R/global.R

In gggenomes: A Grammar of Graphics for Comparative Genomics

# Environment that holds various global variables and settings for gggenomes,
# such as known file formats. It is not exported and should not be directly
# manipulated by other packages.
gggenomes_global <- new.env(parent = emptyenv())

# Mapping of file formats, extensions, contexts, and parsers
#
# parser is a function name, like "read_tsv", ...
#
# context=NA defines fallback parser that is used if no parser is defined for
# the specific context
gggenomes_global$def_formats <- tibble::tribble(
  ~format, ~ext, ~context, ~parser,
  "ambigious", qc(txt, tsv, csv), NA, "read_ambigious",
  "fasta", qc(fa, fas, fasta, ffn, fna, faa), qc(seqs), qc(read_seq_len),
  "fai", qc(fai), qc(seqs), qc(read_fai),
  "gff3", qc(gff, gff3, gff2, gtf), qc(feats, seqs), qc(read_gff3, read_seq_len),
  "gbk", qc(gbk, gb, gbff, gpff), qc(feats, seqs), qc(read_gbk, read_seq_len),
  "bed", qc(bed), "feats", "read_bed",
  "blast", qc(m8, o6, o7), qc(feats, links), qc(read_blast, read_blast),
  "paf", qc(paf), qc(feats, links), qc(read_paf, read_paf),
  "alitv", qc(json), qc(feats, seqs, links),
  qc(read_alitv_genes, read_alitv_seqs, read_alitv_links),
  "vcf", qc(vcf), qc(feats), qc(read_vcf)
)

# Default column names for different formats
gggenomes_global$def_names <- list(
  gff3 = qc(seq_id, source, type, start, end, score, strand, phase, attributes),
  paf = qc(
    seq_id, length, start, end, strand, seq_id2, length2, start2, end2,
    map_match, map_length, map_quality
  ),
  blast = qc(
    seq_id, seq_id2, pident, length, mismatch, gapopen, start, end,
    start2, end2, evalue, bitscore
  ),
  bed = qc(seq_id, start, end, name, score, strand),
  fai = qc(seq_id, seq_desc, length),
  seq_len = qc(seq_id, seq_desc, length),
  vcf = qc(seq_id, start, feat_id, ref, alt, qual, filter, info, format)
)

gggenomes_global$def_types <- list(
  gff3 = "ccciicccc",
  paf = "ciiicciiiiid",
  blast = "ccdiiiiiiidd",
  bed = "ciicdc",
  fai = "ci---",
  seq_len = "cci",
  vcf = "cicccdccc"
)

utils::globalVariables(c(".", "seq_id", "bin_id", "start", "end"))