/* genePredToFakePsl - create fake .psl of mRNA aligned to dna from genePred file or table. */

/* Copyright (C) 2013 The Regents of the University of California 
 * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "options.h"
#include "portable.h"
#include "hash.h"
#include "hdb.h"
#include "genbank.h"
#include "genePred.h"
#include "genePredReader.h"
#include "psl.h"


/* Command line switches. */
static char *chromSizes = NULL;  /* read chrom sizes from file instead of database . */
static char *qSizes = NULL;  /* read query sizes from file */
static struct hash *qSizeHash = NULL;  /* key is name, value is size */

/* Command line option specifications */
static struct optionSpec optionSpecs[] = {
    {"chromSize", OPTION_STRING},
    {"qSizes", OPTION_STRING},
    {NULL, 0}
};

void usage()
/* Explain usage and exit. */
{
errAbort(
  "genePredToFakePsl - Create a psl of fake-mRNA aligned to gene-preds from a file or table.\n"
  "usage:\n"
  "   genePredToFakePsl [options] db fileTbl pslOut cdsOut\n"
  "\n"
  "If fileTbl is an existing file, then it is used.\n"
  "Otherwise, the table by this name is used.\n"
  "\n"
  "pslOut specifies the fake-mRNA output psl filename.\n"
  "\n"
  "cdsOut specifies the output cds tab-separated file which contains\n"
  "genbank-style CDS records showing cdsStart..cdsEnd\n"  
  "e.g. NM_123456 34..305\n"
  "options:\n"
  "   -chromSize=sizefile\tRead chrom sizes from file instead of database\n"
  "             sizefile contains two white space separated fields per line:\n"
  "		chrom name and size\n"
  "   -qSizes=qSizesFile\tRead in query sizes to fixup qSize and qStarts\n"

  "\n");
}

static void cnvGenePredCds(struct genePred *gp, int qSize, FILE *cdsFh)
/* determine CDS and output */
{
struct genbankCds cds;
genePredToCds(gp, &cds);
fprintf(cdsFh,"%s\t%d..%d\n", gp->name, cds.start+1, cds.end); /* genbank cds is closed 1-based */
}

static void cnvGenePred(struct hash *chromHash, struct genePred *gp, FILE *pslFh, FILE *cdsFh)
/* convert a genePred to a psl and CDS */
{
int chromSize = hashIntValDefault(chromHash, gp->chrom, 0);
if (chromSize == 0)
    errAbort("Couldn't find chromosome/scaffold '%s' in chromInfo", gp->chrom);
int qSize = 0;
if (qSizes != NULL)
    qSize = hashIntValDefault(qSizeHash, gp->name, 0);
struct psl *psl = genePredToPsl(gp, chromSize, qSize);
pslTabOut(psl, pslFh);
pslFree(&psl);
if (gp->cdsStart < gp->cdsEnd)
    cnvGenePredCds(gp, qSize, cdsFh);
}

static struct hash *getChromHash(char *db)
/* Return a hash of chrom names and sizes, from either -chromSize=file or db */
{
struct hash *chromHash = NULL;
if (chromSizes != NULL)
    chromHash = hChromSizeHashFromFile(chromSizes);
else
    chromHash = hChromSizeHash(db);
return chromHash;
}

static void fakePslFromGenePred(char *db, char *fileTbl, char *pslOut, char *cdsOut)
/* check a genePred */
{
struct genePredReader *gpr;
struct genePred *gp;
FILE *pslFh = mustOpen(pslOut, "w");
FILE *cdsFh = mustOpen(cdsOut, "w");

struct hash *chromHash = getChromHash(db);

if (fileExists(fileTbl))
    {
    gpr = genePredReaderFile(fileTbl, NULL);
    }
else
    {
    struct sqlConnection *conn = hAllocConn(db);
    gpr = genePredReaderQuery(conn, fileTbl, NULL);
    hFreeConn(&conn);
    }

while ((gp = genePredReaderNext(gpr)) != NULL)
    {
    cnvGenePred(chromHash, gp, pslFh, cdsFh);
    }
genePredReaderFree(&gpr);
carefulClose(&pslFh);
carefulClose(&cdsFh);
}

int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
chromSizes = optionVal("chromSize", NULL);
qSizes = optionVal("qSizes", NULL);
if (argc != 5)
    usage();
if (qSizes != NULL)
    qSizeHash = hChromSizeHashFromFile(qSizes);
fakePslFromGenePred(argv[1],argv[2],argv[3],argv[4]);
return 0;
}