// Read the first 10 sequences from the database to determine its type
uint4 determineDbAlphabetType(char* filename)
{
int4 sequenceCount = 0;
char* sequence;
uint4 sequenceLength;
// Open FASTA file for reading
readFasta_open(filename);
// Move through the FASTA file reading descriptions and sequences
while (readFasta_readSequence() && sequenceCount < 10)
{
// Get sequence just read
sequence = readFasta_sequenceBuffer;
sequenceLength = readFasta_sequenceLength;
// Determine the alphabet of the current sequence
if (encoding_determineAlphabetType(sequence, sequenceLength) == encoding_protein)
{
// If contains protein letters, return protein type
readFasta_close();
return encoding_protein;
}
sequenceCount++;
}
// Close fasta reader and return nucleotide type
readFasta_close();
return encoding_nucleotide;
}
int main(int argc, char *argv[]) {
char *filename, *sequence, *description, *sequenceCopy;
int sequenceLength;
// User must provide FASTA format file at command line
if (argc < 2) {
fprintf(stderr, "Useage: dust <FASTA file>\n");
exit(-1);
}
filename = argv[1];
// Initialize encoding routines
encoding_initialize(encoding_nucleotide);
// Open FASTA file for reading
readFasta_open(filename);
// Read each sequence from the file
while (readFasta_readSequence()) {
// Get sequence just read
sequence = readFasta_sequenceBuffer;
description = readFasta_descriptionBuffer;
sequenceLength = readFasta_sequenceLength;
// Make in-memory copy of it
sequenceCopy = (char *)global_malloc(sequenceLength);
strcpy(sequenceCopy, sequence);
// Perform dust filtering
dust_dustSequence(sequence);
// Print description and filtering sequence
printf(">%s\n%s\n", description, sequence);
}
}
int4 main(int argc, char* argv[])
{
char *sequence, *filename;
uint4 sequenceLength;
int4 totalWilds = 0, alphabetType;
struct memSingleBlock* wildcardEdits;
struct wildcardEdit* wildcardEdit;
char *wildcardData = NULL, *startWildcardData = NULL;
// User must provide FASTA format file at command line
if (argc < 2)
{
fprintf(stderr, "Useage: formatdb <FASTA file>\n");
exit(-1);
}
filename = argv[1];
// Initialize array to store wildcard edits
wildcardEdits = memSingleBlock_initialize(sizeof(struct wildcardEdit), 10);
// Determine if database is protein or nucleotide
alphabetType = determineDbAlphabetType(filename);
if (alphabetType == encoding_protein)
{
printf("PROTEIN database detected.\n");
}
else if (alphabetType == encoding_nucleotide)
{
printf("NUCLEOTIDE database detected.\n");
}
// Initialize codes array
encoding_initialize(alphabetType);
// Initialize writing to formatted database
writedb_initialize(filename, alphabetType);
// Open FASTA file for reading
readFasta_open(filename);
printf("Formatting database...");
fflush(stdout);
// Move through the FASTA file reading descriptions and sequences
while (readFasta_readSequence())
{
// Get sequence just read
sequence = readFasta_sequenceBuffer;
sequenceLength = readFasta_sequenceLength;
// Encode the sequence
encoding_encodeSequence(sequence, sequenceLength, alphabetType);
// Convert nucleotide sequences to byte-packed format
if (alphabetType == encoding_nucleotide)
{
// Replace any wilds with a random character
totalWilds += encoding_replaceWildcards(wildcardEdits, sequence, sequenceLength);
// Declare memory to hold wildcard data
startWildcardData = global_realloc(startWildcardData,
sizeof(char) * wildcardEdits->numEntries * 5);
wildcardData = startWildcardData;
// For each wildcard edit, encode details using chars and vbytes
memSingleBlock_resetCurrent(wildcardEdits);
while ((wildcardEdit = memSingleBlock_getCurrent(wildcardEdits)) != NULL)
{
// Record wild character
*wildcardData = wildcardEdit->code;
wildcardData++;
// Convert the position to a vbyte
vbyte_putVbyte(wildcardData, wildcardEdit->position);
}
}
else
{
startWildcardData = wildcardData = NULL;
}
// printf("[%s](%d)", readFasta_descriptionBuffer, readFasta_descriptionLength); fflush(stdout);
// Add sequence to the formatted collection
writedb_addSequence(sequence, sequenceLength, readFasta_descriptionBuffer,
readFasta_descriptionLength, startWildcardData,
wildcardData - startWildcardData, NULL, 0);
// Print status dots
if (writedb_sequenceCount % 10000 == 0)
{
printf(".");
fflush(stdout);
}
}
// Close fasta reader
readFasta_close();
// Finalize writing to the formatted collection
writedb_close();
printf("done.\n");
printf("%d sequences processed.\n", writedb_sequenceCount);
printf("%llu letters processed.\n", writedb_numberOfLetters);
printf("%d wildcards encoded.\n", totalWilds);
printf("%d volume(s) created.\n", writedb_volume + 1);
printf("Longest/shortest sequence was %d/%d letters\n",
writedb_maximumSequenceLength, writedb_minimumSequenceLength);
fflush(stdout);
return 0;
}
