func TranslateQuerySeqs(
query *bytes.Reader, action SearchOperator) (*bytes.Reader, error) {
buf := new(bytes.Buffer)
f := fasta.NewWriter(buf)
reader := fasta.NewReader(query)
for i := 0; true; i++ {
sequence, err := reader.Read()
if err == io.EOF {
break
}
if err != nil {
return nil, err
}
origSeq := sequence.Bytes()
n := sequence.Name
// generate 6 ORFs
transSeqs := Translate(origSeq)
for _, s := range transSeqs {
result := seq.NewSequenceString(n, string(Reduce(s)))
f.Write(result)
}
}
return bytes.NewReader(buf.Bytes()), nil
}
func translateQueries(reader *fasta.Reader, f *fasta.Writer) error {
sequence, err := reader.Read()
if err == io.EOF {
return nil
}
if err != nil {
fatalf("Could not read input fasta query: %s\n", err)
}
origSeq := sequence.Bytes()
n := sequence.Name
// generate 6 ORFs
transSeqs := cablastp.Translate(origSeq)
for _, s := range transSeqs {
// reduce each one
result := seq.NewSequenceString(n, string(cablastp.Reduce(s)))
f.Write(result)
}
f.Flush()
return nil
}
func ReduceQuerySeqs(
query *bytes.Reader) (*bytes.Reader, error) {
buf := new(bytes.Buffer)
f := fasta.NewWriter(buf)
reader := fasta.NewReader(query)
for i := 0; true; i++ {
sequence, err := reader.Read()
if err == io.EOF {
break
}
if err != nil {
return nil, err
}
rs := Reduce(sequence.Bytes())
n := sequence.Name
result := seq.NewSequenceString(n, string(rs))
f.Write(result)
}
f.Flush()
return bytes.NewReader(buf.Bytes()), nil
}
func processCompressedQueries(db *cablastp.DB, queryDBConf *cablastp.DBConf, inputQueryFilename string, searchBuf *bytes.Buffer) error {
cablastp.Vprintln("Compressing queries into a database...")
dbDirLoc := "./tmp_query_database" // TODO this should be a parameter
qDBDirLoc, err := compressQueries(inputQueryFilename, queryDBConf, dbDirLoc)
handleFatalError("Error compressing queries", err)
cablastp.Vprintln("Opening DB for reading")
qDB, err := cablastp.NewReadDB(qDBDirLoc)
handleFatalError("Error opening query database", err)
cablastp.Vprintln("Opening compressed queries for search...")
compQueryFilename := qDB.CoarseFastaLocation()
compQueries, err := getInputFasta(compQueryFilename)
handleFatalError("Error opening compressed query file", err)
queryBuf := new(bytes.Buffer)
f := fasta.NewWriter(queryBuf)
reader := fasta.NewReader(compQueries)
for origSeqID := 0; true; origSeqID++ {
sequence, err := reader.Read()
if err == io.EOF {
break
}
if err != nil {
fatalf("Could not read input fasta query: %s\n", err)
}
origSeq := sequence.Bytes()
n := sequence.Name
// generate 6 ORFs
transSeqs := cablastp.Translate(origSeq)
for _, s := range transSeqs {
// reduce each one
result := seq.NewSequenceString(n, string(cablastp.Reduce(s)))
f.Write(result)
}
f.Flush()
transCoarseQueries := bytes.NewReader(queryBuf.Bytes())
cablastp.Vprintln("\nBlasting query on coarse database...")
err = blastCoarse(db, transCoarseQueries, searchBuf)
handleFatalError("Error blasting coarse database", err)
cablastp.Vprintln("Decompressing coarse blast hits...")
expandedSequences, err := expandBlastHits(db, searchBuf)
handleFatalError("Error decompressing coarse blast hits", err)
if len(expandedSequences) == 0 {
cablastp.Vprintln("No results from coarse search")
} else {
cablastp.Vprintln("Making FASTA from coarse blast hits...")
searchBuf.Reset()
err = writeFasta(expandedSequences, searchBuf)
handleFatalError("Could not create FASTA input from coarse hits", err)
cablastp.Vprintln("Expanding coarse query...")
expQuery, err := expandCoarseSequence(qDB, origSeqID, &sequence)
handleFatalError("Could not expand coarse queries", err)
fineQueryBuf := new(bytes.Buffer)
fineWriter := fasta.NewWriter(fineQueryBuf)
for _, fineQuery := range expQuery {
fineQueryBytes := fineQuery.FastaSeq().Bytes() // <- Is This the same as fineQuery.Residues()?
fineName := fineQuery.Name
writeSeq := seq.NewSequenceString(fineName, string(fineQueryBytes))
fineWriter.Write(writeSeq)
}
fineWriter.Flush()
transFineQueries := bytes.NewReader(fineQueryBuf.Bytes())
cablastp.Vprintln("Building fine BLAST target database...")
targetTmpDir, err := makeFineBlastDB(db, searchBuf)
handleFatalError("Could not create fine database to search on", err)
cablastp.Vprintln("Blasting original query on fine database...")
err = blastFine(db, targetTmpDir, transFineQueries)
handleFatalError("Error blasting fine database", err)
err = os.RemoveAll(targetTmpDir)
handleFatalError("Could not remove fine database", err)
}
queryBuf.Reset()
}
cablastp.Vprintln("Cleaning up...")
err = os.RemoveAll(dbDirLoc)
handleFatalError("Could not remove query database", err)
return nil
}
