From 09fc426b677831819f5a7824fdb54907a886fb58 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Wed, 16 Nov 2022 17:13:03 +0100 Subject: [PATCH] Refactoring related to iterators --- cmd/obitools/obiclean/main.go | 4 ++-- cmd/obitools/obicomplement/main.go | 4 ++-- cmd/obitools/obiconvert/main.go | 4 ++-- cmd/obitools/obicount/main.go | 2 +- cmd/obitools/obidistribute/main.go | 2 +- cmd/obitools/obigrep/main.go | 4 ++-- cmd/obitools/obimultiplex/main.go | 9 +++++---- cmd/obitools/obipairing/main.go | 5 +++-- cmd/obitools/obipcr/main.go | 4 ++-- cmd/obitools/obirefidx/main.go | 4 ++-- cmd/obitools/obitag/main.go | 4 ++-- cmd/obitools/obiuniq/main.go | 4 ++-- pkg/obiformats/batch_of_files_reader.go | 2 +- pkg/obiformats/ecopcr_read.go | 4 ++-- pkg/obiformats/embl_read.go | 6 +++--- pkg/obiformats/fastseq_read.go | 4 ++-- pkg/obiformats/fastseq_write_fasta.go | 10 +++++----- pkg/obiformats/fastseq_write_fastq.go | 10 +++++----- pkg/obiformats/genbank_read.go | 14 +++++++------- pkg/obiformats/universal_read.go | 10 +++++----- pkg/obiformats/universal_write.go | 16 ++++++++-------- pkg/obiiter/batchiterator.go | 14 +++++++------- pkg/obitools/obiconvert/sequence_reader.go | 16 ++++++++-------- pkg/obitools/obiconvert/sequence_writer.go | 14 +++++++------- pkg/obitools/obidistribute/distribute.go | 6 +++--- pkg/obitools/obigrep/grep.go | 2 +- pkg/obitools/obimultiplex/demultiplex.go | 4 ++-- pkg/obitools/obipairing/options.go | 4 ++-- pkg/obitools/obitag/options.go | 2 +- 29 files changed, 95 insertions(+), 93 deletions(-) diff --git a/cmd/obitools/obiclean/main.go b/cmd/obitools/obiclean/main.go index 24b3ace..4788b3a 100644 --- a/cmd/obitools/obiclean/main.go +++ b/cmd/obitools/obiclean/main.go @@ -14,9 +14,9 @@ func main() { _, args, _ := optionParser(os.Args) - fs, _ := obiconvert.ReadBioSequencesBatch(args...) + fs, _ := obiconvert.ReadBioSequences(args...) cleaned := obiclean.IOBIClean(fs) - obiconvert.WriteBioSequencesBatch(cleaned, true) + obiconvert.WriteBioSequences(cleaned, true) } diff --git a/cmd/obitools/obicomplement/main.go b/cmd/obitools/obicomplement/main.go index c910797..3645d98 100644 --- a/cmd/obitools/obicomplement/main.go +++ b/cmd/obitools/obicomplement/main.go @@ -14,8 +14,8 @@ func main() { _, args, _ := optionParser(os.Args) - fs, _ := obiconvert.ReadBioSequencesBatch(args...) + fs, _ := obiconvert.ReadBioSequences(args...) comp := fs.MakeIWorker(obiiter.ReverseComplementWorker(true)) - obiconvert.WriteBioSequencesBatch(comp, true) + obiconvert.WriteBioSequences(comp, true) } diff --git a/cmd/obitools/obiconvert/main.go b/cmd/obitools/obiconvert/main.go index 800f6f7..e88a62f 100644 --- a/cmd/obitools/obiconvert/main.go +++ b/cmd/obitools/obiconvert/main.go @@ -13,6 +13,6 @@ func main() { _, args, _ := optionParser(os.Args) - fs, _ := obiconvert.ReadBioSequencesBatch(args...) - obiconvert.WriteBioSequencesBatch(fs, true) + fs, _ := obiconvert.ReadBioSequences(args...) + obiconvert.WriteBioSequences(fs, true) } diff --git a/cmd/obitools/obicount/main.go b/cmd/obitools/obicount/main.go index 3447c4d..3801f27 100644 --- a/cmd/obitools/obicount/main.go +++ b/cmd/obitools/obicount/main.go @@ -33,7 +33,7 @@ func main() { _, args, _ := optionParser(os.Args) - fs, _ := obiconvert.ReadBioSequencesBatch(args...) + fs, _ := obiconvert.ReadBioSequences(args...) nvariant, nread, nsymbol := fs.Count(true) if obicount.CLIIsPrintingVariantCount() { diff --git a/cmd/obitools/obidistribute/main.go b/cmd/obitools/obidistribute/main.go index 7f1b094..1c636a7 100644 --- a/cmd/obitools/obidistribute/main.go +++ b/cmd/obitools/obidistribute/main.go @@ -14,6 +14,6 @@ func main() { _, args, _ := optionParser(os.Args) - fs, _ := obiconvert.ReadBioSequencesBatch(args...) + fs, _ := obiconvert.ReadBioSequences(args...) obidistribute.DistributeSequence(fs) } diff --git a/cmd/obitools/obigrep/main.go b/cmd/obitools/obigrep/main.go index 46e4557..0b38bdd 100644 --- a/cmd/obitools/obigrep/main.go +++ b/cmd/obitools/obigrep/main.go @@ -36,7 +36,7 @@ func main() { _, args, _ := optionParser(os.Args) - sequences, _ := obiconvert.ReadBioSequencesBatch(args...) + sequences, _ := obiconvert.ReadBioSequences(args...) selected := obigrep.IFilterSequence(sequences) - obiconvert.WriteBioSequencesBatch(selected, true) + obiconvert.WriteBioSequences(selected, true) } diff --git a/cmd/obitools/obimultiplex/main.go b/cmd/obitools/obimultiplex/main.go index 154ea8d..120385c 100644 --- a/cmd/obitools/obimultiplex/main.go +++ b/cmd/obitools/obimultiplex/main.go @@ -1,10 +1,11 @@ package main import ( - log "github.com/sirupsen/logrus" "os" "runtime/pprof" + log "github.com/sirupsen/logrus" + "git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions" "git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert" "git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimultiplex" @@ -30,8 +31,8 @@ func main() { _, args, _ := optionParser(os.Args) - sequences, _ := obiconvert.ReadBioSequencesBatch(args...) - amplicons, _ := obimultiplex.IExtractBarcodeBatches(sequences) - obiconvert.WriteBioSequencesBatch(amplicons, true) + sequences, _ := obiconvert.ReadBioSequences(args...) + amplicons, _ := obimultiplex.IExtractBarcode(sequences) + obiconvert.WriteBioSequences(amplicons, true) amplicons.Wait() } diff --git a/cmd/obitools/obipairing/main.go b/cmd/obitools/obipairing/main.go index 358a5a3..aa349d9 100644 --- a/cmd/obitools/obipairing/main.go +++ b/cmd/obitools/obipairing/main.go @@ -1,10 +1,11 @@ package main import ( - log "github.com/sirupsen/logrus" "os" "runtime/trace" + log "github.com/sirupsen/logrus" + "git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions" "git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert" "git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing" @@ -40,5 +41,5 @@ func main() { obipairing.WithStats(), obioptions.CLIParallelWorkers(), ) - obiconvert.WriteBioSequencesBatch(paired, true) + obiconvert.WriteBioSequences(paired, true) } diff --git a/cmd/obitools/obipcr/main.go b/cmd/obitools/obipcr/main.go index 889eee2..14e5b01 100644 --- a/cmd/obitools/obipcr/main.go +++ b/cmd/obitools/obipcr/main.go @@ -33,7 +33,7 @@ func main() { _, args, _ := optionParser(os.Args) - sequences, _ := obiconvert.ReadBioSequencesBatch(args...) + sequences, _ := obiconvert.ReadBioSequences(args...) amplicons, _ := obipcr.PCR(sequences) - obiconvert.WriteBioSequencesBatch(amplicons, true) + obiconvert.WriteBioSequences(amplicons, true) } diff --git a/cmd/obitools/obirefidx/main.go b/cmd/obitools/obirefidx/main.go index 47d5bcc..12e6db3 100644 --- a/cmd/obitools/obirefidx/main.go +++ b/cmd/obitools/obirefidx/main.go @@ -14,9 +14,9 @@ func main() { _, args, _ := optionParser(os.Args) - fs, _ := obiconvert.ReadBioSequencesBatch(args...) + fs, _ := obiconvert.ReadBioSequences(args...) indexed := obirefidx.IndexReferenceDB(fs) - written, _ := obiconvert.WriteBioSequencesBatch(indexed, false) + written, _ := obiconvert.WriteBioSequences(indexed, false) written.Consume() } diff --git a/cmd/obitools/obitag/main.go b/cmd/obitools/obitag/main.go index b8af4a1..02eec69 100644 --- a/cmd/obitools/obitag/main.go +++ b/cmd/obitools/obitag/main.go @@ -33,8 +33,8 @@ func main() { _, args, _ := optionParser(os.Args) - fs, _ := obiconvert.ReadBioSequencesBatch(args...) + fs, _ := obiconvert.ReadBioSequences(args...) identified := obitag.AssignTaxonomy(fs) - obiconvert.WriteBioSequencesBatch(identified, true) + obiconvert.WriteBioSequences(identified, true) } diff --git a/cmd/obitools/obiuniq/main.go b/cmd/obitools/obiuniq/main.go index 3421880..58f3c83 100644 --- a/cmd/obitools/obiuniq/main.go +++ b/cmd/obitools/obiuniq/main.go @@ -36,7 +36,7 @@ func main() { _, args, _ := optionParser(os.Args) - sequences, _ := obiconvert.ReadBioSequencesBatch(args...) + sequences, _ := obiconvert.ReadBioSequences(args...) unique := obiuniq.Unique(sequences) - obiconvert.WriteBioSequencesBatch(unique, true) + obiconvert.WriteBioSequences(unique, true) } diff --git a/pkg/obiformats/batch_of_files_reader.go b/pkg/obiformats/batch_of_files_reader.go index 2d5aa4c..4ea693f 100644 --- a/pkg/obiformats/batch_of_files_reader.go +++ b/pkg/obiformats/batch_of_files_reader.go @@ -13,7 +13,7 @@ func ReadSequencesBatchFromFiles(filenames []string, options ...WithOption) obiiter.IBioSequenceBatch { if reader == nil { - reader = ReadSequencesBatchFromFile + reader = ReadSequencesFromFile } batchiter := obiiter.MakeIBioSequenceBatch(0) diff --git a/pkg/obiformats/ecopcr_read.go b/pkg/obiformats/ecopcr_read.go index 69237cf..a313af0 100644 --- a/pkg/obiformats/ecopcr_read.go +++ b/pkg/obiformats/ecopcr_read.go @@ -119,7 +119,7 @@ func __read_ecopcr_bioseq__(file *__ecopcr_file__) (*obiseq.BioSequence, error) return bseq, nil } -func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch { +func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch { tag := make([]byte, 11) n, _ := reader.Read(tag) @@ -224,5 +224,5 @@ func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiiter.IB reader = greader } - return ReadEcoPCRBatch(reader, options...), nil + return ReadEcoPCR(reader, options...), nil } diff --git a/pkg/obiformats/embl_read.go b/pkg/obiformats/embl_read.go index 402710a..a669a4f 100644 --- a/pkg/obiformats/embl_read.go +++ b/pkg/obiformats/embl_read.go @@ -201,7 +201,7 @@ func _ReadFlatFileChunk(reader io.Reader, readers chan _FileChunk) { // 6 5 43 2 1 // // ?//? -func ReadEMBLBatch(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch { +func ReadEMBL(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch { opt := MakeOptions(options) entry_channel := make(chan _FileChunk, opt.BufferSize()) @@ -224,7 +224,7 @@ func ReadEMBLBatch(reader io.Reader, options ...WithOption) obiiter.IBioSequence return newIter } -func ReadEMBLBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) { +func ReadEMBLFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) { var reader io.Reader var greader io.Reader var err error @@ -242,5 +242,5 @@ func ReadEMBLBatchFromFile(filename string, options ...WithOption) (obiiter.IBio reader = greader } - return ReadEMBLBatch(reader, options...), nil + return ReadEMBL(reader, options...), nil } diff --git a/pkg/obiformats/fastseq_read.go b/pkg/obiformats/fastseq_read.go index beed274..05c9380 100644 --- a/pkg/obiformats/fastseq_read.go +++ b/pkg/obiformats/fastseq_read.go @@ -87,7 +87,7 @@ func _FastseqReader(seqfile C.fast_kseq_p, } -func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) { +func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) { opt := MakeOptions(options) name := C.CString(filename) @@ -132,7 +132,7 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiiter.I return newIter, err } -func ReadFastSeqBatchFromStdin(options ...WithOption) obiiter.IBioSequenceBatch { +func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequenceBatch { opt := MakeOptions(options) newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize()) diff --git a/pkg/obiformats/fastseq_write_fasta.go b/pkg/obiformats/fastseq_write_fasta.go index 36a5c2e..bfb996d 100644 --- a/pkg/obiformats/fastseq_write_fasta.go +++ b/pkg/obiformats/fastseq_write_fasta.go @@ -61,7 +61,7 @@ func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader) []b return bs.Bytes() } -func WriteFastaBatch(iterator obiiter.IBioSequenceBatch, +func WriteFasta(iterator obiiter.IBioSequenceBatch, file io.Writer, options ...WithOption) (obiiter.IBioSequenceBatch, error) { opt := MakeOptions(options) @@ -136,13 +136,13 @@ func WriteFastaBatch(iterator obiiter.IBioSequenceBatch, return newIter, nil } -func WriteFastaBatchToStdout(iterator obiiter.IBioSequenceBatch, +func WriteFastaToStdout(iterator obiiter.IBioSequenceBatch, options ...WithOption) (obiiter.IBioSequenceBatch, error) { options = append(options, OptionDontCloseFile()) - return WriteFastaBatch(iterator, os.Stdout, options...) + return WriteFasta(iterator, os.Stdout, options...) } -func WriteFastaBatchToFile(iterator obiiter.IBioSequenceBatch, +func WriteFastaToFile(iterator obiiter.IBioSequenceBatch, filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) { @@ -155,5 +155,5 @@ func WriteFastaBatchToFile(iterator obiiter.IBioSequenceBatch, options = append(options, OptionCloseFile()) - return WriteFastaBatch(iterator, file, options...) + return WriteFasta(iterator, file, options...) } diff --git a/pkg/obiformats/fastseq_write_fastq.go b/pkg/obiformats/fastseq_write_fastq.go index 5217b6f..845636e 100644 --- a/pkg/obiformats/fastseq_write_fastq.go +++ b/pkg/obiformats/fastseq_write_fastq.go @@ -51,7 +51,7 @@ type FileChunck struct { order int } -func WriteFastqBatch(iterator obiiter.IBioSequenceBatch, +func WriteFastq(iterator obiiter.IBioSequenceBatch, file io.Writer, options ...WithOption) (obiiter.IBioSequenceBatch, error) { opt := MakeOptions(options) @@ -129,13 +129,13 @@ func WriteFastqBatch(iterator obiiter.IBioSequenceBatch, return newIter, nil } -func WriteFastqBatchToStdout(iterator obiiter.IBioSequenceBatch, +func WriteFastqToStdout(iterator obiiter.IBioSequenceBatch, options ...WithOption) (obiiter.IBioSequenceBatch, error) { options = append(options, OptionDontCloseFile()) - return WriteFastqBatch(iterator, os.Stdout, options...) + return WriteFastq(iterator, os.Stdout, options...) } -func WriteFastqBatchToFile(iterator obiiter.IBioSequenceBatch, +func WriteFastqToFile(iterator obiiter.IBioSequenceBatch, filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) { @@ -148,5 +148,5 @@ func WriteFastqBatchToFile(iterator obiiter.IBioSequenceBatch, options = append(options, OptionCloseFile()) - return WriteFastqBatch(iterator, file, options...) + return WriteFastq(iterator, file, options...) } diff --git a/pkg/obiformats/genbank_read.go b/pkg/obiformats/genbank_read.go index 07c4c5d..bc4020d 100644 --- a/pkg/obiformats/genbank_read.go +++ b/pkg/obiformats/genbank_read.go @@ -20,10 +20,10 @@ type gbstate int const ( inHeader gbstate = 0 - inEntry = 1 - inDefinition = 2 - inFeature = 3 - inSequence = 4 + inEntry gbstate = 1 + inDefinition gbstate = 2 + inFeature gbstate = 3 + inSequence gbstate = 4 ) func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) { @@ -107,7 +107,7 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) { } -func ReadGenbankBatch(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch { +func ReadGenbank(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch { opt := MakeOptions(options) entry_channel := make(chan _FileChunk, opt.BufferSize()) @@ -130,7 +130,7 @@ func ReadGenbankBatch(reader io.Reader, options ...WithOption) obiiter.IBioSeque return newIter } -func ReadGenbankBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) { +func ReadGenbankFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) { var reader io.Reader var greader io.Reader var err error @@ -148,5 +148,5 @@ func ReadGenbankBatchFromFile(filename string, options ...WithOption) (obiiter.I reader = greader } - return ReadGenbankBatch(reader, options...), nil + return ReadGenbank(reader, options...), nil } diff --git a/pkg/obiformats/universal_read.go b/pkg/obiformats/universal_read.go index 0625d56..780d1d5 100644 --- a/pkg/obiformats/universal_read.go +++ b/pkg/obiformats/universal_read.go @@ -42,7 +42,7 @@ func GuessSeqFileType(firstline string) string { } } -func ReadSequencesBatchFromFile(filename string, +func ReadSequencesFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) { var file *os.File var reader io.Reader @@ -85,14 +85,14 @@ func ReadSequencesBatchFromFile(filename string, switch filetype { case "fastq", "fasta": file.Close() - is, _ := ReadFastSeqBatchFromFile(filename, options...) + is, _ := ReadFastSeqFromFile(filename, options...) return is, nil case "ecopcr": - return ReadEcoPCRBatch(reader, options...), nil + return ReadEcoPCR(reader, options...), nil case "embl": - return ReadEMBLBatch(reader, options...), nil + return ReadEMBL(reader, options...), nil case "genbank": - return ReadGenbankBatch(reader, options...), nil + return ReadGenbank(reader, options...), nil default: log.Fatalf("File %s has guessed format %s which is not yet implemented", filename, filetype) diff --git a/pkg/obiformats/universal_write.go b/pkg/obiformats/universal_write.go index 52e9f32..addf020 100644 --- a/pkg/obiformats/universal_write.go +++ b/pkg/obiformats/universal_write.go @@ -10,7 +10,7 @@ import ( "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter" ) -func WriteSequenceBatch(iterator obiiter.IBioSequenceBatch, +func WriteSequence(iterator obiiter.IBioSequenceBatch, file io.Writer, options ...WithOption) (obiiter.IBioSequenceBatch, error) { @@ -27,12 +27,12 @@ func WriteSequenceBatch(iterator obiiter.IBioSequenceBatch, if len(batch.Slice()) > 0 { if batch.Slice()[0].HasQualities() { - newIter, err = WriteFastqBatch(iterator, file, options...) + newIter, err = WriteFastq(iterator, file, options...) } else { - newIter, err = WriteFastaBatch(iterator, file, options...) + newIter, err = WriteFasta(iterator, file, options...) } } else { - newIter, err = WriteFastaBatch(iterator, file, options...) + newIter, err = WriteFasta(iterator, file, options...) } return newIter, err @@ -45,13 +45,13 @@ func WriteSequenceBatch(iterator obiiter.IBioSequenceBatch, return obiiter.NilIBioSequenceBatch, fmt.Errorf("input iterator not ready") } -func WriteSequencesBatchToStdout(iterator obiiter.IBioSequenceBatch, +func WriteSequencesToStdout(iterator obiiter.IBioSequenceBatch, options ...WithOption) (obiiter.IBioSequenceBatch, error) { options = append(options, OptionDontCloseFile()) - return WriteSequenceBatch(iterator, os.Stdout, options...) + return WriteSequence(iterator, os.Stdout, options...) } -func WriteSequencesBatchToFile(iterator obiiter.IBioSequenceBatch, +func WriteSequencesToFile(iterator obiiter.IBioSequenceBatch, filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) { @@ -63,5 +63,5 @@ func WriteSequencesBatchToFile(iterator obiiter.IBioSequenceBatch, } options = append(options, OptionCloseFile()) - return WriteSequenceBatch(iterator, file, options...) + return WriteSequence(iterator, file, options...) } diff --git a/pkg/obiiter/batchiterator.go b/pkg/obiiter/batchiterator.go index cd3fc26..6f39d61 100644 --- a/pkg/obiiter/batchiterator.go +++ b/pkg/obiiter/batchiterator.go @@ -631,7 +631,7 @@ func (iterator IBioSequenceBatch) FilterOn(predicate obiseq.SequencePredicate, return trueIter.Rebatch(size) } -// Load every sequences availables from an IBioSequenceBatch iterator into +// Load all sequences availables from an IBioSequenceBatch iterator into // a large obiseq.BioSequenceSlice. func (iterator IBioSequenceBatch) Load() obiseq.BioSequenceSlice { @@ -656,12 +656,12 @@ func IBatchOver(data obiseq.BioSequenceSlice, buffsize = sizes[1] } - trueIter := MakeIBioSequenceBatch(buffsize) + newIter := MakeIBioSequenceBatch(buffsize) - trueIter.Add(1) + newIter.Add(1) go func() { - trueIter.WaitAndClose() + newIter.WaitAndClose() }() go func() { @@ -673,12 +673,12 @@ func IBatchOver(data obiseq.BioSequenceSlice, if next > ldata { next = ldata } - trueIter.Push(MakeBioSequenceBatch(batchid, data[i:next])) + newIter.Push(MakeBioSequenceBatch(batchid, data[i:next])) batchid++ } - trueIter.Done() + newIter.Done() }() - return trueIter + return newIter } diff --git a/pkg/obitools/obiconvert/sequence_reader.go b/pkg/obitools/obiconvert/sequence_reader.go index e1568d6..708b46b 100644 --- a/pkg/obitools/obiconvert/sequence_reader.go +++ b/pkg/obitools/obiconvert/sequence_reader.go @@ -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 { diff --git a/pkg/obitools/obiconvert/sequence_writer.go b/pkg/obitools/obiconvert/sequence_writer.go index 3e9d8b8..8ea4e2d 100644 --- a/pkg/obitools/obiconvert/sequence_writer.go +++ b/pkg/obitools/obiconvert/sequence_writer.go @@ -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...) } } diff --git a/pkg/obitools/obidistribute/distribute.go b/pkg/obitools/obidistribute/distribute.go index 1eb1c94..f2cc6ad 100644 --- a/pkg/obitools/obidistribute/distribute.go +++ b/pkg/obitools/obidistribute/distribute.go @@ -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(), diff --git a/pkg/obitools/obigrep/grep.go b/pkg/obitools/obigrep/grep.go index a406189..4404194 100644 --- a/pkg/obitools/obigrep/grep.go +++ b/pkg/obitools/obigrep/grep.go @@ -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()) diff --git a/pkg/obitools/obimultiplex/demultiplex.go b/pkg/obitools/obimultiplex/demultiplex.go index 30e4e23..1ae0e07 100644 --- a/pkg/obitools/obimultiplex/demultiplex.go +++ b/pkg/obitools/obimultiplex/demultiplex.go @@ -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()) diff --git a/pkg/obitools/obipairing/options.go b/pkg/obitools/obipairing/options.go index 414733a..2f5c129 100644 --- a/pkg/obitools/obipairing/options.go +++ b/pkg/obitools/obipairing/options.go @@ -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 } diff --git a/pkg/obitools/obitag/options.go b/pkg/obitools/obitag/options.go index 68d9136..ce46985 100644 --- a/pkg/obitools/obitag/options.go +++ b/pkg/obitools/obitag/options.go @@ -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)