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/protein/spLoadRankProp/spLoadRankProp.c src/hg/protein/spLoadRankProp/spLoadRankProp.c index e291e9b..7c672cb 100644 --- src/hg/protein/spLoadRankProp/spLoadRankProp.c +++ src/hg/protein/spLoadRankProp/spLoadRankProp.c @@ -1,190 +1,190 @@ /* spLoadRankProp - load rankProp table */ /* 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 "jksql.h" #include "hdb.h" #include "spMapper.h" #include "rankProp.h" #include "rankPropProt.h" #include "linefile.h" #include "hgRelate.h" #include "verbose.h" #include "obscure.h" /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"append", OPTION_BOOLEAN}, {"keep", OPTION_BOOLEAN}, {"noLoad", OPTION_BOOLEAN}, {"noMapFile", OPTION_STRING}, {"unirefFile", OPTION_STRING}, {NULL, 0} }; boolean gAppend = FALSE; /* append to table? */ boolean gKeep = FALSE; /* keep tab file */ boolean gLoad = TRUE; /* load databases */ char *gNoMapFile = NULL; /* output dropped sp ids to this file */ void usage() /* Explain usage and exit. */ { errAbort( "spLoadRankProp - load swissprot rankProp table.\n" "usage:\n" " spLoadRankProp database table rankPropFile\n" "Options:\n" " -unirefFile=tab - tab-separated file containing uniref information.\n" " If specified, used to map accessions to known genes associated with\n" " all proteins in a uniref entry.\n" " -append - append to the table instead of recreating it\n" " -keep - keep tab file used to load database\n" " -noLoad - don't load database, implies -keep\n" " -noMapFile=file - write list of swissprots or uniref ids that couldn't\n" " be mapped. First column is id, second column is R if it wasn't found\n" " in uniref, or K if it couldn't be associated with a known gene\n" " -verbose=n - n >= 3 lists mappings\n" "\n" "Load a file in the format:\n" " prot1Acc prot2Acc ranking eVal12 eVal21\n" "these will be converted to known gene ids\n" "\n" ); } char createString[] = "CREATE TABLE %s (\n" " query varchar(255) not null, # known genes id of query protein\n" " target varchar(255) not null, # known genes id of target protein\n" " score float not null, # rankp score\n" " #Indices\n" " INDEX(query(12))\n" ");\n"; void processRow(char **row, struct spMapper *mapper, int *zeroScoreCntPtr) /* Parse and process on row of a rankProp file, converting ids to known gene * ids. Only save if score is greater than zero */ { struct rankPropProt rpRec; rankPropProtStaticLoad(row, &rpRec); if (rpRec.score == 0.0) { verbose(2, "zero score for %s <=> %s\n", rpRec.qSpId, rpRec.tSpId); (*zeroScoreCntPtr)++; } else { spMapperMapPair(mapper, rpRec.qSpId, rpRec.tSpId, rpRec.score); } } void outputHit(FILE *tabFh, struct kgPair *kgPair) /* output rankProp record for a kg query/target pair */ { /* output both directions */ struct rankProp outRec; outRec.score = kgPair->score; outRec.query = kgPair->kg1Entry->id; outRec.target = kgPair->kg2Entry->id; rankPropTabOut(&outRec, tabFh); if (!sameString(kgPair->kg1Entry->id, kgPair->kg2Entry->id)) { outRec.query = kgPair->kg2Entry->id; outRec.target = kgPair->kg1Entry->id; rankPropTabOut(&outRec, tabFh); } } void outputHits(FILE *tabFh, struct spMapper *mapper) /* output save pairs and scores */ { struct kgPair *kgPair; for (kgPair = mapper->kgPairList; kgPair != NULL; kgPair = kgPair->next) outputHit(tabFh, kgPair); } void processRankProp(struct spMapper *mapper, char *rankPropFile, char *unirefFile) /* process rankProp file, loading into mapper */ { struct lineFile *inLf = lineFileOpen(rankPropFile, TRUE); char *row[RANKPROPPROT_NUM_COLS]; int zeroScoreCnt = 0; /* copy file, converting ids */ while (lineFileNextRowTab(inLf, row, RANKPROPPROT_NUM_COLS)) processRow(row, mapper, &zeroScoreCnt); lineFileClose(&inLf); if (mapper->qtNoUnirefMapCnt > 0) verbose(1, "%d pairs dropped due to missing uniref entries\n", mapper->qtNoUnirefMapCnt); if (mapper->noUnirefMapCnt) verbose(1, "%d missing uniref entries\n", mapper->noUnirefMapCnt); if (mapper->qtMapCnt > 0) verbose(1, "%d pairs dropped due to no swissprot to known genes mapping\n", mapper->qtMapCnt); if (mapper->noSpIdMapCnt > 0) verbose(1, "%d swissprot ids not mapped known genes\n", mapper->noSpIdMapCnt); if (zeroScoreCnt > 0) verbose(1, "%d entries dropped due to zero score\n", zeroScoreCnt); verbose(1, "%d pairs mapped\n", mapper->qtMapCnt); if (gNoMapFile != NULL) spMapperPrintNoMapInfo(mapper, gNoMapFile); } /* output rankProp record for a kg query/target pair */ void spLoadRankProp(char *database, char *table, char *rankPropFile, char *unirefFile) /* load a rankProp table */ { char query[1024]; struct sqlConnection *conn = sqlConnect(database); char *organism = hScientificName(database); struct spMapper *mapper = spMapperNew(conn, 1, unirefFile, organism); FILE *tabFh; processRankProp(mapper, rankPropFile, unirefFile); tabFh = hgCreateTabFile(".", table); outputHits(tabFh, mapper); if (gLoad) { sqlSafef(query, sizeof(query), createString, table); if (gAppend) sqlMaybeMakeTable(conn, table, query); else sqlRemakeTable(conn, table, query); } if (gLoad) hgLoadTabFileOpts(conn, ".", table, SQL_TAB_FILE_ON_SERVER, &tabFh); else carefulClose(&tabFh); if (!gKeep) hgRemoveTabFile(".", table); sqlDisconnect(&conn); spMapperFree(&mapper); freeMem(organism); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc != 4) usage("wrong # args"); gAppend = optionExists("append"); gKeep = optionExists("keep"); gLoad = !optionExists("noLoad"); gNoMapFile = optionVal("noMapFile", NULL); if (!gLoad) gKeep = TRUE; spLoadRankProp(argv[1], argv[2], argv[3], optionVal("unirefFile", NULL)); return 0; }