Golang bio.NewError函数代码示例

// Join p to the sequence at the end specified by where.
func (self *Seq) Join(p *Seq, where int) (err error) {
	if self.circular {
		return bio.NewError("Cannot join circular sequence: receiver.", 0, self)
	} else if p.circular {
		return bio.NewError("Cannot join circular sequence: parameter.", 0, p)
	}

	switch where {
	case seq.Start:
		p = p.Copy().(*Seq)
		p.S.Align(seq.End)
		self.S.Align(seq.Start)
		self.S.LeftPad = p.S.LeftPad
	case seq.End:
		p = p.Copy().(*Seq)
		p.S.Align(seq.Start)
		self.S.Align(seq.End)
		self.S.RightPad = p.S.RightPad
	default:
		return bio.NewError("Undefined location.", 0, where)
	}

	tt, offset := sequtils.Join(self.S.Letters, p.S.Letters, where)
	self.offset = offset
	self.S.Letters = tt.([]alphabet.Pack)

	return
}

// Read a single sequence and return it or an error.
// TODO: Does not read multi-line fastq.
func (self *Reader) Read() (s seq.Sequence, err error) {
	var (
		buff, line, label []byte
		isPrefix          bool
		seqBuff           []alphabet.QLetter
		t                 seqio.SequenceAppender
	)

	inQual := false

	for {
		if buff, isPrefix, err = self.r.ReadLine(); err == nil {
			if isPrefix {
				line = append(line, buff...)
				continue
			} else {
				line = buff
			}

			line = bytes.TrimSpace(line)
			if len(line) == 0 {
				continue
			}
			switch {
			case !inQual && line[0] == '@':
				t = self.readHeader(line)
				label, line = line, nil
			case !inQual && line[0] == '+':
				if len(label) == 0 {
					return nil, bio.NewError("fastq: no header line parsed before +line in fastq format", 0)
				}
				if len(line) > 1 && bytes.Compare(label[1:], line[1:]) != 0 {
					return nil, bio.NewError("fastq: quality header does not match sequence header", 0)
				}
				inQual = true
			case !inQual:
				line = bytes.Join(bytes.Fields(line), nil)
				seqBuff = make([]alphabet.QLetter, len(line))
				for i := range line {
					seqBuff[i].L = alphabet.Letter(line[i])
				}
			case inQual:
				line = bytes.Join(bytes.Fields(line), nil)
				if len(line) != len(seqBuff) {
					return nil, bio.NewError("fastq: sequence/quality length mismatch", 0)
				}
				for i := range line {
					seqBuff[i].Q = alphabet.DecodeToQphred(line[i], self.enc)
				}
				t.AppendQLetters(seqBuff...)

				return t, nil
			}
		} else {
			return
		}
	}

	panic("cannot reach")
}

// Write a single sequence and return the number of bytes written and any error.
func (self *Writer) Write(s *seq.Seq) (n int, err error) {
	if s.Quality == nil {
		return 0, bio.NewError("No quality associated with sequence", 0, s)
	}
	if s.Len() == s.Quality.Len() {
		self.template[1] = []byte(s.ID)
		self.template[3] = s.Seq
		if self.QID {
			self.template[4] = append(append([]byte("\n+"), []byte(s.ID)...), '\n')
		} else {
			self.template[4] = []byte("\n+\n")
		}
		self.template[5] = self.encodeQuality(s.Quality.Qual)
		var tn int
		for _, t := range self.template {
			tn, err = self.w.Write(t)
			n += tn
			if err != nil {
				return
			}
		}
	} else {
		return 0, bio.NewError("Sequence length and quality length do not match", 0, s)
	}

	return
}

func (p *Promise) fulfill(value interface{}) (err error) {
	r, set := p.messageState()

	if r.Err != nil {
		err = bio.NewError("Tried to fulfill a failed promise", 0, r.Err)
	} else {
		if !set || p.mutable {
			r.Value = value
			err = nil
		} else {
			err = bio.NewError("Tried to fulfill an already set immutable promise", 0)
		}
	}

	if err != nil && p.relay {
		if r.Err != nil {
			err = bio.NewError("Promise already failed - cannot relay", 0, r.Err)
		} else {
			r.Err = err
		}
	}

	p.message <- r

	return
}

func (self *Seq) Join(s *Seq, where int) (j *Seq, err error) {
	var (
		ts []byte
		ID string
	)

	if self.Circular {
		return nil, bio.NewError("Cannot join circular molecule.", 0, self)
	}

	if !self.Inplace && self.Quality != nil && self.Quality.Inplace {
		return nil, bio.NewError("Inplace operation on Quality with non-Inplace operation on parent Seq.", 0, self)
	}

	switch where {
	case Prepend:
		ID = s.ID + "+" + self.ID
		ts = make([]byte, len(s.Seq), len(s.Seq)+len(self.Seq))
		copy(ts, s.Seq)
		ts = append(ts, self.Seq...)
	case Append:
		ID = self.ID + "+" + s.ID
		if self.Inplace {
			ts = append(self.Seq, s.Seq...)
		} else {
			ts = make([]byte, len(self.Seq), len(s.Seq)+len(self.Seq))
			copy(ts, self.Seq)
			ts = append(ts, s.Seq...)
		}
	}

	var q *Quality
	if self.Quality != nil && s.Quality != nil {
		q, err = self.Quality.Join(s.Quality, where)
		if err != nil {
			return
		}
	}

	if self.Inplace {
		j = self
		j.ID = ID
		j.Seq = ts
		j.Quality = q // self.Quality will become nil if either sequence lacks Quality
	} else {
		j = &Seq{
			ID:      ID,
			Seq:     ts,
			Strand:  self.Strand,
			Moltype: self.Moltype,
			Quality: q,
		}
	}
	if where == Prepend {
		j.Offset -= s.Len()
	}

	return
}

func (self *Seq) Trunc(start, end int) (s *Seq, err error) {
	var ts []byte

	if !self.Inplace && self.Quality != nil && self.Quality.Inplace {
		return nil, bio.NewError("Inplace operation on Quality with non-Inplace operation on parent Seq.", 0, self)
	}

	if start < self.Offset || end < self.Offset ||
		start > len(self.Seq)+self.Offset || end > len(self.Seq)+self.Offset {
		return nil, bio.NewError("Start or end position out of range.", 0, self)
	}

	if start <= end {
		if self.Inplace {
			ts = self.Seq[start-self.Offset : end-self.Offset]
		} else {
			ts = append([]byte(nil), self.Seq[start-self.Offset:end-self.Offset]...)
		}
	} else if self.Circular {
		if self.Inplace {
			ts = append(self.Seq[start-self.Offset:], self.Seq[:end-self.Offset]...) // not quite inplace for this op
		} else {
			ts = make([]byte, len(self.Seq)-start-self.Offset, len(self.Seq)+end-start)
			copy(ts, self.Seq[start-self.Offset:])
			ts = append(ts, self.Seq[:end-self.Offset]...)
		}
	} else {
		return nil, bio.NewError("Start position greater than end position for non-circular molecule.", 0, self)
	}

	var q *Quality
	if self.Quality != nil {
		q, err = self.Quality.Trunc(start, end)
		if err != nil {
			err = bio.NewError("Quality.Trunc() returned error", 0, err)
			return
		}
	}

	if self.Inplace {
		s = self
		s.Seq = ts
		s.Circular = false
		s.Quality = q
	} else {
		s = &Seq{
			ID:       self.ID,
			Seq:      ts,
			Offset:   start,
			Strand:   self.Strand,
			Circular: false,
			Moltype:  self.Moltype,
			Quality:  q,
		}
	}

	return
}

// Pack a QLetter into a QPack. a.Len() == 4.
func (self QLetter) Pack(a Nucleic) (QPack, error) {
	if a.Len() != 4 {
		return 0, bio.NewError("Invalid alphabet", 0, self)
	}
	if !a.IsValid(self.L) {
		return QPack(byte(self.Q) << 2), bio.NewError("Invalid letter", 0, self)
	}
	return QPack(byte(self.Q)<<2 | byte(a.IndexOf(self.L)&0x3)), nil
}

// Convert coordinates in a packed sequence into a feat.Feature.
func featureOf(contigs *seq.Seq, from, to int, comp bool) (feature *feat.Feature, err error) {
	if comp {
		from, to = contigs.Len()-to, contigs.Len()-from
	}
	if from >= to {
		return nil, bio.NewError(fmt.Sprintf("%s: from > to", contigs.ID), 0, nil)
	}

	// DPHit coordinates sometimes over/underflow.
	// This is a lazy hack to work around it, should really figure
	// out what is going on.
	if from < 0 {
		from = 0
	}
	if to > contigs.Len() {
		to = contigs.Len()
	}

	// Take midpoint of segment -- lazy hack again, endpoints
	// sometimes under / overflow
	bin := (from + to) / (2 * binSize)
	binCount := (contigs.Len() + binSize - 1) / binSize

	if bin < 0 || bin >= binCount {
		return nil, bio.NewError(fmt.Sprintf("%s: bin %d out of range 0..%d", contigs.ID, bin, binCount-1), 0, nil)
	}

	contigIndex := contigs.Meta.(seqMap).binMap[bin]

	if contigIndex < 0 || contigIndex >= len(contigs.Meta.(seqMap).contigs) {
		return nil, bio.NewError(fmt.Sprintf("%s: contig index %d out of range 0..%d", contigs.ID, contigIndex, len(contigs.Meta.(seqMap).contigs)), 0, nil)
	}

	length := to - from

	if length < 0 {
		return nil, bio.NewError(fmt.Sprintf("%s: length < 0", contigs.ID), 0, nil)
	}

	contig := contigs.Meta.(seqMap).contigs[contigIndex]
	contigFrom := from - contig.from
	contigTo := contigFrom + length

	if contigFrom < 0 {
		contigFrom = 0
	}

	if contigTo > contig.seq.Len() {
		contigTo = contig.seq.Len()
	}

	return &feat.Feature{
		ID:    contig.seq.ID,
		Start: contigFrom,
		End:   contigTo,
	}, nil
}

// Join p to the sequence at the end specified by where.
func (self *Seq) Join(p *Seq, where int) (err error) {
	if self.circular {
		return bio.NewError("Cannot join circular sequence: receiver.", 1, self)
	} else if p.circular {
		return bio.NewError("Cannot join circular sequence: parameter.", 1, p)
	}

	tt, offset := sequtils.Join(self.S, p.S, where)
	self.offset = offset
	self.S = tt.([]alphabet.Letter)

	return
}

// Read a single sequence and return it or an error.
// TODO: Does not read interleaved fastq.
func (self *Reader) Read() (sequence *seq.Seq, err error) {
	var line, label, seqBody, qualBody []byte
	sequence = &seq.Seq{}

	inQual := false
READ:
	for {
		line, err = self.r.ReadBytes('\n')
		if err == nil {
			if len(line) > 0 && line[len(line)-1] == '\r' {
				line = line[:len(line)-1]
			}
			line = bytes.TrimSpace(line)
			if len(line) == 0 {
				continue
			}
			switch {
			case !inQual && line[0] == '@':
				label = line[1:]
			case !inQual && line[0] == '+':
				if len(label) == 0 {
					return nil, bio.NewError("No ID line parsed at +line in fastq format", 0)
				}
				if len(line) > 1 && bytes.Compare(label, line[1:]) != 0 {
					return nil, bio.NewError("Quality ID does not match sequence ID", 0)
				}
				inQual = true
			case !inQual:
				line = bytes.Join(bytes.Fields(line), nil)
				seqBody = append(seqBody, line...)
			case inQual:
				line = bytes.Join(bytes.Fields(line), nil)
				qualBody = append(qualBody, line...)
				if len(qualBody) >= len(seqBody) {
					break READ
				}
			}
		} else {
			return
		}
	}

	if len(seqBody) != len(qualBody) {
		return nil, bio.NewError("Quality length does not match sequence length", 0)
	}

	labelString := string(label)
	sequence = seq.New(labelString, seqBody, seq.NewQuality(labelString, self.decodeQuality(qualBody)))

	return
}

// Join p to the sequence at the end specified by where.
func (self *QSeq) Join(p *QSeq, where int) (err error) {
	if self.circular {
		return bio.NewError("Cannot join circular sequence: receiver.", 1, self)
	} else if p.circular {
		return bio.NewError("Cannot join circular sequence: parameter.", 1, p)
	}

	var tt interface{}

	tt, self.offset = sequtils.Join(self.S, p.S, where)
	self.S = tt.([]alphabet.QPack)

	return
}

// Convert a string of bases into a Kmer, returns an error if string length does not match word length
func (self *Index) KmerOf(kmertext string) (kmer Kmer, err error) {
	if len(kmertext) != self.k {
		return 0, bio.NewError("Sequence length does not match Kmer length", 0, self.k, kmertext)
	}

	for _, v := range kmertext {
		x := lookUp.ValueToCode[v]
		if x < 0 {
			return 0, bio.NewError("Kmer contains illegal character", 0, kmertext)
		}
		kmer = (kmer << 2) | Kmer(x)
	}

	return
}

func checkPackedAlpha(alpha alphabet.Nucleic) error {
	if alpha.Len() != 4 {
		return bio.NewError("Cannot create packed sequence with alphabet length != 4", 0, alpha)
	}
	for _, v := range alphabet.BytesToLetters([]byte(alpha.String())) {
		if c, ok := alpha.Complement(v); ok && alpha.IndexOf(v) != alpha.IndexOf(c)^0x3 {
			// TODO: Resolution to the following problem:
			// Normal nucleotide alphabets (ACGT/ACGU) are safe with this in either case sensitive or
			// insensitive. Other alphabets may not be, in this case specify case sensitive.
			return bio.NewError("alphabet order not consistent with bit operations for packed.", 0, alpha)
		}
	}

	return nil
}

// Return an array of positions for the Kmer string kmertext
func (self *Index) GetPositionsString(kmertext string) (positions []int, err error) {
	switch {
	case len(kmertext) != self.k:
		return nil, bio.NewError("Sequence length does not match Kmer length", 0, self.k, kmertext)
	case !self.indexed:
		return nil, bio.NewError("Index not built: call Build()", 0, self)
	}

	var kmer Kmer
	if kmer, err = self.KmerOf(kmertext); err != nil {
		return nil, err
	}

	return self.GetPositionsKmer(kmer)
}

func NewSeq(id string, subids []string, b [][]alphabet.Letter, alpha alphabet.Peptide, cons protein.Consensifyer) (*Seq, error) {
	switch lids, lseq := len(subids), len(b); {
	case lids == 0 && len(b) == 0:
	case lseq != 0 && lids == len(b[0]):
		if lids == 0 {
			subids = make([]string, len(b[0]))
			for i := range subids {
				subids[i] = fmt.Sprintf("%s:%d", id, i)
			}
		}
	default:
		return nil, bio.NewError("alignment: id/seq number mismatch", 0)
	}

	return &Seq{
		ID:         id,
		SubIDs:     append([]string(nil), subids...),
		S:          append([][]alphabet.Letter(nil), b...),
		alphabet:   alpha,
		Consensify: cons,
		Stringify: func(s seq.Polymer) string {
			t := s.(*Seq).Consensus(false)
			return t.String()
		},
	}, nil
}