Skip to content

Commit

Permalink
Start correcting nexus parser #3
Browse files Browse the repository at this point in the history
  • Loading branch information
@fredericlemoine
fredericlemoine committed May 3, 2019
1 parent 585c4fd commit ff15423
Show file tree
Hide file tree
Showing 3 changed files with 76 additions and 35 deletions.
2 changes: 2 additions & 0 deletions io/nexus/nexus_lexer.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -147,6 +147,8 @@ func (s *Scanner) scanIdent() (tok Token, lit string) {
return DATATYPE, buf.String()
case "MISSING":
return MISSING, buf.String()
case "MATCHCHAR":
return MATCHCHAR, buf.String()
case "GAP":
return GAP, buf.String()
case "MATRIX":
Expand Down
100 changes: 69 additions & 31 deletions io/nexus/nexus_parser.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ import (
"fmt"
"io"
"strconv"
"strings"

"github.com/evolbioinfo/goalign/align"
aio "github.com/evolbioinfo/goalign/io"
Expand Down Expand Up @@ -59,6 +60,7 @@ func (p *Parser) Parse() (al align.Alignment, err error) {
var nchar, ntax, taxantax int64
datatype := "dna"
missing := '*'
matchchar := '.'
gap := '-'
var taxlabels map[string]bool = nil
var names []string
Expand Down Expand Up @@ -112,7 +114,7 @@ func (p *Parser) Parse() (al align.Alignment, err error) {
err = p.parseUnsupportedBlock()
case DATA:
// DATA/CHARACTERS BLOCK
names, sequences, nchar, ntax, datatype, missing, gap, err = p.parseData()
names, sequences, nchar, ntax, datatype, missing, gap, matchchar, err = p.parseData()
default:
// If an unsupported block is seen, we just skip it
aio.PrintMessage(fmt.Sprintf("Unsupported block %q, skipping", lit2))
Expand All @@ -130,10 +132,10 @@ func (p *Parser) Parse() (al align.Alignment, err error) {
return
}

if gap != '-' || missing != '*' {
err = fmt.Errorf("We only accept - gaps (not %c) && * missing (not %c) so far", gap, missing)
return
}
// if gap != '-' || missing != '*' {
// err = fmt.Errorf("We only accept - gaps (have %c) && * missing (have %c) so far", gap, missing)
// return
// }

// We initialize alignment structure using goalign structure
if names != nil && sequences != nil {
Expand All @@ -152,6 +154,9 @@ func (p *Parser) Parse() (al align.Alignment, err error) {
err = fmt.Errorf("Number of character in sequence #%d (%d) does not correspond to definition %d", i, len(seq), nchar)
return
}
seq = strings.Replace(seq, string(gap), string(align.GAP), -1)
seq = strings.Replace(seq, string(missing), string(align.OTHER), -1)
seq = strings.Replace(seq, string(matchchar), string(align.POINT), -1)
if err = al.AddSequence(name, seq, ""); err != nil {
return
}
Expand Down Expand Up @@ -240,8 +245,10 @@ func (p *Parser) parseTaxa() (int64, map[string]bool, error) {
stoplabels = true
case IDENT:
taxlabels[lit2] = true
case ENDOFLINE:
continue
default:
err = fmt.Errorf("Unknown token %q in taxlabel list", lit2)
err = fmt.Errorf("Unknown token %q (%v) in taxlabel list", lit2, tok2)
stoplabels = true
}
}
Expand All @@ -265,9 +272,10 @@ func (p *Parser) parseTaxa() (int64, map[string]bool, error) {
}

// DATA / Characters BLOCK
func (p *Parser) parseData() (names []string, sequences map[string]string, nchar, ntax int64, datatype string, missing, gap rune, err error) {
func (p *Parser) parseData() (names []string, sequences map[string]string, nchar, ntax int64, datatype string, missing, gap, matchchar rune, err error) {
datatype = "dna"
missing = '*'
matchchar = '.'
gap = '-'
stopdata := false
sequences = make(map[string]string)
Expand Down Expand Up @@ -353,46 +361,72 @@ func (p *Parser) parseData() (names []string, sequences map[string]string, nchar
if tok3 != EQUAL {
err = fmt.Errorf("Expecting '=' after DATATYPE, got %q", lit3)
stopformat = true
}
tok4, lit4 := p.scanIgnoreWhitespace()
if tok4 == IDENT {
datatype = lit4
} else {
err = fmt.Errorf("Expecting identifier after 'DATATYPE=', got %q", lit4)
stopformat = true
tok4, lit4 := p.scanIgnoreWhitespace()
if tok4 == IDENT {
datatype = lit4
} else {
err = fmt.Errorf("Expecting identifier after 'DATATYPE=', got %q", lit4)
stopformat = true
}
}
case MISSING:
tok3, lit3 := p.scanIgnoreWhitespace()
if tok3 != EQUAL {
err = fmt.Errorf("Expecting '=' after MISSING, got %q", lit3)
stopformat = true
} else {
tok4, lit4 := p.scanIgnoreWhitespace()
if tok4 != IDENT {
err = fmt.Errorf("Expecting Integer value after 'MISSING=', got %q", lit4)
stopformat = true
} else {
if len(lit4) != 1 {
err = fmt.Errorf("Expecting a single character after MISSING=', got %q", lit4)
stopformat = true
} else {
missing = []rune(lit4)[0]
}
}
}
tok4, lit4 := p.scanIgnoreWhitespace()
if tok4 != IDENT {
err = fmt.Errorf("Expecting Integer value after 'MISSING=', got %q", lit4)
stopformat = true
}
if len(lit4) != 1 {
err = fmt.Errorf("Expecting a single character after MISSING=', got %q", lit4)
stopformat = true
}
missing = []rune(lit4)[0]
case GAP:
tok3, lit3 := p.scanIgnoreWhitespace()
if tok3 != EQUAL {
err = fmt.Errorf("Expecting '=' after GAP, got %q", lit3)
stopformat = true
} else {
tok4, lit4 := p.scanIgnoreWhitespace()
if tok4 != IDENT {
err = fmt.Errorf("Expecting an identifier after 'GAP=', got %q", lit4)
stopformat = true
} else {
if len(lit4) != 1 {
err = fmt.Errorf("Expecting a single character after GAP=', got %q", lit4)
stopformat = true
} else {
gap = []rune(lit4)[0]
}
}
}
tok4, lit4 := p.scanIgnoreWhitespace()
if tok4 != IDENT {
err = fmt.Errorf("Expecting an identifier after 'GAP=', got %q", lit4)
stopformat = true
}
if len(lit4) != 1 {
err = fmt.Errorf("Expecting a single character after GAP=', got %q", lit4)
case MATCHCHAR:
tok3, lit3 := p.scanIgnoreWhitespace()
if tok3 != EQUAL {
err = fmt.Errorf("Expecting '=' after MATCHCHAR, got %q", lit3)
stopformat = true
} else {
tok4, lit4 := p.scanIgnoreWhitespace()
if tok4 != IDENT {
err = fmt.Errorf("Expecting character value after 'MATCHCHAR=', got %q", lit4)
stopformat = true
} else {
if len(lit4) != 1 {
err = fmt.Errorf("Expecting a single character after MATCHCHAR=', got %q", lit4)
stopformat = true
} else {
matchchar = []rune(lit4)[0]
}
}
}
gap = []rune(lit4)[0]
default:
if err = p.parseUnsupportedKey(lit2); err != nil {
stopformat = true
Expand All @@ -410,6 +444,10 @@ func (p *Parser) parseData() (names []string, sequences map[string]string, nchar
for !stopmatrix {
tok2, lit2 := p.scanIgnoreWhitespace()
switch tok2 {
case OPENBRACK:
if tok2, lit2, err = p.consumeComment(tok2, lit2); err != nil {
stopmatrix = true
}
case IDENT, NUMERIC:
// We remove whitespaces in sequences if any
// and take into account possibly interleaved
Expand Down
9 changes: 5 additions & 4 deletions io/nexus/nexus_token.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,10 +29,11 @@ const (
NTAX // Dimensions : Number of taxa
NCHAR // Dimensions : Length of alignment

FORMAT // Format
DATATYPE // Format datatype=dna
MISSING // Format missing=? missing char
GAP // Format gap=- gap character
FORMAT // Format
DATATYPE // Format datatype=dna
MISSING // Format missing=? missing char
GAP // Format gap=- gap character
MATCHCHAR // Format matchchar=. matching character compared to first seq

MATRIX // Matrix
END // End
Expand Down

0 comments on commit ff15423

Please sign in to comment.