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Module I · Chord

1.1 Tables and field meanings1.2 Produce and import comparisons1.3 Build the layers step by step1.4 Direction, curvature and clearance1.5 Filter and summarize links1.6 Full source-file workflow1.7 Complete chord showcase

Module II · Collinear

2.1 Reuse chord input tables2.2 Switch coordinates and add layers2.3 Routes, clearance and the ruler2.4 Compare CDS neighbourhoods2.5 Focus, anchors and segments2.6 Complete collinear showcase

Module III · Plasmid

3.1 DNA, annotations and 13 references3.2 From a circle to annotation layers3.3 Features, primers and restriction3.4 Thirteen plasmid references3.5 Complete plasmid cases

Consult as needed · Data and layers

Prepare tables and coordinatesImport and convert dataImport nucleotide and protein alignmentsProject protein intervals to genomic coordinatesFeatures, stacking and genomic decorationLabels and local placementQuantitative tracksMappings, scales, guides and themesSet values by sequence and strandCommon adjustments and grammarExport, preview and diagnostics

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Read one or more BLAST tabular output files into ribbon_data format

On this page

• Usage
• Arguments
• Value
• Details
• See also
• Examples

Both file and files accept literal path vectors or wildcard patterns. Repeated resolved paths are read once, in first-occurrence order. Standard -outfmt 6 and -outfmt 7 use the default 12 tabular fields; the historical extended 17-column format is optional. Omitting -outfmt entirely produces pairwise text, which this tabular reader does not parse.

Usage

Code

read_blast(
  file = NULL,
  files = NULL,
  format = c("auto", "outfmt6", "outfmt7", "custom"),
  col_names = NULL,
  comment = "#",
  source_file = FALSE,
  ...
)

Arguments

file

Optional path vector or glob patterns; read before files.

files

Optional character vector of BLAST tabular output files (literal paths and/or wildcard patterns). All matched files are read and combined into one data.frame.

format

Character. "auto" (default) detects the column layout from the file; "outfmt6" requires the standard 12-column layout, "outfmt7" parses its # Fields: declaration, and "custom" requires col_names.

col_names

Optional character vector naming the columns in the file, used with format = "custom" or to override auto-detection.

comment

Character comment character, default "#" (BLAST outfmt 7 header lines start with #).

source_file

Logical. Add a .source_file column when reading one or more files, default FALSE.

...

Additional arguments passed to utils::read.table() (e.g. na.strings).

Value

A data.frame with the required ribbon columns first (qaccver, saccver, qstart, qend, sstart, send) followed by any preserved optional columns. A ggchord_import attribute records files, per-file output row counts and the one-based inclusive coordinate convention.

Details

The reader also parses BLASTp tabular output. It preserves the producer's numeric endpoints and does not infer or convert amino-acid/nucleotide units. Protein intervals require an explicit CDS projection before genomic plotting; reading a protein HSP does not establish an ungapped nucleotide correspondence. See project_ggchord_features() and project_ggchord_links().

See also

ggchord_data_contract

Examples

Code

if (FALSE) { # \dontrun{
library(dplyr)
# Standard 12-column records; requires the source checkout or tutorial input bundle.
source <- read_blast("examples/blastn-standard/MT108731.1__MT118296.1.tsv")
links <- source |>
  select(qaccver, saccver, qstart, qend, sstart, send)
} # }