func aminoFromStructure(chain *pdb.Chain) seq.Sequence {
var name string
if len(chain.Entry.Cath) > 0 {
name = chain.Entry.Cath
} else if len(chain.Entry.Scop) > 0 {
name = chain.Entry.Scop
} else {
name = fmt.Sprintf("%s%c", chain.Entry.IdCode, chain.Ident)
}
s := seq.Sequence{
Name: name,
Residues: make([]seq.Residue, 0, 50),
}
lasti := 0
for _, r := range chain.Models[0].Residues {
if lasti != r.SequenceNum {
s.Residues = append(s.Residues, r.Name)
lasti = r.SequenceNum
}
}
return s
}
func main() {
pdbEntry := util.PDBRead(flag.Arg(0))
fasEntries := make([]seq.Sequence, 0, 5)
if !flagSeparateChains {
var fasEntry seq.Sequence
if len(pdbEntry.Chains) == 1 {
fasEntry.Name = chainHeader(pdbEntry.OneChain())
} else {
fasEntry.Name = fmt.Sprintf("%s", strings.ToLower(pdbEntry.IdCode))
}
seq := make([]seq.Residue, 0, 100)
for _, chain := range pdbEntry.Chains {
if isChainUsable(chain) {
seq = append(seq, chain.Sequence...)
}
}
fasEntry.Residues = seq
if len(fasEntry.Residues) == 0 {
util.Fatalf("Could not find any amino acids.")
}
fasEntries = append(fasEntries, fasEntry)
} else {
for _, chain := range pdbEntry.Chains {
if !isChainUsable(chain) {
continue
}
fasEntry := seq.Sequence{
Name: chainHeader(chain),
Residues: chain.Sequence,
}
fasEntries = append(fasEntries, fasEntry)
}
}
if len(fasEntries) == 0 {
util.Fatalf("Could not find any chains with amino acids.")
}
var fasOut io.Writer
if flag.NArg() == 1 {
fasOut = os.Stdout
} else {
if len(flagSplit) > 0 {
util.Fatalf("The '--split' option is incompatible with a single " +
"output file.")
}
fasOut = util.CreateFile(util.Arg(1))
}
if len(flagSplit) == 0 {
util.Assert(fasta.NewWriter(fasOut).WriteAll(fasEntries),
"Could not write FASTA file '%s'", fasOut)
} else {
for _, entry := range fasEntries {
fp := path.Join(flagSplit, fmt.Sprintf("%s.fasta", entry.Name))
out := util.CreateFile(fp)
w := fasta.NewWriter(out)
util.Assert(w.Write(entry), "Could not write to '%s'", fp)
util.Assert(w.Flush(), "Could not write to '%s'", fp)
}
}
}
// ReadSequence is exported for use in other packages that read FASTA-like
// files.
//
// The 'translate' function is used when sequences are checked for valid
// characters.
//
// If you're just reading FASTA files, this method SHOULD NOT be used.
func (r *Reader) ReadSequence(translate Translator) (seq.Sequence, error) {
s := seq.Sequence{}
seenHeader := false
// Before entering the main loop, we have to check to see if we've
// already read this entry's header.
if r.nextHeader != nil {
s.Name = trimHeader(r.nextHeader)
r.nextHeader = nil
seenHeader = true
}
for {
line, err := r.buf.ReadBytes('\n')
if err == io.EOF {
if len(line) == 0 {
return s, io.EOF
}
} else if err != nil {
return seq.Sequence{}, fmt.Errorf("Error on line %d: %s",
r.line, err)
}
line = bytes.TrimSpace(line)
// If it's empty, increment the counter and skip ahead.
if len(line) == 0 {
r.line++
continue
}
// If the line starts with PIR junk, ignore the line.
if bytes.HasPrefix(line, []byte("C;")) ||
bytes.HasPrefix(line, []byte("structure")) ||
bytes.HasPrefix(line, []byte("sequence")) {
r.line++
continue
}
// If we haven't seen the header yet, this better be it.
if !seenHeader {
if line[0] != '>' {
return seq.Sequence{},
fmt.Errorf("Expected '>', got '%c' on line %d.",
line[0], r.line)
}
// Trim the '>' and load this line into the header.
s.Name = trimHeader(line)
seenHeader = true
r.line++
continue
} else if line[0] == '>' {
// This means we've begun reading the next entry.
// So slap this line into 'nextHeader' and return the current entry.
r.nextHeader = line
r.line++
return s, nil
}
// Finally, time to start reading the sequence.
// If we trust the sequences, then we can just append this line
// willy nilly. Otherwise we've got to check each character.
if s.Residues == nil {
s.Residues = make([]seq.Residue, 0, 50)
}
if r.TrustSequences {
for _, b := range line {
s.Residues = append(s.Residues, seq.Residue(b))
}
} else {
for _, b := range line {
bNew, ok := translate(b)
if !ok {
return seq.Sequence{},
fmt.Errorf("Invalid character '%c' on line %d.",
b, r.line)
}
// If the zero byte is returned from translate, then we
// don't keep this residue around.
if bNew > 0 {
s.Residues = append(s.Residues, bNew)
}
}
}
r.line++
}
panic("unreachable")
}