int main(int argc, char *argv[]) /* Process command line. */ { char *scoreSchemeFile = NULL; optionHash(&argc, argv); if (argc != 5) usage(); if (optionExists("fa")) { qIsFa = TRUE; qFaList = faReadAllMixed(argv[3]); } if (optionExists("tfa")) { tIsFa = TRUE; tFaList = faReadAllMixed(argv[2]); } scoreSchemeFile = optionVal("scoreScheme", scoreSchemeFile); if (scoreSchemeFile != NULL) scoreScheme = axtScoreSchemeRead(scoreSchemeFile); else scoreScheme = axtScoreSchemeDefault(); lavToAxt(argv[1], argv[2], argv[3], argv[4]); return 0; }
static void seqReaderLoadFasta(struct seqReader *seqReader) /* load a FASTA file into a seqReader object */ { seqReader->seqTbl = hashNew(21); struct dnaSeq *seq, *seqs = faReadAllMixed(seqReader->spec); while ((seq = slPopHead(&seqs)) != NULL) hashAdd(seqReader->seqTbl, seq->name, seq); }
void faToNib(int options, char *in, char *out) /* faToNib - Convert from .fa to .nib format. */ { struct dnaSeq *seq = faReadAllMixed(in); if (slCount(seq) > 1) errAbort("faToNib only works on fa files containing a single sequence."); if (optionExists("hardMask")) maskLower(seq); nibWriteMasked(options, seq, out); }