func main() {
buf := new(bytes.Buffer)
if flag.NArg() < 2 {
flag.Usage()
}
// If the quiet flag isn't set, enable verbose output.
if !flagQuiet {
cablastp.Verbose = true
}
inputFastaQuery, err := getInputFasta()
if err != nil {
fatalf("Could not read input fasta query: %s\n", err)
}
db, err := cablastp.NewReadDB(flag.Arg(0))
if err != nil {
fatalf("Could not open '%s' database: %s\n", flag.Arg(0), err)
}
cablastp.Vprintln("\nBlasting query on coarse database...")
if err := blastCoarse(db, inputFastaQuery, buf); err != nil {
fatalf("Error blasting coarse database: %s\n", err)
}
cablastp.Vprintln("Decompressing blast hits...")
expandedSequences, err := expandBlastHits(db, buf)
if err != nil {
fatalf("%s\n", err)
}
// Write the contents of the expanded sequences to a fasta file.
// It is then passed as the "-subject" parameter to blastp.
var tmpFine string
if tmpFine, err = writeFasta(expandedSequences); err != nil {
fatalf("Could not create FASTA input from coarse hits: %s\n", err)
}
// Finally, run the query against the fine fasta database and pass on the
// stdout and stderr...
cablastp.Vprintln("Blasting query on fine database...")
if _, err := inputFastaQuery.Seek(0, os.SEEK_SET); err != nil {
fatalf("Could not seek to start of query fasta input: %s\n", err)
}
if err := blastFine(db, tmpFine, inputFastaQuery); err != nil {
fatalf("Error blasting fine database: %s\n", err)
}
// Delete the temporary fine database.
if !flagNoCleanup {
if err := os.Remove(tmpFine); err != nil {
fatalf("Could not delete fine fasta database: %s\n", err)
}
}
cleanup(db)
}
func main() {
if flag.NArg() < 2 {
flag.Usage()
}
// If the quiet flag isn't set, enable verbose output.
if !flagQuiet {
cablastp.Verbose = true
}
// Open the fasta file specified for writing.
outFasta, err := os.Create(flag.Arg(1))
if err != nil {
fatalf("Could not write to '%s': %s\n", flag.Arg(1), err)
}
fastaWriter := fasta.NewWriter(outFasta)
fastaWriter.Asterisk = true
// Create a new database for writing. If we're appending, we load
// the coarse database into memory, and setup the database for writing.
db, err := cablastp.NewReadDB(flag.Arg(0))
if err != nil {
fatalf("Could not open '%s' database: %s\n", flag.Arg(0), err)
}
cablastp.Vprintln("")
// Start the CPU profile after all of the data has been read.
if len(flagCpuProfile) > 0 {
f, err := os.Create(flagCpuProfile)
if err != nil {
fatalf("%s\n", err)
}
pprof.StartCPUProfile(f)
}
numSeqs := db.ComDB.NumSequences()
for orgSeqId := 0; orgSeqId < numSeqs; orgSeqId++ {
oseq, err := db.ComDB.ReadSeq(db.CoarseDB, orgSeqId)
if err != nil {
fatalf("Error reading seq id '%d': %s\n", orgSeqId, err)
}
if err := fastaWriter.Write(oseq.FastaSeq()); err != nil {
cablastp.Vprintf("Error writing seq '%s': %s\n", oseq.Name, err)
}
}
cleanup(db)
if err = fastaWriter.Flush(); err != nil {
fatalf("%s\n", err)
}
if err = outFasta.Close(); err != nil {
fatalf("%s\n", err)
}
}
func main() {
buf := new(bytes.Buffer)
if flag.NArg() < 2 {
flag.Usage()
}
if len(flagRPSPath) == 0 {
fmt.Fprintln(os.Stderr, "The '--rpspath' flag must be set.")
flag.Usage()
}
// If the quiet flag isn't set, enable verbose output.
if !flagQuiet {
cablastp.Verbose = true
}
inputFastaQuery, err := getInputFasta()
if err != nil {
fatalf("Could not read input fasta query: %s\n", err)
}
db, err := cablastp.NewReadDB(flag.Arg(0))
if err != nil {
fatalf("Could not open '%s' database: %s\n", flag.Arg(0), err)
}
cablastp.Vprintln("\nBlasting query on coarse database...")
if err := blastCoarse(db, inputFastaQuery, buf); err != nil {
fatalf("Error blasting coarse database: %s\n", err)
}
cablastp.Vprintln("Decompressing blast hits...")
expandedSequences, err := expandBlastHits(db, buf)
if err != nil {
fatalf("%s\n", err)
}
// Write the contents of the expanded sequences to a fasta file.
// It is then passed as the "-subject" parameter to blastp.
buf.Reset()
if err := writeFasta(expandedSequences, buf); err != nil {
fatalf("Could not create FASTA input from coarse hits: %s\n", err)
}
// Create the fine blast db in a temporary directory
cablastp.Vprintln("Building fine BLAST database...")
tmpDir, err := makeFineBlastDB(db, buf)
if err != nil {
fatalf("Could not create fine database to search on: %s\n", err)
}
// Finally, run the query against the fine fasta database and pass on
// stdout and stderr...
cablastp.Vprintln("Blasting query on fine database...")
if _, err := inputFastaQuery.Seek(0, os.SEEK_SET); err != nil {
fatalf("Could not seek to start of query fasta input: %s\n", err)
}
if err := blastFine(db, tmpDir, inputFastaQuery); err != nil {
fatalf("Error blasting fine database: %s\n", err)
}
// Delete the temporary fine database.
if !flagNoCleanup {
if err := os.RemoveAll(tmpDir); err != nil {
fatalf("Could not delete fine BLAST database: %s\n", err)
}
}
cleanup(db)
}
