0.16.6 documentation

Complete canonical API text; task articles explain the workflows. Tutorials

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Setup and learning paths

HomeInstall and prepare the environmentChoose your learning module

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

Learning map and reference

Articles and complete workflowsFunction referenceReproducible galleryFrequently asked questionsMigrate to the candidate APITerminology and design sourcesDevelopment status and changes

Read one or more FASTA files into seq_data format

On this page

• Usage
• Arguments
• Value
• See also
• Examples

file reads a single FASTA file; files reads multiple files at once and combines them. files accepts a character vector of literal paths and/or wildcard patterns (e.g. "examples/fasta/*.fna").

Usage

Code

read_fasta_lengths(
  file = NULL,
  files = NULL,
  header_delim = NULL,
  source_file = FALSE
)

Arguments

file

Optional path vector or glob patterns; read before files.

files

Optional character vector of FASTA files (literal paths and/or wildcard patterns). All matched files are read and combined.

header_delim

Optional character. When given, each header is split at every occurrence of this delimiter and only the first piece is kept.

source_file

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

Value

A data.frame with columns accver and length. A ggchord_import attribute records files and per-file output row counts.

See also

ggchord_data_contract

Examples

Code

if (FALSE) { # \dontrun{
library(dplyr)
# Requires the source checkout or tutorial input bundle.
source <- read_fasta_lengths("examples/fasta/MT108731.1.fna")
seqs <- source |>
  select(accver, length)
} # }