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/getRna/getRna.c src/hg/getRna/getRna.c index 8786776..81ba169 100644 --- src/hg/getRna/getRna.c +++ src/hg/getRna/getRna.c @@ -1,296 +1,296 @@ /* getRna - get mrna sequences */ /* 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 "options.h" #include "hdb.h" #include "jksql.h" #include "genbank.h" #include "linefile.h" #include "fa.h" /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"cdsUpper", OPTION_BOOLEAN}, {"cdsUpperAll", OPTION_BOOLEAN}, {"inclVer", OPTION_BOOLEAN}, {"peptides", OPTION_BOOLEAN}, {"seqTbl", OPTION_STRING}, {"extFileTbl", OPTION_STRING}, {NULL, 0} }; /* command line options */ static boolean cdsUpper = FALSE; static boolean cdsUpperAll = FALSE; static boolean inclVer = FALSE; static boolean peptides = FALSE; char *seqTbl = NULL; char *extFileTbl = NULL; /* derived from command line, it clearer as -cdsUpperAll and -peptides defines * multiple behaviors */ boolean warnOnNoCds = FALSE; boolean skipNoCds = FALSE; static int errCnt = 0; static void usage() /* Explain usage and exit. */ { errAbort( "getRna - Get mrna for GenBank or RefSeq sequences found in a database\n" "usage:\n" " getRna [options] database accFile outfa\n" "\n" "Get mrna for all accessions in accFile, writing to a fasta file. If accession\n" " has a version, that version is returned or an error generated\n" "\n" "Options:\n" " -cdsUpper - lookup CDS and output it as upper case. If CDS annotation\n" " can't be obtained, the sequence is skipped with a warning.\n" " -cdsUpperAll - like -cdsUpper, except keep sequeneces without CDS\n" " -inclVer - include version with sequence id.\n" " -peptides - translate mRNAs to peptides\n" " -seqTbl=tbl - use this table instead of gbSeq and seq. Many other options don't work if this is used.\n" " -extFileTbl=tbl - use this table instead of gbExtFile and extFile\n" "\n"); } static void parseAccVersion(char* requestedAcc, char acc[GENBANK_ACC_BUFSZ], char ver[GENBANK_ACC_BUFSZ]) /* parse accession and optional version */ { char* verDot = strchr(requestedAcc, '.'); if (verDot != NULL) { genbankDropVer(acc, requestedAcc); safecpy(ver, GENBANK_ACC_BUFSZ, verDot+1); } else { safecpy(acc, GENBANK_ACC_BUFSZ, requestedAcc); ver[0] = '\0'; } } static struct dnaSeq* getSeq(struct sqlConnection *conn, char* acc) /* get sequence from fasta file */ { HGID seqId; char *faSeq = hGetSeqAndId(conn, acc, &seqId); if (faSeq == NULL) { fprintf(stderr, "%s\tsequence not in database\n", acc); errCnt++; return NULL; } return faFromMemText(faSeq); } static char *getCdsString(struct sqlConnection *conn, char *acc) /* get the CDS string for an accession, or null if not found */ { char query[256]; sqlSafef(query, sizeof(query), "SELECT cds.name FROM gbCdnaInfo,cds WHERE (gbCdnaInfo.acc = '%s') AND (gbCdnaInfo.cds != 0) AND (gbCdnaInfo.cds = cds.id)", acc); return sqlQuickString(conn, query); } static boolean getCds(struct sqlConnection *conn, char *acc, int mrnaLen, struct genbankCds *cds) /* get the CDS range for an mRNA, warning and return FALSE if can't obtain * CDS or it is longer than mRNA. */ { char *cdsStr = getCdsString(conn, acc); if (cdsStr == NULL) { if (warnOnNoCds) fprintf(stderr, "%s\tno CDS defined\n", acc); return FALSE; } if (!genbankCdsParse(cdsStr, cds)) { if (warnOnNoCds) fprintf(stderr, "%s\tcan't parse CDS: %s\n", acc, cdsStr); free(cdsStr); return FALSE; } if (cds->end > mrnaLen) { if (warnOnNoCds) fprintf(stderr, "%s\tCDS exceeds mRNA length: %s\n", acc, cdsStr); free(cdsStr); return FALSE; } free(cdsStr); return TRUE; } static void upperCaseCds(struct dnaSeq *dna, struct genbankCds *cds) /* uppercase the CDNS */ { tolowers(dna->dna); toUpperN(dna->dna+cds->start, (cds->end-cds->start)); } int getVersion(struct sqlConnection *conn, char *acc) /* get version for acc, or 0 if not found */ { char query[256]; sqlSafef(query, sizeof(query), "SELECT version FROM gbCdnaInfo WHERE (gbCdnaInfo.acc = '%s')", acc); return sqlQuickNum(conn, query); } static void processVersion(struct sqlConnection *conn, char acc[GENBANK_ACC_BUFSZ], char ver[GENBANK_ACC_BUFSZ]) /* If the acc has a version, check that the correct version was included. If * a version is requested in the fasta, update acc argument. */ { int dbVerNum = getVersion(conn, acc); char dbVerStr[32]; safef(dbVerStr, sizeof(dbVerStr), "%d", dbVerNum); if ((strlen(ver) > 0) && !sameString(dbVerStr, ver)) { fprintf(stderr, "%s.%s requested, database has version %s\n", acc, ver, dbVerStr); errCnt++; } if (inclVer) { char accTmp[GENBANK_ACC_BUFSZ]; safef(accTmp, sizeof(accTmp), "%s.%d", acc, dbVerNum); safecpy(acc, GENBANK_ACC_BUFSZ, accTmp); } } static void writePeptide(FILE *outFa, char *acc, struct dnaSeq *dna, struct genbankCds *cds) /* translate the sequence to a peptide and output */ { char *pep = needMem(dna->size); /* more than needed */ char hold = dna->dna[cds->end]; dna->dna[cds->end] = '\0'; dnaTranslateSome(dna->dna+cds->start, pep, dna->size); dna->dna[cds->end] = hold; faWriteNext(outFa, acc, pep, strlen(pep)); freeMem(pep); } static void getAccMrna(char *requestedAcc, struct sqlConnection *conn, FILE *outFa) /* get mrna for an accession */ { char acc[GENBANK_ACC_BUFSZ]; char ver[GENBANK_ACC_BUFSZ]; boolean cdsOk = TRUE; struct genbankCds cds; parseAccVersion(requestedAcc, acc, ver); struct dnaSeq *dna = getSeq(conn, acc); if (dna == NULL) return; if (cdsUpper || peptides) { cdsOk = getCds(conn, acc, dna->size, &cds); if ((!cdsOk) && skipNoCds) { dnaSeqFree(&dna); return; } } if (cdsOk && cdsUpper) upperCaseCds(dna, &cds); if (inclVer || (strlen(ver) > 0)) processVersion(conn, acc, ver); if (peptides) writePeptide(outFa, acc, dna, &cds); else faWriteNext(outFa, acc, dna->dna, dna->size); dnaSeqFree(&dna); } static void getAccSeqTable(char *acc, struct sqlConnection *conn, FILE *outFa) /* get mrna for an accession from a seqTable */ { struct dnaSeq *dna = hDnaSeqMustGetConn(conn, acc, seqTbl, extFileTbl); faWriteNext(outFa, acc, dna->dna, dna->size); dnaSeqFree(&dna); } static void getRna(char *database, char *accFile, char *outFaFile) /* obtain mrna for a list of accessions */ { struct sqlConnection *conn = sqlConnect(database); struct lineFile *accLf = lineFileOpen(accFile, TRUE); FILE *outFa = mustOpen(outFaFile, "w"); char *line; int lineSize; while (lineFileNext(accLf, &line, &lineSize)) { if (seqTbl == NULL) getAccMrna(trimSpaces(line), conn, outFa); else getAccSeqTable(trimSpaces(line), conn, outFa); } if (ferror(outFa)) errAbort("error writing %s", outFaFile); carefulClose(&outFa); lineFileClose(&accLf); sqlDisconnect(&conn); } int main(int argc, char *argv[]) /* Process command line. */ { char *database, *accFile, *outFaFile; optionInit(&argc, argv, optionSpecs); if (argc != 4) usage(); database = argv[1]; accFile = argv[2]; outFaFile = argv[3]; if ((optionExists("seqTbl") && !optionExists("extFileTbl")) || (!optionExists("seqTbl") && optionExists("extFileTbl"))) errAbort("must specified both or neither of -seqTbl and -extFileTbl"); seqTbl = optionVal("seqTbl", seqTbl); extFileTbl = optionVal("extFileTbl", extFileTbl); cdsUpper = optionExists("cdsUpper"); cdsUpperAll = optionExists("cdsUpperAll"); if ((seqTbl != NULL) && (cdsUpper || cdsUpperAll)) errAbort("-cdsUpper and -cdsUpperAll not support with -seqTbl"); warnOnNoCds = !cdsUpperAll; skipNoCds = cdsUpper; if (cdsUpperAll) cdsUpper = TRUE; inclVer = optionExists("inclVer"); if ((seqTbl != NULL) && inclVer) errAbort("-inclVer not support with -seqTbl, version is always included"); peptides = optionExists("peptides"); if ((seqTbl != NULL) && peptides) errAbort("-peptides not support with -seqTbl"); if (peptides) skipNoCds = TRUE; if (peptides && (cdsUpper || cdsUpperAll)) errAbort("can't specify -peptides with -cdsUpper or -cdsUpperAll"); getRna(database, accFile, outFaFile); return (errCnt == 0) ? 0 : 1; }