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Read the contigs in a Sequencher project

read_spf_contigs.Rd

Lists every contig in a Sequencher project file (.SPF) with its name, consensus sequence and the reads assembled into it.

Usage

read_spf_contigs(path, deleted = FALSE)

Arguments

path

Path to a Sequencher project file.

deleted

If TRUE, also return contigs deleted from the project whose records are still in the file.

Value

A list with one element per contig, named after the contigs. Each element is a list with

  • name: the contig's name in the project;

  • consensus: the saved consensus sequence as IUPAC codes, without gaps;

  • consensus_gapped: the same consensus with - for alignment columns where it has no base;

  • reads: the names of the reads in the contig, matching names() of the list read_spf() returns, so each copy of a read imported twice has its own name;

  • references: the names of any reference sequences in the contig;

  • unresolved: the number of members that could not be traced to a read or reference, for example reads deleted from the project;

  • deleted: whether the contig was deleted from the project, as for reads in read_spf().

Details

The consensus is the one Sequencher saved with the project, so it reflects the reads and edits at the time the project was last saved; it is not recomputed from the reads. spf_format describes how contigs are stored. The position and orientation of each read within its contig are not read yet.

See also

read_spf(), spf_format

Examples

spf <- "project.SPF"
if (file.exists(spf)) {
  contigs <- read_spf_contigs(spf)
  names(contigs)
  lengths(lapply(contigs, `[[`, "reads"))
}