void chopFaLines(char *inName, char *outName)
/* chopFaLines - Read in FA file with long lines and rewrite it with shorter lines. */
{
FILE *in = mustOpen(inName, "r");
FILE *out = mustOpen(outName, "w");
char *commentLine;
struct dnaSeq *seq;
while (faReadNext(in, NULL, TRUE, &commentLine, &seq))
{
commentLine = trimSpaces(commentLine+1);
uglyf(">%s\n", commentLine);
mustWrite(uglyOut, seq->dna, 100);
uglyf("\n");
uglyAbort("All for now");
faWriteNext(out, commentLine, seq->dna, seq->size);
}
}
boolean detailTest(struct psl *psl)
/* Detailed pass/fail test. */
{
int size = pslBlockTotalSize(psl);
int badFactor = psl->misMatch + psl->tNumInsert + psl->qNumInsert + 2*log(1+psl->tBaseInsert + psl->qBaseInsert);
int milliBad = roundingScale(1000, badFactor, size);
if (sameString(psl->qName, "ti|18649044"))
{
static int maxc = 10;
uglyf("%s: size %d, badFactor %d, milliBad %d\n", psl->qName, size, badFactor, milliBad);
if (--maxc == 0)
uglyAbort("All for now");
}
#ifdef NEVER
#endif /* NEVER */
if (milliBad < 85)
return FALSE;
return TRUE;
}
void cdwCheckDataset(char *outputFile)
/* cdwCheckDataset - Look at all the submissions for a given dataset and print helpful stats.. */
{
FILE *f = mustOpen(outputFile,"w");
struct sqlConnection *conn = sqlConnect("cdw");
char query[1024];
struct cdwSubmitDir *submitDir;
// Get the id associated with the submission directory.
if (gWorkingDir == NULL)
{
char cwd[1024];
getcwd(cwd, sizeof(cwd));
sqlSafef(query, sizeof(query), "select * from cdwSubmitDir where url = '%s';", cwd);
submitDir = cdwSubmitDirLoadByQuery(conn, query);
}
else
{
sqlSafef(query, sizeof(query), "select * from cdwSubmitDir where url = '%s';", gWorkingDir);
submitDir = cdwSubmitDirLoadByQuery(conn, query);
}
if (!submitDir)
uglyAbort("There are no submissions associated with the submission directory provided.");
// Get all cdwSubmit entries associated with the submission directory.
sqlSafef(query, sizeof(query), "select * from cdwSubmit where submitDirId = '%i';", submitDir->id);
struct cdwSubmit *submitList = cdwSubmitLoadByQuery(conn, query);
struct cdwSubmit *submission;
// Keep track of the # of submissions, meta files and mani files.
int count = 0;
long long int totalFiles = 0, totalBytes = 0; // Count the total files and bytes.
struct slName *submitters = NULL, *user; // Keep track of the submitters.
// Loop over all cdwSubmit entries and gather/print out stats.
for (submission = submitList; ; submission = submission->next)
{
++count;
sqlSafef(query,sizeof(query), "select * from cdwUser where id = '%i';", (int)submission->userId);
struct cdwUser *user = cdwUserLoadByQuery(conn,query);
if(!slNameInList(submitters, user->email)) // If a submitter has not been seen add it.
slNameAddHead(&submitters, user->email);
// Print out submission stats.
fprintf(f, "Sub #: %i | Sub id: %i | New files: %i | New bytes: %lld | Mani id: %i |",
count, submission->id, submission->newFiles, submission->newBytes, submission->manifestFileId);
fprintf(f, " Meta id: %i | Files with new meta data values: %i | User email: %s | Wrangler: %s\n",
submission->metaFileId, submission->metaChangeCount, user->email, submission->wrangler);
totalFiles += submission->newFiles;
totalBytes += submission->newBytes;
if (submission->next == NULL)
break;
}
sqlSafef(query, sizeof(query), "select distinct metaFileId from cdwSubmit where submitDirId=%i", submitDir->id);
fprintf(f,"Total submissions:\t%i\n", count);
fprintf(f,"Total files:\t%lld\n",totalFiles);
// Math magic for pretty printing the file size.
long long int tBytes, gBytes, mBytes, kBytes, bytes;
tBytes = totalBytes/1000000000000;
gBytes = (totalBytes - tBytes * 1000000000000)/1000000000;
mBytes = (totalBytes - tBytes * 1000000000000 - gBytes * 1000000000)/1000000;
kBytes = (totalBytes - tBytes * 1000000000000 - gBytes * 1000000000 - mBytes * 1000000)/1000;
bytes = totalBytes - tBytes * 1000000000000 - gBytes * 1000000000 - mBytes * 1000000 - kBytes * 1000;
fprintf(f,"Total bytes:\t%lld T %lld G %lld M %lld K %lld B\n", tBytes, gBytes, mBytes, kBytes, bytes);
fprintf(f,"Submitters: ");
// Print out the submitters, ideally it will only be one person but in practice... Not so much.
for (user = submitters; ; user = user->next)
{
fprintf(f,"%s", user->name);
if (user->next == NULL)
break;
fprintf(f,", ");
}
fprintf(f,"\n");
sqlDisconnect(&conn);
}
