boolean anyCdnaSeq(char *name, struct dnaSeq **retDna, struct wormCdnaInfo *retInfo)
/* Get a single cDNA sequence. Optionally (if retInfo is non-null) get additional
* info about the sequence. */
{
static FILE *cdnaFa;
static struct snof *cdnaSnof = NULL;
long offset;
char *faComment;
char **pFaComment = (retInfo == NULL ? NULL : &faComment);
if (cdnaSnof == NULL)
{
char buf[512];
cdnaSnof = snofMustOpen(cdnaName);
sprintf(buf, "%s%s", cdnaName, ".fa");
cdnaFa = mustOpen(buf, "rb");
}
if (!snofFindOffset(cdnaSnof, name, &offset))
return FALSE;
fseek(cdnaFa, offset, SEEK_SET);
if (!faReadNext(cdnaFa, name, TRUE, pFaComment, retDna))
return FALSE;
if (retInfo != NULL)
{
/* Kludge - only look up info if format is more or less right. */
int fieldCount = countChars(faComment, '|');
if (fieldCount >= 8)
wormFaCommentIntoInfo(faComment, retInfo);
else
zeroBytes(retInfo, sizeof(*retInfo));
}
return TRUE;
}
boolean nextWormCdnaAndInfo(struct wormCdnaIterator *it, struct dnaSeq **retSeq,
struct wormCdnaInfo *retInfo)
/* Return next sequence and associated info from database. */
{
char *faComment;
if (!faReadNext(it->faFile, "unknown", TRUE, &faComment, retSeq))
return FALSE;
wormFaCommentIntoInfo(faComment, retInfo);
return TRUE;
}
boolean wormCdnaSeq(char *name, struct dnaSeq **retDna, struct wormCdnaInfo *retInfo)
/* Get a single worm cDNA sequence. Optionally (if retInfo is non-null) get additional
* info about the sequence. */
{
long offset;
char *faComment;
char **pFaComment = (retInfo == NULL ? NULL : &faComment);
wormCdnaCache();
if (!snofFindOffset(cdnaSnof, name, &offset))
return FALSE;
fseek(cdnaFa, offset, SEEK_SET);
if (!faReadNext(cdnaFa, name, TRUE, pFaComment, retDna))
return FALSE;
wormFaCommentIntoInfo(faComment, retInfo);
return TRUE;
}
boolean wormCdnaInfo(char *name, struct wormCdnaInfo *retInfo)
/* Get info about cDNA sequence. */
{
char commentBuf[512];
char *comment;
long offset;
wormCdnaCache();
if (!snofFindOffset(cdnaSnof, name, &offset))
return FALSE;
fseek(cdnaFa, offset, SEEK_SET);
mustGetLine(cdnaFa, commentBuf, sizeof(commentBuf));
if (commentBuf[0] != '>')
errAbort("Expecting line starting with > in cDNA fa file.\nGot %s", commentBuf);
comment = cloneString(commentBuf);
wormFaCommentIntoInfo(comment, retInfo);
return TRUE;
}
boolean wormInfoForGene(char *orfName, struct wormCdnaInfo *retInfo)
/* Return info if any on ORF, or NULL if none exists. freeMem() return value. */
{
FILE *f;
char fileName[512];
char lineBuf[512];
int nameLen;
char *info = NULL;
char *synName = NULL;
int lineCount = 0;
/* Make this one work for orfs as well as gene names */
if (wormIsGeneName(orfName))
{
synName = wormGeneFirstOrfName(orfName);
if (synName != NULL)
orfName = synName;
}
sprintf(fileName, "%sorfInfo", wormFeaturesDir());
nameLen = strlen(orfName);
f = mustOpen(fileName, "r");
while (fgets(lineBuf, sizeof(lineBuf), f))
{
++lineCount;
if (strncmp(lineBuf, orfName, nameLen) == 0 && lineBuf[nameLen] == ' ')
{
info = cloneString(lineBuf);
break;
}
}
freeMem(synName);
fclose(f);
if (info == NULL)
return FALSE;
wormFaCommentIntoInfo(info, retInfo);
return TRUE;;
}
