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Correctly handle empty files

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Former-commit-id: d166aa352ce4bf32739ddc2f7d1c9967918822fd
This commit is contained in:
Eric Coissac
2023-10-16 15:34:06 +02:00
parent e8c55a2b6b
commit 6a6a6f6f2c
4 changed files with 19 additions and 35 deletions
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19
pkg/obiformats/embl_read.go
View File

@ -4,13 +4,10 @@ import (
"bufio"
"bytes"
"io"
"os"
"path"
"strconv"
"strings"
gzip "github.com/klauspost/pgzip"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
@ -276,23 +273,21 @@ func ReadEMBL(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
func ReadEMBLFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
var reader io.Reader
var greader io.Reader
var err error
options = append(options, OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))))
reader, err = os.Open(filename)
reader, err = Ropen(filename)
if err == 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
}
// Test if the flux is compressed by gzip
//greader, err = gzip.NewReader(reader)
greader, err = gzip.NewReaderN(reader, 1<<24, 2)
if err == nil {
reader = greader
}
return ReadEMBL(reader, options...), nil
}

11
pkg/obiformats/fastaseq_read.go
View File

@ -114,19 +114,8 @@ func FastaChunkReader(r io.Reader, size int, cutHead bool) (chan FastxChunk, err
end := []byte{}
for err == nil && n > 0 {
// fmt.Println("============end=========================")
// fmt.Println(string(end))
// fmt.Println("------------buff------------------------")
// fmt.Println(string(buff))
buff = Concatenate(end, buff)
// fmt.Println("------------buff--pasted----------------")
// fmt.Println(string(buff))
buff, end = lastFastaCut(buff)
// fmt.Println("----------------buff--cutted------------")
// fmt.Println(string(buff))
// fmt.Println("------------------end-------------------")
// fmt.Println(string(end))
// fmt.Println("========================================")
if len(buff) > 0 {
out <- FastxChunk{
Bytes: bytes.Clone(buff),

19
pkg/obiformats/genbank_read.go
View File

@ -4,14 +4,11 @@ import (
"bufio"
"bytes"
"io"
"os"
"path"
"regexp"
"strconv"
"strings"
gzip "github.com/klauspost/pgzip"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
@ -173,23 +170,21 @@ func ReadGenbank(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
func ReadGenbankFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
var reader io.Reader
var greader io.Reader
var err error
options = append(options, OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))))
reader, err = os.Open(filename)
reader, err = Ropen(filename)
if err == 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
}
// Test if the flux is compressed by gzip
//greader, err = gzip.NewReader(reader)
greader, err = gzip.NewReaderN(reader, 1<<24, 2)
if err == nil {
reader = greader
}
return ReadGenbank(reader, options...), nil
}

5
pkg/obiformats/universal_read.go
View File

@ -148,6 +148,11 @@ func ReadSequencesFromFile(filename string,
file, err = Ropen(filename)
if err == ErrNoContent {
log.Infof("file %s is empty", filename)
return ReadEmptyFile(options...)
}
if err != nil {
log.Fatalf("open file error: %v", err)
return obiiter.NilIBioSequence, err