func (self *Reader) commentMetaline(line string) (f *feat.Feature, err error) {
// Load these into a slice in a MetaField of the Feature
fields := strings.Split(string(line), " ")
switch fields[0] {
case "gff-version":
self.Version, err = strconv.Atoi(fields[1])
if err != nil {
self.Version = DefaultVersion
}
return self.Read()
case "source-version":
if len(fields) > 1 {
self.SourceVersion = strings.Join(fields[1:], " ")
return self.Read()
} else {
return nil, bio.NewError("Incomplete source-version metaline", 0, fields)
}
case "date":
if len(fields) > 1 {
self.Date, err = time.Parse(self.TimeFormat, strings.Join(fields[1:], " "))
return self.Read()
} else {
return nil, bio.NewError("Incomplete date metaline", 0, fields)
}
case "Type":
if len(fields) > 1 {
self.Type = bio.ParseMoltype(fields[1])
return self.Read()
} else {
return nil, bio.NewError("Incomplete Type metaline", 0, fields)
}
case "sequence-region":
if len(fields) > 3 {
var start, end int
start, err = strconv.Atoi(fields[2])
if err != nil {
return nil, err
} else {
if self.OneBased {
start = bio.OneToZero(start)
}
}
end, err = strconv.Atoi(fields[3])
if err != nil {
return nil, err
}
f = &feat.Feature{
Meta: &feat.Feature{
ID: fields[1],
Start: start,
End: end,
},
}
} else {
return nil, bio.NewError("Incomplete sequence-region metaline", 0, fields)
}
case "DNA", "RNA", "Protein":
if len(fields) > 1 {
var s *seq.Seq
s, err = self.metaSequence(fields[0], fields[1])
if err != nil {
return
} else {
f = &feat.Feature{Meta: s}
}
} else {
return nil, bio.NewError("Incomplete sequence metaline", 0, fields)
}
default:
f = &feat.Feature{Meta: line}
}
return
}
// Read a single feature or part and return it or an error.
func (self *Reader) Read() (f *feat.Feature, err error) {
var (
line string
elems []string
s int8
ok bool
)
for {
line, err = self.r.ReadString('\n')
if err != nil {
return
}
if len(line) > 0 && line[len(line)-1] == '\r' {
line = line[:len(line)-1]
}
line = strings.TrimSpace(line)
if len(line) == 0 { // ignore blank lines
continue
} else if strings.HasPrefix(line, "##") {
f, err = self.commentMetaline(line[2:])
return
} else if line[0] != '#' { // ignore comments
elems = strings.SplitN(line, "\t", 10)
break
}
}
if s, ok = charToStrand[elems[strandField]]; !ok {
s = 0
}
startPos, se := strconv.Atoi(elems[startField])
if se != nil {
startPos = 0
} else {
if self.OneBased {
startPos = bio.OneToZero(startPos)
}
}
endPos, se := strconv.Atoi(elems[endField])
if se != nil {
endPos = 0
}
fr, se := strconv.Atoi(elems[frameField])
if se != nil {
fr = -1
}
score, se := strconv.ParseFloat(elems[scoreField], 64)
var scorePtr *float64
if se != nil {
scorePtr = nil
} else {
scorePtr = &score
}
f = &feat.Feature{
ID: elems[nameField] + ":" + strconv.Itoa(startPos) + ".." + strconv.Itoa(endPos),
Location: elems[nameField],
Source: elems[sourceField],
Start: startPos,
End: endPos,
Feature: elems[featureField],
Score: scorePtr,
Frame: int8(fr),
Strand: s,
Moltype: self.Type, // currently we default to bio.DNA
}
if len(elems) > attributeField {
f.Attributes = elems[attributeField]
}
if len(elems) > commentField {
f.Comments = elems[commentField]
}
return
}