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case "fastq", "fasta":
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file.Close()
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is, err := ReadFastSeqFromFile(filename, options...)
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return is, err
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case "ecopcr":
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return ReadEcoPCR(reader, options...), nil
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case "embl":
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return ReadEMBL(reader, options...), nil
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case "genbank":
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return ReadGenbank(reader, options...), nil
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default:
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log.Fatalf("File %s has guessed format %s which is not yet implemented",
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filename, filetype)
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}
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return obiiter.NilIBioSequence, nil
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}
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