/* WormDNA - stuff that finds C. elegans sequence data. * * This file is copyright 2000 Jim Kent, but license is hereby * granted for all use - public, private or commercial. */ #ifndef WORMDNA_H #define WORMDNA_H #ifndef DNAUTIL_H #include "dnautil.h" #endif #ifndef DNASEQ_H #include "dnaseq.h" #endif #ifndef NT4_H #include "nt4.h" #endif #ifndef GDF_H #include "gdf.h" #endif struct wormCdnaInfo /* Extra info stored in cDNA database other than string. */ { char *motherString; /* Holds memory for other strings. */ char *name; /* Name of cDNA. */ char *gene; /* Something like unc-1 */ char orientation; /* + or - (relative to gene transcription direction) */ char *product; /* Something like "cyclin-dependent kinase" */ int cdsStart, cdsEnd; /* Start and stop of coding region within cDNA. */ boolean knowStart, knowEnd; /* Start known? End known? */ boolean isEmbryonic; /* True if derived from embryo culture. */ boolean isAdult; /* True if derived from adult culture. */ boolean isMale; /* True if males only. */ boolean isHermaphrodite; /* True if hermaphrodites only. */ char *description; /* One line description. */ }; boolean wormCdnaInfo(char *name, struct wormCdnaInfo *retInfo); /* Get info about cDNA sequence. */ void wormFaCommentIntoInfo(char *faComment, struct wormCdnaInfo *retInfo); /* Process line from .fa file containing information about cDNA into binary * structure. */ void wormFreeCdnaInfo(struct wormCdnaInfo *ci); /* Free the mother string in the cdnaInfo. (The info structure itself normally isn't * dynamically allocated. */ boolean wormInfoForGene(char *orfName, struct wormCdnaInfo *retInfo); /* Return info if any on gene/ORF, or NULL if none exists. wormFreeCdnaInfo retInfo when done. */ boolean wormCdnaSeq(char *name, struct dnaSeq **retDna, struct wormCdnaInfo *retInfo); /* Get a single worm cDNA sequence. Optionally (if retInfo is non-null) get additional * info about the sequence. */ void wormCdnaUncache(); /* Get rid of any resources used caching or quickly accessing * worm cDNA */ /* Stuff for searching entire database of worm cDNA */ struct wormCdnaIterator { FILE *faFile; }; boolean wormSearchAllCdna(struct wormCdnaIterator **retSi); /* Set up to search entire database or worm cDNA */ void freeWormCdnaIterator(struct wormCdnaIterator **pIt); /* Free up iterator returned by wormSearchAllCdna() */ struct dnaSeq *nextWormCdna(struct wormCdnaIterator *it); /* Return next sequence in database */ boolean nextWormCdnaAndInfo(struct wormCdnaIterator *it, struct dnaSeq **retSeq, struct wormCdnaInfo *retInfo); /* Return next sequence and associated info from database. */ char *wormFeaturesDir(); /* Return the features directory. (Includes trailing slash.) */ char *wormChromDir(); /* Return the directory with the chromosomes. */ char *wormCdnaDir(); /* Return directory with cDNA data. */ char *wormSangerDir(); /* Return directory with Sanger specific gene predictions. */ char *wormGenieDir(); /* Return directory with Genie specific gene predictions. */ char *wormXenoDir(); /* Return directory with cross-species alignments. */ boolean wormIsGeneName(char *name); /* See if it looks like a worm gene name - that is * abc-12 * letters followed by a dash followed by a number. */ boolean wormIsOrfName(char *in); /* Check to see if the input is formatted correctly to be * an ORF. */ struct slName *wormGeneToOrfNames(char *name); /* Returns list of cosmid.N type ORF names that are known by abc-12 type name. */ char *wormGeneFirstOrfName(char *geneName); /* Return first ORF synonym to gene. */ boolean wormGeneForOrf(char *orfName, char *geneNameBuf, int bufSize); /* Look for gene type (unc-12 or something) synonym for cosmid.N name. */ boolean getWormGeneExonDna(char *name, DNA **retDna); /* get the exon sequence for a gene */ boolean getWormGeneDna(char *name, DNA **retDna, boolean upcExons); /* Get the DNA associated with a gene. Optionally upper case exons. */ void wormLoadNt4Genome(struct nt4Seq ***retNt4Seq, int *retNt4Count); /* Load up entire packed worm genome into memory. */ void wormFreeNt4Genome(struct nt4Seq ***pNt4Seq); /* Free up packed worm genome. */ int wormChromSize(char *chrom); /* Return size of worm chromosome. */ DNA *wormChromPart(char *chromId, int start, int size); /* Return part of a worm chromosome. */ DNA *wormChromPartExonsUpper(char *chromId, int start, int size); /* Return part of a worm chromosome with exons in upper case. */ void wormChromNames(char ***retNames, int *retNameCount); /* Get list of worm chromosome names. */ int wormChromIx(char *name); /* Return index of worm chromosome. */ char *wormChromForIx(int ix); /* Given ix, return worm chromosome official name. */ char *wormOfficialChromName(char *name); /* This returns a pointer to our official string for the chromosome name. * (This allows some routines to do directo pointer comparisons rather * than string comparisons.) */ boolean wormGeneRange(char *name, char **retChromId, char *retStrand, int *retStart, int *retEnd); /* Return chromosome position of a gene, ORF, nameless cluster, or cosmid. Returns * FALSE if no such gene/cluster. */ boolean wormParseChromRange(char *in, char **retChromId, int *retStart, int *retEnd); /* Chop up a string representation of a range within a chromosome and put the * pieces into the return variables. Return FALSE if it isn't formatted right. */ boolean wormIsChromRange(char *in); /* Check to see if the input is formatted correctly to be * a range of a chromosome. */ void wormClipRangeToChrom(char *chrom, int *pStart, int *pEnd); /* Make sure that we stay inside chromosome. */ boolean wormIsNamelessCluster(char *name); /* Returns true if name is of correct format to be a nameless cluster. */ DNA *wormGetNamelessClusterDna(char *name); /* Get DNA associated with nameless cluster */ struct wormFeature /* This holds info on where something is in the genome. */ { struct wormFeature *next; char *chrom; /* One of names returned by */ int start, end; char typeByte; char name[1]; /* Allocated to fit. */ }; struct wormFeature *newWormFeature(char *name, char *chrom, int start, int end, char typeByte); /* Allocate a new feature. */ struct wormFeature *wormCdnasInRange(char *chromId, int start, int end); /* Get info on all cDNAs that overlap the range. */ struct wormFeature *wormGenesInRange(char *chromId, int start, int end); /* Get info on all genes that overlap the range. */ struct wormFeature *wormSomeGenesInRange(char *chromId, int start, int end, char *gdfDir); /* Get info on genes that overlap range in a particular set of gene predictions. */ struct wormFeature *wormCosmidsInRange(char *chromId, int start, int end); /* Get info on all cosmids that overlap the range. */ struct cdaAli *wormCdaAlisInRange(char *chromId, int start, int end); /* Return list of cdna alignments that overlap range. */ FILE *wormOpenGoodAli(); /* Opens good alignment file and reads signature. * (You can then cdaLoadOne() it.) */ struct wormGdfCache /* Helps managed fast indexed access to gene predictions. */ { char **pDir; struct snof *snof; FILE *file; }; extern struct wormGdfCache wormSangerGdfCache; extern struct wormGdfCache wormGenieGdfCache; struct gdfGene *wormGetGdfGene(char *name); /* Get the named gdfGene. */ struct gdfGene *wormGetSomeGdfGene(char *name, struct wormGdfCache *cache); /* Get a single gdfGene of given name. */ struct gdfGene *wormGetGdfGeneList(char *baseName, int baseNameSize); /* Get all gdfGenes that start with a given name. */ struct gdfGene *wormGetSomeGdfGeneList(char *baseName, int baseNameSize, struct wormGdfCache *cache); /* Get all gdfGenes that start with a given name. */ struct gdfGene *wormGdfGenesInRange(char *chrom, int start, int end, struct wormGdfCache *geneFinder); /* Get list of genes in range according to given gene finder. */ void wormUncacheGdf(); /* Free up resources associated with fast GDF access. */ void wormUncacheSomeGdf(struct wormGdfCache *cache); /* Uncache some gene prediction set. */ #endif /* WORMDNA_H */