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Refactoring related to iterators

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This commit is contained in:
Eric Coissac
2022-11-16 17:13:03 +01:00
parent 6f853da9df
commit 09fc426b67
29 changed files with 95 additions and 93 deletions
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16
pkg/obitools/obiconvert/sequence_reader.go
View File

@@ -67,7 +67,7 @@ func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
return list_of_files, nil
}
func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, error) {
func ReadBioSequences(filenames ...string) (obiiter.IBioSequenceBatch, error) {
var iterator obiiter.IBioSequenceBatch
var reader func(string, ...obiformats.WithOption) (obiiter.IBioSequenceBatch, error)
@@ -97,13 +97,13 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
log.Printf("Reading sequences from stdin in %s\n", CLIInputFormat())
switch CLIInputFormat() {
case "ecopcr":
iterator = obiformats.ReadEcoPCRBatch(os.Stdin, opts...)
iterator = obiformats.ReadEcoPCR(os.Stdin, opts...)
case "embl":
iterator = obiformats.ReadEMBLBatch(os.Stdin, opts...)
iterator = obiformats.ReadEMBL(os.Stdin, opts...)
case "genbank":
iterator = obiformats.ReadGenbankBatch(os.Stdin, opts...)
iterator = obiformats.ReadGenbank(os.Stdin, opts...)
default:
iterator = obiformats.ReadFastSeqBatchFromStdin(opts...)
iterator = obiformats.ReadFastSeqFromStdin(opts...)
}
} else {
@@ -116,11 +116,11 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
case "ecopcr":
reader = obiformats.ReadEcoPCRBatchFromFile
case "embl":
reader = obiformats.ReadEMBLBatchFromFile
reader = obiformats.ReadEMBLFromFile
case "genbank":
reader = obiformats.ReadGenbankBatchFromFile
reader = obiformats.ReadGenbankFromFile
default:
reader = obiformats.ReadSequencesBatchFromFile
reader = obiformats.ReadSequencesFromFile
}
if len(list_of_files) > 1 {

14
pkg/obitools/obiconvert/sequence_writer.go
View File

@@ -8,7 +8,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)
func WriteBioSequencesBatch(iterator obiiter.IBioSequenceBatch,
func WriteBioSequences(iterator obiiter.IBioSequenceBatch,
terminalAction bool, filenames ...string) (obiiter.IBioSequenceBatch, error) {
var newIter obiiter.IBioSequenceBatch
@@ -43,20 +43,20 @@ func WriteBioSequencesBatch(iterator obiiter.IBioSequenceBatch,
if len(filenames) == 0 {
switch CLIOutputFormat() {
case "fastq":
newIter, err = obiformats.WriteFastqBatchToStdout(iterator, opts...)
newIter, err = obiformats.WriteFastqToStdout(iterator, opts...)
case "fasta":
newIter, err = obiformats.WriteFastaBatchToStdout(iterator, opts...)
newIter, err = obiformats.WriteFastaToStdout(iterator, opts...)
default:
newIter, err = obiformats.WriteSequencesBatchToStdout(iterator, opts...)
newIter, err = obiformats.WriteSequencesToStdout(iterator, opts...)
}
} else {
switch CLIOutputFormat() {
case "fastq":
newIter, err = obiformats.WriteFastqBatchToFile(iterator, filenames[0], opts...)
newIter, err = obiformats.WriteFastqToFile(iterator, filenames[0], opts...)
case "fasta":
newIter, err = obiformats.WriteFastaBatchToFile(iterator, filenames[0], opts...)
newIter, err = obiformats.WriteFastaToFile(iterator, filenames[0], opts...)
default:
newIter, err = obiformats.WriteSequencesBatchToFile(iterator, filenames[0], opts...)
newIter, err = obiformats.WriteSequencesToFile(iterator, filenames[0], opts...)
}
}

6
pkg/obitools/obidistribute/distribute.go
View File

@@ -40,11 +40,11 @@ func DistributeSequence(sequences obiiter.IBioSequenceBatch) {
switch obiconvert.CLIOutputFormat() {
case "fastq":
formater = obiformats.WriteFastqBatchToFile
formater = obiformats.WriteFastqToFile
case "fasta":
formater = obiformats.WriteFastaBatchToFile
formater = obiformats.WriteFastaToFile
default:
formater = obiformats.WriteSequencesBatchToFile
formater = obiformats.WriteSequencesToFile
}
dispatcher := sequences.Distribute(CLISequenceClassifier(),

2
pkg/obitools/obigrep/grep.go
View File

@@ -22,7 +22,7 @@ func IFilterSequence(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBat
obioptions.CLIBatchSize())
go func() {
_, err := obiconvert.WriteBioSequencesBatch(discarded,
_, err := obiconvert.WriteBioSequences(discarded,
true,
CLIDiscardedFileName())

4
pkg/obitools/obimultiplex/demultiplex.go
View File

@@ -10,7 +10,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
)
func IExtractBarcodeBatches(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSequenceBatch, error) {
func IExtractBarcode(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSequenceBatch, error) {
opts := make([]obingslibrary.WithOption, 0, 10)
@@ -44,7 +44,7 @@ func IExtractBarcodeBatches(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSeq
obioptions.CLIBatchSize())
go func() {
_, err := obiconvert.WriteBioSequencesBatch(unidentified,
_, err := obiconvert.WriteBioSequences(unidentified,
true,
CLIUnidentifiedFileName())

4
pkg/obitools/obipairing/options.go
View File

@@ -47,12 +47,12 @@ func OptionSet(options *getoptions.GetOpt) {
}
func IBatchPairedSequence() (obiiter.IPairedBioSequenceBatch, error) {
forward, err := obiconvert.ReadBioSequencesBatch(_ForwardFiles...)
forward, err := obiconvert.ReadBioSequences(_ForwardFiles...)
if err != nil {
return obiiter.NilIPairedBioSequenceBatch, err
}
reverse, err := obiconvert.ReadBioSequencesBatch(_ReverseFiles...)
reverse, err := obiconvert.ReadBioSequences(_ReverseFiles...)
if err != nil {
return obiiter.NilIPairedBioSequenceBatch, err
}

2
pkg/obitools/obitag/options.go
View File

@@ -39,7 +39,7 @@ func CLIRefDBName() string {
}
func CLIRefDB() obiseq.BioSequenceSlice {
refdb, err := obiformats.ReadSequencesBatchFromFile(_RefDB)
refdb, err := obiformats.ReadSequencesFromFile(_RefDB)
if err != nil {
log.Panicf("Cannot open the reference library file : %s\n", _RefDB)