getFastaSeqFromFilePath: Genomic DNA sequence for one SeqID

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Genomic DNA sequence for one SeqID

Description

Get the genomic DNA nucleotide sequence for one chromosome from a file or folder

Usage

getFastaSeqFromFilePath(filePath, seqID, verbose = FALSE)

Arguments

filePath	complete path name to a FASTA file or a folder of FASTA files as a character string.
seqID	character string of one SeqID sequence identifier.
verbose	logical, show status of the search progress.

Details

A (hopefully easy) function to find and read the DNA sequence for any single chromosome. In the case of a small genome contained in a single file, this finds the named chromosome descriptor in the FASTA file, and returns that nucleotide sequence. In the case of very large genomes with separate files for each chromosome, this searches the given path for the appropriately named FASTA file. There are hardcoded assumptions that the file names and sequence descriptors in the FASTA file(s) correspond exacly with the SeqID terms in the SeqMap.

Value

one chromosome of DNA nucleotides, as a Biostrings DNAString, or NULL if the file/SeqID search fails.

Author(s)

Bob Morrison

See Also

loadFasta, for reading arbitray FASTA files. MapSets, for details on synchronizing SpeciesIDs, SeqIDs, and FASTA descriptors.

robertdouglasmorrison/DuffyTools documentation built on April 13, 2025, 8:51 p.m.