533112afe2a2005e80cdb1f82904ea65032d4302 braney Sat Oct 2 11:37:34 2021 -0700 split hg/lib into two separate libaries, one only used by the cgis diff --git src/hg/cgilib/gencodeIntron.c src/hg/cgilib/gencodeIntron.c new file mode 100644 index 0000000..34ba349 --- /dev/null +++ src/hg/cgilib/gencodeIntron.c @@ -0,0 +1,226 @@ +/* gencodeIntron.c was originally generated by the autoSql program, which also + * generated gencodeIntron.h and gencodeIntron.sql. This module links the database and + * the RAM representation of objects. */ + +/* Copyright (C) 2014 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + +#include "common.h" +#include "linefile.h" +#include "dystring.h" +#include "jksql.h" +#include "gencodeIntron.h" + + +void gencodeIntronStaticLoad(char **row, struct gencodeIntron *ret) +/* Load a row from gencodeIntron table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->chrom = row[0]; +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = row[3]; +ret->status = row[4]; +strcpy(ret->strand, row[5]); +ret->transcript = row[6]; +ret->geneId = row[7]; +} + +struct gencodeIntron *gencodeIntronLoad(char **row) +/* Load a gencodeIntron from row fetched with select * from gencodeIntron + * from database. Dispose of this with gencodeIntronFree(). */ +{ +struct gencodeIntron *ret; + +AllocVar(ret); +ret->chrom = cloneString(row[0]); +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = cloneString(row[3]); +ret->status = cloneString(row[4]); +strcpy(ret->strand, row[5]); +ret->transcript = cloneString(row[6]); +ret->geneId = cloneString(row[7]); +return ret; +} + +struct gencodeIntron *gencodeIntronLoadAll(char *fileName) +/* Load all gencodeIntron from a whitespace-separated file. + * Dispose of this with gencodeIntronFreeList(). */ +{ +struct gencodeIntron *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[8]; + +while (lineFileRow(lf, row)) + { + el = gencodeIntronLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct gencodeIntron *gencodeIntronLoadAllByChar(char *fileName, char chopper) +/* Load all gencodeIntron from a chopper separated file. + * Dispose of this with gencodeIntronFreeList(). */ +{ +struct gencodeIntron *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[8]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = gencodeIntronLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct gencodeIntron *gencodeIntronLoadByQuery(struct sqlConnection *conn, char *query, int rowOffset) +/* Load all gencodeIntron from table that satisfy the query given. + * Where query is of the form 'select * from example where something=something' + * or 'select example.* from example, anotherTable where example.something = + * anotherTable.something'. + * Dispose of this with gencodeIntronFreeList(). */ +{ +struct gencodeIntron *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = gencodeIntronLoad(row+rowOffset); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void gencodeIntronSaveToDb(struct sqlConnection *conn, struct gencodeIntron *el, char *tableName, int updateSize) +/* Save gencodeIntron as a row to the table specified by tableName. + * As blob fields may be arbitrary size updateSize specifies the approx size + * of a string that would contain the entire query. Arrays of native types are + * converted to comma separated strings and loaded as such, User defined types are + * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */ +{ +struct dyString *update = newDyString(updateSize); +sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s','%s','%s','%s','%s')", + tableName, el->chrom, el->chromStart, el->chromEnd, el->name, el->status, el->strand, el->transcript, el->geneId); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + + +struct gencodeIntron *gencodeIntronCommaIn(char **pS, struct gencodeIntron *ret) +/* Create a gencodeIntron out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new gencodeIntron */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->chrom = sqlStringComma(&s); +ret->chromStart = sqlUnsignedComma(&s); +ret->chromEnd = sqlUnsignedComma(&s); +ret->name = sqlStringComma(&s); +ret->status = sqlStringComma(&s); +sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); +ret->transcript = sqlStringComma(&s); +ret->geneId = sqlStringComma(&s); +*pS = s; +return ret; +} + +void gencodeIntronFree(struct gencodeIntron **pEl) +/* Free a single dynamically allocated gencodeIntron such as created + * with gencodeIntronLoad(). */ +{ +struct gencodeIntron *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freeMem(el->status); +freeMem(el->transcript); +freeMem(el->geneId); +freez(pEl); +} + +void gencodeIntronFreeList(struct gencodeIntron **pList) +/* Free a list of dynamically allocated gencodeIntron's */ +{ +struct gencodeIntron *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + gencodeIntronFree(&el); + } +*pList = NULL; +} + +void gencodeIntronOutput(struct gencodeIntron *el, FILE *f, char sep, char lastSep) +/* Print out gencodeIntron. Separate fields with sep. Follow last field with lastSep. */ +{ +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->chrom); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->chromStart); +fputc(sep,f); +fprintf(f, "%u", el->chromEnd); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->name); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->status); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->strand); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->transcript); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->geneId); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ + +void gencodeIntronTableCreate(struct sqlConnection *conn, char *tableName, int indexSize) +/* Create a gencodeIntron table with the given name */ +{ +char *createString = +"CREATE TABLE %s (\n" +" chrom varchar(255) not null, # Chromosome\n" +" chromStart int unsigned not null, # Start position in chromosome\n" +" chromEnd int unsigned not null, # End position in chromosome\n" +" name varchar(255) not null, # Intron ID\n" +" status enum('not_tested', 'RT_positive','RT_negative','RT_wrong_junction','RT_submitted', 'RACE_validated'), # Status\n" +" strand char(1) not null, # + or -\n" +" transcript varchar(255) not null, # Transcript ID from GTF\n" +" geneId varchar(255) not null, # Gene ID from GTF\n" +" INDEX(chrom(%d),chromStart),\n" +" INDEX(chrom(%d),chromEnd)\n" +")\n"; +struct dyString *dy = newDyString(1024); +sqlDyStringPrintf(dy, createString, tableName, indexSize, indexSize, indexSize); +sqlRemakeTable(conn, tableName, dy->string); +dyStringFree(&dy); +} +