2a5a5ee4f6ec1c8f915175db9f4c806d06a9a69a
krish
  Fri Dec 17 22:22:59 2010 -0800
first draft of FASTA pair alignment to PSL converter
diff --git src/hg/fastaToPsl/fastaToPsl.c src/hg/fastaToPsl/fastaToPsl.c
new file mode 100644
index 0000000..c8cbbe5
--- /dev/null
+++ src/hg/fastaToPsl/fastaToPsl.c
@@ -0,0 +1,86 @@
+/* fastaToPsl - Convert FASTA alignments to PSL format. */
+#include "common.h"
+#include "fa.h"
+#include "linefile.h"
+#include "hash.h"
+#include "options.h"
+#include "dystring.h"
+#include "errabort.h"
+#include "psl.h"
+#include "sqlNum.h"
+#include "obscure.h"
+
+static char const rcsid[] = "$Id: spideyToPsl.c,v 1.4 2008/02/21 02:13:24 markd Exp $";
+
+void usage()
+/* Explain usage and exit. */
+{
+errAbort(
+  "fastaToPsl - Convert FASTA pair alignments to PSL format\n"
+  "usage:\n"
+  "   fastaToPsl [options] in.fa out.psl\n"
+  "\n"
+  "where in.fa is the FASTA pair alignment. \n"
+  );
+}
+
+
+/* command line */
+static struct optionSpec optionSpec[] = {
+    {NULL, 0}
+};
+
+void fastaToPsl(char *inName, char *outName)
+/* fastaToPsl - Convert axt to psl format. */
+{
+struct lineFile *inLF;
+DNA *tmpSeq;
+char *tmpHeader;
+int tmpSize;
+boolean read;
+struct psl* pslAlign;
+
+DNA *qSeq;
+int qSize;
+char *qHeader;
+
+DNA *tSeq;
+int tSize;
+char *tHeader;
+
+inLF  = lineFileOpen(inName, TRUE);
+
+/* read the query sequence */
+read = faMixedSpeedReadNext(inLF, &tmpSeq, &qSize, &tmpHeader);
+if (!read) errAbort("Could not read query FASTA entry.");
+qSeq    = cloneString(tmpSeq);
+qHeader = cloneString(tmpHeader);
+
+/* read the target sequence */
+read = faMixedSpeedReadNext(inLF, &tmpSeq, &tSize, &tmpHeader);
+if (!read) errAbort("Could not read target FASTA entry.");
+tSeq    = cloneString(tmpSeq);
+tHeader = cloneString(tmpHeader);
+
+/* try to read next sequence to see if there is one */
+read = faMixedSpeedReadNext(inLF, &tmpSeq, &tmpSize, &tmpHeader);
+if (read) warn("WARN: Found more than two FASTA entries, only processing the first two.");
+
+pslAlign = pslFromAlign(qHeader, countNonDash(qSeq, qSize), 0, qSize, qSeq,
+                        tHeader, countNonDash(tSeq, tSize), 0, tSize, tSeq,
+                        "+", 0);
+pslWriteAll(pslAlign, outName, TRUE);
+
+lineFileClose(&inLF);
+}
+
+int main(int argc, char *argv[])
+/* Process command line. */
+{
+optionInit(&argc, argv, optionSpec);
+if (argc != 3)
+    usage();
+//gUntranslated = optionExists("untranslated");
+fastaToPsl(argv[1], argv[2]);
+return 0;
+}