mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
remove bad files
Former-commit-id: 44bd45070e43c60ff37a7c579ca4ae1517ec7bcc
This commit is contained in:
537
test.go
537
test.go
@ -1,537 +0,0 @@
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package main
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import (
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"bytes"
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"fmt"
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"io"
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"log"
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"regexp"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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"github.com/gabriel-vasile/mimetype"
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"golang.org/x/exp/slices"
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)
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func OBIMimeTypeGuesser(stream io.Reader) (*mimetype.MIME, io.Reader, error) {
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fastaDetector := func(raw []byte, limit uint32) bool {
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ok, err := regexp.Match("^>[^ ]", raw)
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return ok && err == nil
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}
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fastqDetector := func(raw []byte, limit uint32) bool {
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ok, err := regexp.Match("^@[^ ]", raw)
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return ok && err == nil
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}
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ecoPCR2Detector := func(raw []byte, limit uint32) bool {
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ok := bytes.HasPrefix(raw, []byte("#@ecopcr-v2"))
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return ok
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}
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genbankDetector := func(raw []byte, limit uint32) bool {
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ok2 := bytes.HasPrefix(raw, []byte("LOCUS "))
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ok1, err := regexp.Match("^[^ ]* +Genetic Sequence Data Bank *\n", raw)
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return ok2 || (ok1 && err == nil)
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}
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emblDetector := func(raw []byte, limit uint32) bool {
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ok := bytes.HasPrefix(raw, []byte("ID "))
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return ok
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}
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mimetype.Lookup("text/plain").Extend(fastaDetector, "text/fasta", ".fasta")
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mimetype.Lookup("text/plain").Extend(fastqDetector, "text/fastq", ".fastq")
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mimetype.Lookup("text/plain").Extend(ecoPCR2Detector, "text/ecopcr2", ".ecopcr")
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mimetype.Lookup("text/plain").Extend(genbankDetector, "text/genbank", ".seq")
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mimetype.Lookup("text/plain").Extend(emblDetector, "text/embl", ".dat")
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// Create a buffer to store the read data
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buf := make([]byte, 1024*128)
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n, err := stream.Read(buf)
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if err != nil && err != io.EOF {
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return nil, nil, err
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}
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// Detect the MIME type using the mimetype library
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mimeType := mimetype.Detect(buf)
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if mimeType == nil {
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return nil, nil, err
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}
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// Create a new reader based on the read data
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newReader := io.MultiReader(bytes.NewReader(buf[:n]), stream)
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return mimeType, newReader, nil
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}
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var xxx1 = `00422_612GNAAXX:7:73:6614:3284#0/1
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ccgaatatcttagataccccactatgcttagccctaaacataaacattcaataaacaaga
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atgttcgccagagtactactagcaacagcctgaaactcaaagcacttg
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>HELIUM_000100422_612GNAAXX:7:13:11063:8138#0/1
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ccgcctcctttagataccccactatgcttagccctaaacacaagtaattattataacaaa
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attattcgccagagtactaccggcaatagcttaaaactcacagaactt
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>HELIUM_000100422_612GNAAXX:7:2:7990:17026#0/1
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ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgcttt
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tcaggctgttgctagtagtactctggcgaccattcttgtttattgatt
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>HELIUM_000100422_612GNAAXX:7:3:19649:11224#0/1
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ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgagtt
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tcaggctgttgctagtagtactctggcgaacattcttgtttattgaat
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>HELIUM_000100422_612GNAAXX:7:3:8446:7884#0/1
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ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgagtt
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tcaggctgttgctagtagtactctggcgaacattcttgtttattgaat
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>HELIUM_000100422_612GNAAXX:7:108:8714:2464#0/1
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ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaa
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attattcgccagagtactaccggcaatagcttaaaactcaaaggactt
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>HELIUM_000100422_612GNAAXX:7:28:3969:15209#0/1
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ccaattaacttagataccccactatgcctagccttaaacacaaatagttatgcaaacaaa
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actattcgccagagtactaccggcaatagcttaaaactcaacgcactg
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>HELIUM_000100422_612GNAAXX:7:44:3269:3608#0/1
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gaagtagtagaacaggctcctctagaagggt`
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var xxx2 = `>HELIUM_000100422_612GNAAXX:7:13:11063:8138#0/1
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ccgcctcctttagataccccactatgcttagccctaaacacaagtaattattataacaaa
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attattcgccagagtactaccggcaatagcttaaaactcacagaactt
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>HELIUM_000100422_612GNAAXX:7:2:7990:17026#0/1
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ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgcttt
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tcaggctgttgctagtagtactctggcgaccattcttgtttattgatt
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>HELIUM_000100422_612GNAAXX:7:3:19649:11224#0/1
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ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgagtt
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tcaggctgttgctagtagtactctggcgaacattcttgtttattgaat
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>HELIUM_000100422_612GNAAXX:7:3:8446:7884#0/1
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ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgagtt
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tcaggctgttgctagtagtactctggcgaacattcttgtttattgaat
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>HELIUM_000100422_612GNAAXX:7:108:8714:2464#0/1
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ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaa
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attattcgccagagtactaccggcaatagcttaaaactcaaaggactt
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>HELIUM_000100422_612GNAAXX:7:28:3969:15209#0/1
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ccaattaacttagataccccactatgcctagccttaaacacaaatagttatgcaaacaaa
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actattcgccagagtactaccggcaatagcttaaaactcaacgcactg
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>HELIUM_000100422_612GNAAXX:7:44:3269:3608#0/1
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gaagtagtagaacaggctcctctagaagggt`
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var xxx3 = `00422_612GNAAXX:7:73:6614:3284#0/1
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ccgaatatcttagataccccactatgcttagccctaaacataaacattcaataaacaaga
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atgttcgccagagtactactagcaacagcctgaaactcaaagcacttg
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>HELIUM_000100422_612GNAAXX:7:13:11063:8138#0/1
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ccgcctcctttagataccccactatgcttagccctaaacacaagtaattattataacaaa
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attattcgccagagtactaccggcaatagcttaaaactcacagaactt
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>HELIUM_000100422_612GNAAXX:7:2:7990:17026#0/1
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ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgcttt
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tcaggctgttgctagtagtactctggcgaccattcttgtttattgatt
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>HELIUM_000100422_612GNAAXX:7:3:19649:11224#0/1
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ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgagtt
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tcaggctgttgctagtagtactctggcgaacattcttgtttattgaat
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>HELIUM_000100422_612GNAAXX:7:3:8446:7884#0/1
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ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgagtt
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tcaggctgttgctagtagtactctggcgaacattcttgtttattgaat
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>HELIUM_000100422_612GNAAXX:7:108:8714:2464#0/1
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ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaa
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attattcgccagagtactaccggcaatagcttaaaactcaaaggactt
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>HELIUM_000100422_612GNAAXX:7:28:3969:15209#0/1
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ccaattaacttagataccccactatgcctagccttaaacacaaatagttatgcaaacaaa
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actattcgccagagtactaccggcaatagcttaaaactcaacgcactg`
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var yyy1 = `@HELIUM_000100422_612GNAAXX:7:1:9007:3289#0/1 {"demultiplex_error":"cannot assign the sequence to a sample"}
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ccatctctcttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaagaactc
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+
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CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCACCCCCCCCCBCCACC779?############################################
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@HELIUM_000100422_612GNAAXX:7:1:8849:9880#0/1 {"demultiplex_error":"cannot match any primer pair"}
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gatcggaagagcggttcagcaggaatgccgagaccgatatcgtatgccgtcttctgcttgaaaaaaaaaacaaaataggagagtagactcactgccagtggtcgtcag
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`
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func LastFastqCut(buffer []byte) ([]byte, []byte) {
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imax := len(buffer)
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cut := imax
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state := 0
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restart := imax - 1
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for i := restart; i >= 0 && state < 7; i-- {
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C := buffer[i]
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is_end_of_line := C == '\r' || C == '\n'
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is_space := C == ' ' || C == '\t'
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is_sep := is_space || is_end_of_line
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switch state {
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case 0:
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if C == '+' {
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// Potential start of quality part step 1
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state = 1
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restart = i
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}
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case 1:
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if is_end_of_line {
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// Potential start of quality part step 2
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state = 2
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} else {
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// it was not the start of quality part
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state = 0
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i = restart
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}
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case 2:
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if is_sep {
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// Potential start of quality part step 2 (stay in the same state)
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state = 2
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} else if (C >= 'a' && C <= 'z') || C == '-' || C == '.' {
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// End of the sequence
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state = 3
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} else {
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// it was not the start of quality part
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state = 0
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i = restart
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}
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case 3:
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if is_end_of_line {
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// Entrering in the header line
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state = 4
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} else if (C >= 'a' && C <= 'z') || C == '-' || C == '.' {
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// progressing along of the sequence
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state = 3
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} else {
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// it was not the sequence part
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state = 0
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i = restart
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}
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case 4:
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if is_end_of_line {
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state = 4
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} else {
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state = 5
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}
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case 5:
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if is_end_of_line {
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// It was not the header line
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state = 0
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i = restart
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} else if C == '@' {
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state = 6
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cut = i
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}
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case 6:
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if is_end_of_line {
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state = 7
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} else {
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state = 0
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i = restart
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}
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}
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}
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if state == 7 {
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return buffer[:cut], bytes.Clone(buffer[cut:])
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}
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return []byte{}, buffer
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}
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func LastSequenceCut(buffer []byte) ([]byte, []byte) {
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imax := len(buffer)
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last := 0
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state := 0
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for i := imax - 1; i >= 0 && state < 2; i-- {
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if state == 0 && buffer[i] == '>' {
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state = 1
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last = i
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} else if state == 1 && (buffer[i] == '\r' || buffer[i] == '\n') {
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state = 2
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} else {
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state = 0
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}
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}
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if state == 2 {
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return buffer[:last], bytes.Clone(buffer[last:])
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}
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return []byte{}, buffer
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}
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func FirstSequenceCut(buffer []byte) ([]byte, []byte) {
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imax := len(buffer)
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last := 0
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state := 0
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for i := 0; i < imax && state < 2; i++ {
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if (state == 0 || state == 1) && (buffer[i] == '\r' || buffer[i] == '\n') {
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state = 1
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} else if (state == 1 || i == 0) && buffer[i] == '>' {
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state = 2
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last = i
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} else {
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state = 0
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}
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}
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if state == 2 {
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return bytes.Clone(buffer[:last]), buffer[last:]
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}
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return buffer, []byte{}
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}
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func FullSequenceCut(buffer []byte) ([]byte, []byte, []byte) {
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before, buffer := FirstSequenceCut(buffer)
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if len(buffer) == 0 {
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return before, []byte{}, []byte{}
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}
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buffer, after := LastSequenceCut(buffer)
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return before, buffer, after
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}
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|
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func Concatenate[S ~[]E, E any](s1, s2 S) S {
|
||||
if len(s1) > 0 {
|
||||
if len(s2) > 0 {
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return append(s1[:len(s1):len(s1)], s2...)
|
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}
|
||||
return s1
|
||||
}
|
||||
return s2
|
||||
}
|
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|
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type FastxChunk struct {
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Bytes []byte
|
||||
index int
|
||||
}
|
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|
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func FastaChunkReader(r io.Reader, size int, cutHead bool) (chan FastxChunk, error) {
|
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out := make(chan FastxChunk)
|
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buff := make([]byte, size)
|
||||
|
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n, err := r.Read(buff)
|
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if n > 0 && err == nil {
|
||||
if n < size {
|
||||
buff = buff[:n]
|
||||
}
|
||||
|
||||
begin, buff := FirstSequenceCut(buff)
|
||||
|
||||
if len(begin) > 0 && !cutHead {
|
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return out, fmt.Errorf("begin is not empty : %s", string(begin))
|
||||
}
|
||||
|
||||
go func(buff []byte) {
|
||||
idx := 0
|
||||
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 = LastSequenceCut(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),
|
||||
index: idx,
|
||||
}
|
||||
idx++
|
||||
} else {
|
||||
fmt.Println("***** Empty buff *****")
|
||||
}
|
||||
|
||||
buff = slices.Grow(buff[:0], size)[0:size]
|
||||
n, err = r.Read(buff)
|
||||
if n < size {
|
||||
buff = buff[:n]
|
||||
}
|
||||
// fmt.Printf("n = %d, err = %v\n", n, err)
|
||||
}
|
||||
|
||||
if len(end) > 0 {
|
||||
out <- FastxChunk{
|
||||
Bytes: bytes.Clone(end),
|
||||
index: idx,
|
||||
}
|
||||
}
|
||||
|
||||
close(out)
|
||||
}(buff)
|
||||
}
|
||||
|
||||
return out, nil
|
||||
}
|
||||
|
||||
func ParseFastaChunk(ch FastxChunk) *obiiter.BioSequenceBatch {
|
||||
fmt.Println(string(ch.Bytes))
|
||||
slice := make(obiseq.BioSequenceSlice, 0, obioptions.CLIBatchSize())
|
||||
|
||||
state := 0
|
||||
start := 0
|
||||
current := 0
|
||||
var identifier string
|
||||
var definition string
|
||||
|
||||
for i := 0; i < len(ch.Bytes); i++ {
|
||||
C := ch.Bytes[i]
|
||||
is_end_of_line := C == '\r' || C == '\n'
|
||||
is_space := C == ' ' || C == '\t'
|
||||
is_sep := is_space || is_end_of_line
|
||||
|
||||
switch state {
|
||||
case 0:
|
||||
if C == '>' {
|
||||
// Beginning of sequence
|
||||
state = 1
|
||||
}
|
||||
case 1:
|
||||
if is_sep {
|
||||
// No identifier -> ERROR
|
||||
return nil
|
||||
} else {
|
||||
// Beginning of identifier
|
||||
state = 2
|
||||
start = i
|
||||
}
|
||||
case 2:
|
||||
if is_sep {
|
||||
// End of identifier
|
||||
identifier = string(ch.Bytes[start:i])
|
||||
state = 3
|
||||
}
|
||||
case 3:
|
||||
if is_end_of_line {
|
||||
// Definition empty
|
||||
definition = ""
|
||||
state = 5
|
||||
} else if !is_space {
|
||||
// Beginning of definition
|
||||
start = i
|
||||
state = 4
|
||||
}
|
||||
case 4:
|
||||
if is_end_of_line {
|
||||
definition = string(ch.Bytes[start:i])
|
||||
state = 5
|
||||
|
||||
}
|
||||
case 5:
|
||||
if !is_end_of_line {
|
||||
// Beginning of sequence
|
||||
start = i
|
||||
current = i
|
||||
state = 6
|
||||
}
|
||||
case 6:
|
||||
if C == '>' {
|
||||
// End of sequence
|
||||
s := obiseq.NewBioSequence(identifier, bytes.Clone(ch.Bytes[start:current]), definition)
|
||||
slice = append(slice, s)
|
||||
state = 1
|
||||
|
||||
} else if !is_sep {
|
||||
if C >= 'A' && C <= 'Z' {
|
||||
C = C + 'a' - 'A'
|
||||
}
|
||||
// Removing white space from the sequence
|
||||
if (C >= 'a' && C <= 'z') || C == '-' || C == '.' {
|
||||
ch.Bytes[current] = C
|
||||
current++
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
fmt.Printf("Index = %d, State = %d\n", ch.index, state)
|
||||
slice = append(slice, obiseq.NewBioSequence(identifier, bytes.Clone(ch.Bytes[start:current]), definition))
|
||||
batch := obiiter.MakeBioSequenceBatch(ch.index, slice)
|
||||
return &batch
|
||||
}
|
||||
|
||||
func ReadFastaSequence(reader io.Reader) obiiter.IBioSequence {
|
||||
out := obiiter.MakeIBioSequence()
|
||||
|
||||
nworker := obioptions.CLIReadParallelWorkers()
|
||||
out.Add(nworker)
|
||||
|
||||
chkchan, err := FastaChunkReader(reader, 1024*500, false)
|
||||
|
||||
if err != nil {
|
||||
log.Panicln("Error:", err)
|
||||
}
|
||||
|
||||
go func() {
|
||||
out.WaitAndClose()
|
||||
}()
|
||||
|
||||
parser := func() {
|
||||
defer out.Done()
|
||||
for chk := range chkchan {
|
||||
seqs := ParseFastaChunk(chk)
|
||||
if seqs != nil {
|
||||
out.Push(*seqs)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for i := 0; i < nworker; i++ {
|
||||
go parser()
|
||||
}
|
||||
|
||||
return out.SortBatches().Rebatch(obioptions.CLIBatchSize())
|
||||
}
|
||||
|
||||
func main() {
|
||||
// if len(os.Args) != 2 {
|
||||
// fmt.Println("Usage: go run main.go <filename>")
|
||||
// return
|
||||
// }
|
||||
|
||||
// filename := os.Args[1]
|
||||
// filename := "100.fasta"
|
||||
// file, err := os.Open(filename)
|
||||
// if err != nil {
|
||||
// fmt.Println("Error:", err)
|
||||
// return
|
||||
// }
|
||||
// defer file.Close()
|
||||
|
||||
// mimeType, input, err := OBIMimeTypeGuesser(file)
|
||||
// if err != nil {
|
||||
// fmt.Println("Error:", err)
|
||||
// return
|
||||
// }
|
||||
|
||||
// fmt.Println("Detected MIME Type:", mimeType.String())
|
||||
|
||||
// ch, err := FastaChunkReader(input, 1024, false)
|
||||
|
||||
// if err != nil {
|
||||
// fmt.Println("Error:", err)
|
||||
// return
|
||||
// }
|
||||
|
||||
// for chk := range ch {
|
||||
// fmt.Printf("--------------------\n")
|
||||
// b := ParseFastaChunk(chk)
|
||||
// fmt.Printf("-------- %d --------\n", b.Order())
|
||||
// for _, b := range b.Slice() {
|
||||
// fmt.Printf("--%s--\t--%s--\t--%s--\n", b.Id(), b.Definition(), b.String())
|
||||
// }
|
||||
// }
|
||||
|
||||
d1, f1 := LastFastqCut([]byte(yyy1))
|
||||
// d2, f2 := LastSequenceCut([]byte(xxx2))
|
||||
// d3, f3 := LastSequenceCut([]byte(xxx3))
|
||||
|
||||
fmt.Println("Last Sequence Cut 1:", string(d1), "---", string(f1))
|
||||
// fmt.Println("Last Sequence Cut 2:", string(d2), "---", string(f2))
|
||||
// fmt.Println("Last Sequence Cut 3:", string(d3), "---", string(f3))
|
||||
|
||||
// d1, b1, f1 := FullSequenceCut([]byte(xxx1))
|
||||
// d2, b2, f2 := FullSequenceCut([]byte(xxx2))
|
||||
// d3, b3, f3 := FullSequenceCut([]byte(xxx3))
|
||||
|
||||
// fmt.Println("Last Sequence Cut:", string(d1), "---", string(b1), "---", string(f1))
|
||||
// fmt.Println("Last Sequence Cut:", string(d2), "---", string(b2), "---", string(f2))
|
||||
// fmt.Println("Last Sequence Cut:", string(d3), "---", string(b3), "---", string(f3))
|
||||
|
||||
// Now you can use "extractedData" to access the read data with the associated MIME type.
|
||||
// For example, you can copy the data into a buffer for further manipulation.
|
||||
}
|
||||
BIN
toto.csv.gz
BIN
toto.csv.gz
Binary file not shown.
@ -1,6 +0,0 @@
|
||||
id,HELIUM_000100422_612GNAAXX:7:100:4828:3492#0/1_sub[28..127],HELIUM_000100422_612GNAAXX:7:113:17236:15166#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:16:12111:9453#0/1_sub[28..127],HELIUM_000100422_612GNAAXX:7:17:3675:13316#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:20:15729:20493#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:22:2603:18023#0/1_sub[28..127],HELIUM_000100422_612GNAAXX:7:25:11714:14251#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:2:15508:17530#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:30:17945:19531#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:34:14122:13731#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:34:17680:16952#0/1_sub[28..127],HELIUM_000100422_612GNAAXX:7:52:12776:11698#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:53:17880:8617#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:58:11419:17203#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:5:15939:5437#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:66:4039:8016#0/1_sub[28..127],HELIUM_000100422_612GNAAXX:7:69:15276:10367#0/1_sub[28..127],HELIUM_000100422_612GNAAXX:7:72:17638:8081#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:7:18108:9040#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:7:2880:4021#0/1_sub[28..127],HELIUM_000100422_612GNAAXX:7:80:10626:19388#0/1_sub[28..127],HELIUM_000100422_612GNAAXX:7:81:18704:12346#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127],HELIUM_000100422_612GNAAXX:7:84:16335:5083#0/1_sub[28..126],HELIUM_000100422_612GNAAXX:7:94:16908:11285#0/1_sub[28..127],HELIUM_000100422_612GNAAXX:7:9:9623:15395#0/1_sub[28..127]
|
||||
15a_F730814,0,0,0,0,0,9165,0,0,0,0,0,0,0,5,0,0,0,0,4,0,0,0,0,0,0,0
|
||||
13a_F730603,22,0,1,0,0,0,0,0,0,0,15,0,0,19,0,25,0,0,9,0,20,0,0,0,8409,0
|
||||
29a_F260619,0,0,13,0,16,6139,0,0,0,0,0,0,0,1,0,0,25,0,0,44,0,0,391,110,0,353
|
||||
26a_F040644,0,72,0,17,0,0,14,18,43,31,0,52,88,481,12830,0,0,15,0,0,0,208,0,14,0,0
|
||||
|
||||
|
Reference in New Issue
Block a user