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/lib/soTerm.c src/hg/lib/soTerm.c index 6629ff7..cb16b45 100644 --- src/hg/lib/soTerm.c +++ src/hg/lib/soTerm.c @@ -1,197 +1,197 @@ /* soTerm - Sequence Ontology terms that we use for compatibility with Ensembl & others. */ /* Copyright (C) 2014 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 "dystring.h" #include "soTerm.h" #define SO_PREFIX "SO:" #define MISO_URL_BASE "http://www.sequenceontology.org/browser/current_svn/term/" struct soStringToId // Map SO term string name to int ID { char *term; // string name for term, e.g. "stop_lost" enum soTerm id; // integer ID for term, e.g. 1578 for "SO:0001578" }; static struct soStringToId soStringToId[] = { { "unknown", soUnknown }, { "frameshift", frameshift }, { "regulatory_region_variant", regulatory_region_variant }, { "stop_retained_variant", stop_retained_variant }, { "exon_loss_variant", exon_loss_variant }, { "splice_acceptor_variant", splice_acceptor_variant }, { "splice_donor_variant", splice_donor_variant }, { "complex_transcript_variant", complex_transcript_variant }, { "stop_lost", stop_lost }, { "coding_sequence_variant", coding_sequence_variant }, { "initiator_codon_variant", initiator_codon_variant }, { "missense_variant", missense_variant }, { "stop_gained", stop_gained }, { "frameshift_variant", frameshift_variant }, { "terminator_codon_variant", terminator_codon_variant }, { "nc_transcript_variant", nc_transcript_variant }, { "mature_miRNA_variant", mature_miRNA_variant }, { "NMD_transcript_variant", NMD_transcript_variant }, { "UTR_variant", UTR_variant }, { "5_prime_UTR_variant", _5_prime_UTR_variant }, { "3_prime_UTR_variant", _3_prime_UTR_variant }, { "incomplete_terminal_codon_variant", incomplete_terminal_codon_variant }, { "intron_variant", intron_variant }, { "intergenic_variant", intergenic_variant }, { "splice_site_variant", splice_site_variant }, { "splice_region_variant", splice_region_variant }, { "upstream_gene_variant", upstream_gene_variant }, { "downstream_gene_variant", downstream_gene_variant }, { "TF_binding_site_variant", TF_binding_site_variant }, { "non_coding_transcript_exon_variant", non_coding_transcript_exon_variant }, { "protein_altering_variant", protein_altering_variant }, { "synonymous_variant", synonymous_variant }, { "inframe_indel", inframe_indel }, { "inframe_insertion", inframe_insertion }, { "inframe_deletion", inframe_deletion }, { "feature_variant", feature_variant }, { "transcript_ablation", transcript_ablation }, { "upstream_transcript_variant", upstream_transcript_variant }, { "downstream_transcript_variant", downstream_transcript_variant }, { "no_sequence_alteration", no_sequence_alteration }, { "genic_downstream_transcript_variant", genic_downstream_transcript_variant }, { "genic_upstream_transcript_variant", genic_upstream_transcript_variant }, { NULL, 0 } }; char *soTermToString(enum soTerm termNumber) /* Translate termNumber to its string equivalent; errAbort if not found. * Do not modify or free result. */ { int i; for (i = 0; soStringToId[i].term != NULL; i++) { if (termNumber == soStringToId[i].id) return soStringToId[i].term; } errAbort("soTermToString: don't recognize term %u", termNumber); return NULL; // never get here } int soTermStringToId(char *soTermStr) /* Translate soTermStr into its numeric ID. Return -1 if soTermStr is not recognized. */ { if (isEmpty(soTermStr)) return -1; int i; for (i = 0; soStringToId[i].term != NULL; i++) { if (sameString(soTermStr, soStringToId[i].term)) return soStringToId[i].id; } return -1; } enum soTerm soTermStringIdToId(char *soIdStr) /* Given a string like "SO:0001627", parse out the numeric ID and convert to enum soTerm. */ { int id = 0; if (startsWith(SO_PREFIX, soIdStr)) { char *numPart = soIdStr + strlen(SO_PREFIX); if (!isAllDigits(numPart)) errAbort("soTermStringToId: expected '"SO_PREFIX"' followed by a number, but got '%s'", soIdStr); else id = atoi(numPart); } else errAbort("soTermStringToId: expected string starting with '"SO_PREFIX"' but got '%s'", soIdStr); return (enum soTerm)id; } char *soTermToMisoLink(enum soTerm term) /* Return an HTML <a> link to the MISO browser page for term * (except if it's soUnknown, just return text not a link). */ { char *link = NULL; if (term == soUnknown) link = cloneString(soTermToString(term)); else { struct dyString *dy = dyStringCreate("<a href='" MISO_URL_BASE SO_PREFIX "%07d' " "target=_blank>%s</a>", term, soTermToString(term)); link = dyStringCannibalize(&dy); } return link; } // Ranking of functional impact, highest first, adapted from recommendations in // http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf : enum soTerm funcImpactOrder[] = { transcript_ablation, exon_loss_variant, frameshift_variant, frameshift, initiator_codon_variant, stop_gained, stop_lost, splice_acceptor_variant, splice_donor_variant, splice_site_variant, inframe_insertion, inframe_deletion, inframe_indel, missense_variant, splice_region_variant, incomplete_terminal_codon_variant, terminator_codon_variant, protein_altering_variant, synonymous_variant, stop_retained_variant, coding_sequence_variant, _5_prime_UTR_variant, _3_prime_UTR_variant, UTR_variant, complex_transcript_variant, // Moved nc above up/downstream for bigDbSnp coloring (nc is colored like UTR), // while Pablo et al's doc has it almost at the bottom.... nc_transcript_variant, genic_upstream_transcript_variant, upstream_transcript_variant, upstream_gene_variant, genic_downstream_transcript_variant, downstream_transcript_variant, downstream_gene_variant, TF_binding_site_variant, regulatory_region_variant, mature_miRNA_variant, feature_variant, intron_variant, intergenic_variant, non_coding_transcript_exon_variant, NMD_transcript_variant, no_sequence_alteration, soUnknown, }; INLINE int getFuncImpactRank(enum soTerm id) /* Return the index of id in a sequence ordered by descending functional impact. */ { int i; for (i = 0; i < ArraySize(funcImpactOrder); i++) if (id == funcImpactOrder[i]) return i; errAbort("soTermCmp: unrecognized soTerm SO:%d", id); return -1; } int soTermCmp(const void *a, const void *b) /* Compare two enum soTerms for sorting by descending order of functional impact. */ { enum soTerm id1 = *(enum soTerm *)a; enum soTerm id2 = *(enum soTerm *)b; int impact1 = getFuncImpactRank(id1); int impact2 = getFuncImpactRank(id2); return impact1 - impact2; }