lib/flydna.c File Reference

#include "common.h"
#include "snof.h"
#include "dnautil.h"
#include "dnaseq.h"
#include "fa.h"
#include "nt4.h"
#include "cda.h"
#include "wormdna.h"
#include "flydna.h"

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Functions
void	flyLoadNt4Genome (struct nt4Seq ***retNt4Seq, int *retNt4Count)
void	flyFreeNt4Genome (struct nt4Seq ***pNt4Seq)
void	flyChromNames (char ***retNames, int *retNameCount)
void	flyFaCommentIntoInfo (char *faComment, struct wormCdnaInfo *retInfo)
boolean	flyCdnaSeq (char *name, struct dnaSeq **retDna, struct wormCdnaInfo *retInfo)
char *	flyFeaturesDir ()
FILE *	flyOpenGoodAli ()
Variables
static char const	rcsid [] = "$Id: flydna.c,v 1.4 2003/05/06 07:33:42 kate Exp $"
static char *	chromNames [] = {"adh"}
static char *	ntFileNames [] = {"c:/biodata/fly/chrom/adh.nt"}

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Function Documentation

boolean flyCdnaSeq	(	char *	name,
		struct dnaSeq **	retDna,
		struct wormCdnaInfo *	retInfo
	)

Definition at line 77 of file flydna.c.

References cdnaFa, cdnaSnof, FALSE, faReadNext(), flyFaCommentIntoInfo(), mustOpen(), SEEK_SET, snofFindOffset(), snofMustOpen(), and TRUE.

{
long offset;
char *faComment;
char **pFaComment = (retInfo == NULL ? NULL : &faComment);
static struct snof *cdnaSnof = NULL;
static FILE *cdnaFa;

if (cdnaSnof == NULL)
        cdnaSnof = snofMustOpen("c:/biodata/fly/cDna/allcdna");
if (cdnaFa == NULL)
        cdnaFa = mustOpen("c:/biodata/fly/cDna/allcdna.fa", "rb");
if (!snofFindOffset(cdnaSnof, name, &offset))
    return FALSE;
fseek(cdnaFa, offset, SEEK_SET);
if (!faReadNext(cdnaFa, name, TRUE, pFaComment, retDna))
    return FALSE;
flyFaCommentIntoInfo(faComment, retInfo);
return TRUE;
}

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void flyChromNames	(	char ***	retNames,
		int *	retNameCount
	)

Definition at line 48 of file flydna.c.

References ArraySize, and chromNames.

{
*retNames = chromNames;
*retNameCount = ArraySize(chromNames);
}

void flyFaCommentIntoInfo	(	char *	faComment,
		struct wormCdnaInfo *	retInfo
	)

Definition at line 55 of file flydna.c.

References zeroBytes().

Referenced by flyCdnaSeq().

{
if (retInfo)
    {
    char *s;
    zeroBytes(retInfo, sizeof(*retInfo));
    /* Separate out first word and use it as name. */
    s = strchr(faComment, ' ');
    if (s != NULL)
            *s++ = 0;
    retInfo->name = faComment+1;
    retInfo->motherString = faComment;
        s = strrchr(retInfo->name, '.');
        retInfo->orientation = '+';
        if (s != NULL)
                retInfo->orientation = (s[1] == '3' ? '-' : '+');
    }
}

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char* flyFeaturesDir

(

)

Definition at line 101 of file flydna.c.

{
return "C:/biodata/fly/features/";
}

void flyFreeNt4Genome

(

struct nt4Seq ***

pNt4Seq

)

Definition at line 35 of file flydna.c.

References ArraySize, freeNt4(), freez(), and ntFileNames.

{
struct nt4Seq **pSeq;
int i;

if ((pSeq = *pNt4Seq) == NULL)
        return;
for (i=0; i<ArraySize(ntFileNames); ++i)
        freeNt4(&pSeq[i]);
freez(pNt4Seq);
}

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void flyLoadNt4Genome	(	struct nt4Seq ***	retNt4Seq,
		int *	retNt4Count
	)

Definition at line 20 of file flydna.c.

References ArraySize, chromNames, loadNt4(), needMem(), and ntFileNames.

{
struct nt4Seq **pSeq;
int i;

pSeq = needMem(ArraySize(ntFileNames) * sizeof(pSeq[0]) );
for (i=0; i<ArraySize(ntFileNames); ++i)
        {
        pSeq[i] = loadNt4(ntFileNames[i], chromNames[i]);
        }
*retNt4Seq = pSeq;
*retNt4Count = ArraySize(ntFileNames);
}

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FILE* flyOpenGoodAli

(

)

Definition at line 107 of file flydna.c.

References cdaOpenVerify().

{
return cdaOpenVerify("C:/biodata/fly/cDNA/good.ali");
}

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Variable Documentation

char* chromNames[] = {"adh"} [static]

Definition at line 17 of file flydna.c.

Referenced by flyChromNames(), flyLoadNt4Genome(), and xenAlignWorm().

char* ntFileNames[] = {"c:/biodata/fly/chrom/adh.nt"} [static]

Definition at line 18 of file flydna.c.

Referenced by flyFreeNt4Genome(), and flyLoadNt4Genome().

char const rcsid[] = "$Id: flydna.c,v 1.4 2003/05/06 07:33:42 kate Exp $" [static]

Definition at line 15 of file flydna.c.

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