4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/recycleDb/bedUp/bedUp.c src/hg/recycleDb/bedUp/bedUp.c index 70cca2f..5654d0a 100644 --- src/hg/recycleDb/bedUp/bedUp.c +++ src/hg/recycleDb/bedUp/bedUp.c @@ -1,305 +1,305 @@ /* bedUp - Load bed submissions after conversion back into new database.. */ /* Copyright (C) 2013 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hash.h" #include "jksql.h" #include "psl.h" #include "clonePos.h" void usage() /* Explain usage and exit. */ { errAbort( "bedUp - Load bed submissions after conversion back into new database.\n" "usage:\n" " bedUp oldDb table newDb old.tab convert.psl missing\n"); } struct bedExt /* Extended bed structure. */ { struct bedExt *next; /* Next in singly linked list. */ char *chrom; /* Human chromosome or FPC contig */ unsigned chromStart; /* Start position in chromosome */ unsigned chromEnd; /* End position in chromosome */ char *name; /* Name. */ char **extraWords; /* Other words in this row of database. */ char *id; /* Unique ID - allocated in hash. */ struct psl *pslList; /* Conversion psl. */ char *oldClone; /* Old clone this used to be at. */ bool converted; /* TRUE if converted to new coors. */ }; char *bedIdS(char *name, char *chrom, char *chromStart) /* Return unique identifier for bed treating number as string. */ { static char buf[128]; sprintf(buf, "%s.%s.%s", name, chrom, chromStart); return buf; } char *bedId(char *name, char *chrom, int chromStart) /* Return unique identifier for bed. */ { char num[16]; sprintf(num, "%d", chromStart); return bedIdS(name, chrom, num); } void unpackPslName(struct lineFile *lf, char *pslName, char **retName, char **retDb, char **retChrom, int *retStart) /* Unpack name in convert psl file. */ { static char buf[128]; char *words[8]; int i; char *e; strncpy(buf, pslName, sizeof(buf)); for (i=0; i<3; ++i) { e = strrchr(buf, '.'); if (e == NULL) errAbort("Expecting name.db.chrom.start line %d of %s", lf->lineIx, lf->fileName); *e++ = 0; words[i] = e; } *retDb = words[2]; *retChrom = words[1]; *retStart = atoi(words[0]); *retName = buf; } struct bedExt *loadTable(char *fileName, struct hash *bedHash, struct hash *chromHash, struct hash *cloneHash) /* Make list and load up tables from file. */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); struct bedExt *bedList = NULL, *bed; char *words[16]; int wordCount; int width; char *s; struct hashEl *hel; while ((wordCount = lineFileChop(lf, words)) != 0) { lineFileExpectWords(lf, 10, wordCount); AllocVar(bed); bed->chrom = hashStoreName(chromHash, words[2]); bed->chromStart = bed->chromEnd = lineFileNeedNum(lf, words, 3); width = lineFileNeedNum(lf, words, 4); bed->chromEnd += width; s = words[5]; chopSuffix(s); bed->oldClone = hashStoreName(cloneHash, s); bed->name = cloneString(words[0]); s = bedId(bed->name, bed->chrom, bed->chromStart); if (hashLookup(bedHash, s)) { warn("%s duplicated, ignoring all but first.", s); freez(&bed); } else { hel = hashAddUnique(bedHash, s, bed); bed->id = hel->name; slAddHead(&bedList, bed); } } lineFileClose(&lf); slReverse(&bedList); return bedList; } void addPsls(char *fileName, char *oldDb, struct hash *bedHash) /* Add relevant psls to beds. */ { struct bedExt *bed; struct lineFile *lf = pslFileOpen(fileName); struct psl *psl; char *s; char *name, *db, *chrom; int chromStart; int total = 0, uniq = 0; while ((psl = pslNext(lf)) != NULL) { unpackPslName(lf, psl->qName, &name, &db, &chrom, &chromStart); if (!sameString(db, oldDb)) errAbort("Old database mismatch %s in command line %s in %s", oldDb, db, fileName); s = bedId(name, chrom, chromStart); bed = hashMustFindVal(bedHash, s); if (bed->pslList == NULL) uniq += 1; slAddHead(&bed->pslList, psl); ++total; } lineFileClose(&lf); printf("%d psls int %s added to %d beds\n", total, fileName, uniq); } void fixFishChrom(char *s) /* Fix chrna_random to chrNA_random, etc for fish. */ { char *e; s += 3; if (islower(s[0])) { e = strchr(s, '_'); if (e == NULL) e = s + strlen(s); toUpperN(s, e-s); } } void addOther(char *oldDb, char *oldTable, struct hash *bedHash) /* Add extra rows to beds. */ { struct sqlConnection *conn = sqlConnect(oldDb); struct sqlResult *sr; char **row; char query[256]; int columnCount; int extraCount, i; char *s; struct bedExt *bed; enum {definedCol = 4}; int rowCount = 0; sqlSafef(query, sizeof query, "select * from %s", oldTable); sr = sqlGetResult(conn, query); columnCount = sqlCountColumns(sr); extraCount = columnCount - definedCol; while ((row = sqlNextRow(sr)) != NULL) { fixFishChrom(row[0]); s = bedIdS(row[3], row[0], row[1]); bed = hashMustFindVal(bedHash, s); if (bed->extraWords != NULL) { warn("Duplicate %s in database, ignoring all but first.", s); continue; } AllocArray(bed->extraWords, extraCount); for (i=definedCol; i<columnCount; ++i) bed->extraWords[i-definedCol] = cloneString(row[i]); ++rowCount; } sqlFreeResult(&sr); sqlDisconnect(&conn); printf("Added %d extra columns to %d rows\n", extraCount, rowCount); } struct clonePos *loadClonePos(char *db, struct hash *clonePosHash) /* Load up clonePos list/hash from database table. */ { struct sqlConnection *conn = sqlConnect(db); struct sqlResult *sr; char **row; char name[128]; struct clonePos *el, *list = NULL; sr = sqlGetResult(conn, NOSQLINJ "select * from clonePos"); while ((row = sqlNextRow(sr)) != NULL) { el = clonePosLoad(row); strcpy(name, el->name); chopSuffix(name); hashAdd(clonePosHash, name, el); slAddHead(&list,el); } sqlFreeResult(&sr); sqlDisconnect(&conn); slReverse(&list); printf("Loaded %d clonePos from %s\n", slCount(list), db); return list; } void convertOne(struct bedExt *bed, struct hash *clonePosHash) /* Convert a single bed if possible. */ { int bestScore = 0, score; struct psl *psl, *bestPsl = NULL; int milliBad; struct clonePos *clonePos; /* Find best psl in list. */ for (psl = bed->pslList; psl != NULL; psl = psl->next) { score = psl->match + psl->repMatch; if (score < round(0.80*psl->qSize)) continue; if ((milliBad = pslCalcMilliBad(psl, FALSE)) > 30) continue; score = round( 0.02*(50-milliBad)*score); clonePos = hashFindVal(clonePosHash, bed->oldClone); if (clonePos != NULL) { if (sameString(clonePos->chrom, psl->tName)) { if (rangeIntersection(psl->tStart, psl->tEnd, clonePos->chromStart, clonePos->chromEnd) > 0) score += 100; } } if (score > bestScore) { bestScore = score; bestPsl = psl; } } if (bestPsl) { bed->converted = TRUE; } } void convertList(struct bedExt *bedList, struct hash *clonePosHash) /* Convert list to new coordinates if possible. */ { struct bedExt *bed; int convertCount = 0; int totalCount = 0; for (bed = bedList; bed != NULL; bed = bed->next) if (bed->extraWords && bed->pslList) { convertOne(bed, clonePosHash); ++totalCount; if (bed->converted) ++convertCount; } printf("%d of %d converted\n", convertCount, totalCount); } void bedUp(char *oldDb, char *oldTable, char *newDb, char *tableFile, char *pslFile, char *missing) /* bedUp - Load bed submissions after conversion back into new database.. */ { struct bedExt *bedList = NULL; struct hash *bedHash = newHash(0); struct hash *chromHash = newHash(5); struct hash *cloneHash = newHash(0); struct hash *clonePosHash = newHash(0); // struct clonePos *clonePosList = NULL; bedList = loadTable(tableFile, bedHash, chromHash, cloneHash); printf("Loaded %d items from %s\n", slCount(bedList), tableFile); addPsls(pslFile, oldDb, bedHash); addOther(oldDb, oldTable, bedHash); // clonePosList = loadClonePos(newDb, clonePosHash); // answer is returned in clonePosHash (void) loadClonePos(newDb, clonePosHash); // ignore returned has pointer convertList(bedList, clonePosHash); } int main(int argc, char *argv[]) /* Process command line. */ { if (argc != 7) usage(); bedUp(argv[1], argv[2], argv[3], argv[4], argv[5], argv[6]); return 0; }