tr2g_fasta: Get transcript and gene info from names in FASTA files
In lambdamoses/BUStoolsR: kallisto | bustools R utilities

tr2g_fasta

R Documentation

Get transcript and gene info from names in FASTA files

Description

FASTA files, such as those for cDNA and ncRNA from Ensembl, might have genome annotation information in the name of each sequence entry. This function extracts the transcript and gene IDs from such FASTA files.

Usage

tr2g_fasta(
  file,
  out_path = ".",
  write_tr2g = TRUE,
  use_gene_name = TRUE,
  use_transcript_version = TRUE,
  use_gene_version = TRUE,
  transcript_biotype_use = "all",
  gene_biotype_use = "all",
  chrs_only = TRUE,
  save_filtered = TRUE,
  compress_fa = FALSE,
  overwrite = FALSE
)

Arguments

`file`	Path to the FASTA file to be read. The file can remain gzipped.
`out_path`	Directory to save the outputs written to disk. If this directory does not exist, then it will be created. Defaults to the current working directory.
`write_tr2g`	Logical, whether to write tr2g to disk. If `TRUE`, then a file `tr2g.tsv` will be written into `out_path`.
`use_gene_name`	Logical, whether to get gene names.
`use_transcript_version`	Logical, whether to include version number in the Ensembl transcript ID. To decide whether to include transcript version number, check whether version numbers are included in the `transcripts.txt` in the `kallisto` output directory. If that file includes version numbers, then trannscript version numbers must be included here as well. If that file does not include version numbers, then transcript version numbers must not be included here.
`use_gene_version`	Logical, whether to include version number in the Ensembl gene ID. Unlike transcript version number, it's up to you whether to include gene version number.
`transcript_biotype_use`	Character, can be "all" or a vector of transcript biotypes to be used. Transcript biotypes aren't entirely the same as gene biotypes. For instance, in Ensembl annotation, `retained_intron` is a transcript biotype, but not a gene biotype. If "cellranger", then a warning will be given. See `data("ensembl_tx_biotypes")` for all available transcript biotypes from Ensembl.
`gene_biotype_use`	Character, can be "all", "cellranger", or a vector of gene biotypes to be used. If "cellranger", then the biotypes used by Cell Ranger's reference are used. See `data("cellranger_biotypes")` for gene biotypes the Cell Ranger reference uses. See `data("ensembl_gene_biotypes")` for all available gene biotypes from Ensembl. Note that gene biotypes and transcript biotypes are not always the same.
`chrs_only`	Logical, whether to include chromosomes only, for GTF and GFF files can contain annotations for scaffolds, which are not incorporated into chromosomes. This will also exclude haplotypes. Defaults to `TRUE`. Only applicable to species found in `genomeStyles()`.
`save_filtered`	If filtering for biotype and chromosomes, whether to save the filtered fasta file. If `TRUE`, the file will be `tx_filtered.fa` in `out_path`.
`compress_fa`	Logical, whether to compress the output fasta file. If `TRUE`, then the fasta file will be gzipped.
`overwrite`	Logical, whether to overwrite if files with names of outputs written to disk already exist.

Details

At present, this function only works with FASTA files from Ensembl, and uses regex to extract vertebrate Ensembl IDs. Sequence names should be formatted as follows:

ENST00000632684.1 cdna chromosome:GRCh38:7:142786213:142786224:1
gene:ENSG00000282431.1 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene
gene_symbol:TRBD1 description:T cell receptor beta diversity 1
[Source:HGNC Symbol;Acc:HGNC:12158]

If your FASTA file sequence names are formatted differently, then you must extract the transcript and gene IDs by some other means. The Bioconductor package Biostrings is recommended; after reading the FASTA file into R, the sequence names can be accessed by the names function.

While normally, you should call sort_tr2g to sort the transcript IDs from the output of the tr2g_* family of functions, If the FASTA file supplied here is the same as the one used to build the kallisto index, then the transcript IDs in the output of this function are in the same order as in the kallisto index, so you can skip sort_tr2g and proceed directly to EC2gene with the output of this function.

Value

A data frame with at least 2 columns: gene for gene ID, transcript for transcript ID, and optionally gene_name for gene names.

Examples

toy_path <- system.file("testdata", package = "BUSpaRse")
file_use <- paste(toy_path, "fasta_test.fasta", sep = "/")
tr2g <- tr2g_fasta(file = file_use, save_filtered = FALSE, write_tr2g = FALSE)

lambdamoses/BUStoolsR documentation built on Aug. 1, 2024, 6:30 a.m.