18776fc865932be3d69aabd64b59ca41d7a26249
markd
  Tue Sep 7 16:24:58 2010 -0700
move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
diff --git src/utils/gtfToGenePred/gtfToGenePred.c src/utils/gtfToGenePred/gtfToGenePred.c
deleted file mode 100644
index b2acca1..0000000
--- src/utils/gtfToGenePred/gtfToGenePred.c
+++ /dev/null
@@ -1,188 +0,0 @@
-/* gtfToGenePred - convert a GTF file to a genePred. */
-#include "common.h"
-#include "linefile.h"
-#include "gff.h"
-#include "genePred.h"
-#include "errCatch.h"
-#include "options.h"
-
-void usage()
-/* Explain usage and exit. */
-{
-errAbort(
-  "gtfToGenePred - convert a GTF file to a genePred\n"
-  "usage:\n"
-  "   gtfToGenePred gtf genePred\n"
-  "\n"
-  "options:\n"
-  "     -genePredExt - create a extended genePred, including frame\n"
-  "      information and gene name\n"
-  "     -allErrors - skip groups with errors rather than aborting.\n"
-  "      Useful for getting infomation about as many errors as possible.\n"
-  "     -infoOut=file - write a file with information on each transcript\n"
-  "     -sourcePrefix=pre - only process entries where the source name has the\n"
-  "      specified prefix.  May be repeated.\n"
-  "     -impliedStopAfterCds - implied stop codon in after CDS\n"
-  "     -geneNameAsName2 - if specified, use gene_name for the name2 field\n"
-  "      instead of gene_id.\n");
-}
-
-static struct optionSpec options[] = {
-    {"genePredExt", OPTION_BOOLEAN},
-    {"allErrors", OPTION_BOOLEAN},
-    {"infoOut", OPTION_STRING},
-    {"sourcePrefix", OPTION_STRING|OPTION_MULTI},
-    {"impliedStopAfterCds", OPTION_BOOLEAN},
-    {"geneNameAsName2", OPTION_BOOLEAN},
-    {NULL, 0},
-};
-boolean clGenePredExt = FALSE;  /* include frame and geneName */
-boolean clAllErrors = FALSE;    /* report as many errors as possible */
-struct slName *clSourcePrefixes; /* list of source prefixes to match */
-unsigned clGxfOptions = 0;       /* options for converting GTF/GFF */
-
-int badGroupCount = 0;  /* count of inconsistent groups found */
-
-
-/* header for info file */
-static char *infoHeader = "#transId\tgeneId\tsource\tchrom\tstart\tend\tstrand\tproteinId\tgeneName\ttranscriptName\n";
-
-static void saveName(char **name, char *newName)
-/* if name references NULL, and newName is not NULL, update name */
-{
-if ((*name == NULL) && (newName != NULL))
-    *name = newName;
-}
-static void writeInfo(FILE *infoFh, struct gffGroup *group)
-/* write a row for a GTF group from the info file */
-{
-
-// scan lineList for group and protein ids
-struct gffLine *ll;
-char *geneId = NULL, *proteinId = NULL, *geneName = NULL, *transcriptName = NULL;
-for (ll = group->lineList; ll != NULL; ll = ll->next)
-    {
-    saveName(&geneId, ll->geneId);
-    saveName(&proteinId, ll->proteinId);
-    saveName(&geneName, ll->geneName);
-    saveName(&transcriptName, ll->transcriptName);
-    }
-
-fprintf(infoFh, "%s\t%s\t%s\t%s\t%d\t%d\t%c\t%s\t%s\t%s\n",
-        group->name, emptyForNull(geneId), group->source,
-        group->seq, group->start, group->end, group->strand,
-        emptyForNull(proteinId), emptyForNull(geneName),
-        emptyForNull(transcriptName));
-}
-
-static void gtfGroupToGenePred(struct gffFile *gtf, struct gffGroup *group, FILE *gpFh,
-                               FILE *infoFh)
-/* convert one gtf group to a genePred */
-{
-unsigned optFields = (clGenePredExt ? genePredAllFlds : 0);
-struct errCatch *errCatch = errCatchNew();
-
-if (errCatchStart(errCatch))
-    {
-    struct genePred *gp = genePredFromGroupedGtf(gtf, group, group->name, optFields, clGxfOptions);
-    if (gp == NULL)
-        {
-        if (clAllErrors)
-            fprintf(stderr,"no exons defined for %s\n", group->name);
-        else
-            errAbort("no exons defined for %s", group->name);
-        badGroupCount++;
-        }
-    else
-        {
-        genePredTabOut(gp, gpFh);
-        genePredFree(&gp);
-        }
-    }
-errCatchEnd(errCatch);
-if (errCatch->gotError)
-    {
-    // drop trailing newline in caught message
-    int l = strlen(errCatch->message->string);
-    if ((l > 0) && (errCatch->message->string[l-1] == '\n'))
-        errCatch->message->string[l-1] = '\0';
-    if (clAllErrors)
-        fprintf(stderr, "%s\n", errCatch->message->string);
-    else
-        errAbort("%s", errCatch->message->string);
-    badGroupCount++;
-    }
-else
-    {
-    if (infoFh != NULL)
-        writeInfo(infoFh, group);
-    }
-errCatchFree(&errCatch); 
-}
-
-static bool sourceMatches(struct gffGroup *group)
-/* see if the source matches on on the list */
-{
-struct slName *pre = NULL;
-for (pre = clSourcePrefixes; pre != NULL; pre = pre->next)
-    if (startsWith(pre->name, group->source))
-        return TRUE;
-return FALSE;
-}
-        
-
-static bool inclGroup(struct gffGroup *group)
-/* check if a group should be included in the output */
-{
-if (clSourcePrefixes != NULL)
-    {
-    if (!sourceMatches(group))
-        return FALSE;
-    }
-return TRUE;
-}
-
-static void gtfToGenePred(char *gtfFile, char *gpFile, char *infoFile)
-/* gtfToGenePred -  convert a GTF file to a genePred.. */
-{
-struct gffFile *gtf = gffRead(gtfFile);
-FILE *gpFh, *infoFh = NULL;
-struct gffGroup *group;
-
-if (!gtf->isGtf)
-    errAbort("%s doesn't appear to be a GTF file (GFF not supported by this program)", gtfFile);
-gffGroupLines(gtf);
-gpFh = mustOpen(gpFile, "w");
-if (infoFile != NULL)
-    {
-    infoFh = mustOpen(infoFile, "w");
-    fputs(infoHeader, infoFh);
-    }
-
-for (group = gtf->groupList; group != NULL; group = group->next)
-    if (inclGroup(group))
-        gtfGroupToGenePred(gtf, group, gpFh, infoFh);
-
-carefulClose(&gpFh);
-gffFileFree(&gtf);
-}
-
-int main(int argc, char *argv[])
-/* Process command line. */
-{
-optionInit(&argc, argv, options);
-if (argc != 3)
-    usage();
-clGenePredExt = optionExists("genePredExt");
-clAllErrors = optionExists("allErrors");
-clSourcePrefixes = optionMultiVal("sourcePrefix", NULL);
-if (optionExists("impliedStopAfterCds"))
-    clGxfOptions |= genePredGxfImpliedStopAfterCds;
-if (optionExists("geneNameAsName2"))
-    clGxfOptions |= genePredGxfGeneNameAsName2;
-
-gtfToGenePred(argv[1], argv[2], optionVal("infoOut", NULL));
-if (badGroupCount > 0)
-    errAbort("%d errors", badGroupCount);
-return 0;
-}
