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Add some code refactoring from the blackboard branch

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This commit is contained in:
Eric Coissac
2024-08-02 12:35:46 +02:00
parent bc1aaaf7d9
commit 1b1cd41fd3
38 changed files with 491 additions and 330 deletions
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pkg/obitools/obiconvert/sequence_reader.go
+13 -6
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@@ -14,7 +14,7 @@ import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
func ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
var err error
list_of_files := orderedset.NewOrderedSet()
for _, fn := range filenames {
@@ -39,7 +39,7 @@ func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
if info.IsDir() {
if path != fn {
subdir, e := _ExpandListOfFiles(true, path)
subdir, e := ExpandListOfFiles(true, path)
if e != nil {
return e
}
@@ -113,19 +113,26 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
log.Printf("Reading sequences from stdin in %s\n", CLIInputFormat())
opts = append(opts, obiformats.OptionsSource("stdin"))
var err error
switch CLIInputFormat() {
case "ecopcr":
iterator = obiformats.ReadEcoPCR(os.Stdin, opts...)
iterator, err = obiformats.ReadEcoPCR(os.Stdin, opts...)
case "embl":
iterator = obiformats.ReadEMBL(os.Stdin, opts...)
iterator, err = obiformats.ReadEMBL(os.Stdin, opts...)
case "genbank":
iterator = obiformats.ReadGenbank(os.Stdin, opts...)
iterator, err = obiformats.ReadGenbank(os.Stdin, opts...)
default:
iterator = obiformats.ReadFastSeqFromStdin(opts...)
}
if err != nil {
return obiiter.NilIBioSequence, err
}
} else {
list_of_files, err := _ExpandListOfFiles(false, filenames...)
list_of_files, err := ExpandListOfFiles(false, filenames...)
if err != nil {
return obiiter.NilIBioSequence, err
}