getFastaSeqFromFilePath: Genomic DNA sequence for one SeqID

Description Usage Arguments Details Value Author(s) See Also


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


getFastaSeqFromFilePath(filePath, seqID, verbose = FALSE)



complete path name to a FASTA file or a folder of FASTA files as a character string.


character string of one SeqID sequence identifier.


logical, show status of the search progress.


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.


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


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 Dec. 7, 2018, 8:02 a.m.