Make a TxToGene object from transcriptome FASTA

Usage

makeTxToGeneFromFasta(file, ignoreVersion = FALSE)

Arguments

file: character(1). File path.
ignoreVersion: logical(1). Ignore identifier (e.g. transcript, gene) versions. When applicable, the identifier containing version numbers will be stored in txIdVersion and geneIdVersion, and the variants without versions will be stored in txId, txIdNoVersion, geneId, and geneIdNoVersion.

Value

TxToGene.

Details

RefSeq transcript FASTA (e.g. "GCF_000001405.39_GRCh38.p13_rna.fna.gz") doesn't contain gene identifiers, and is not supported.

Note

Updated 2024-01-02.

Examples

## Ensembl ====
## > file <- AcidBase::pasteUrl(
## >     "ftp.ensembl.org",
## >     "pub",
## >     "release-102",
## >     "fasta",
## >     "homo_sapiens",
## >     "cdna",
## >     "Homo_sapiens.GRCh38.cdna.all.fa.gz",
## >     protocol = "ftp"
## > )
## > t2g <- makeTxToGeneFromFasta(file)
## > print(t2g)

## GENCODE ====
## GRCh38:
## > file <- AcidBase::pasteUrl(
## >     "ftp.ebi.ac.uk",
## >     "pub",
## >     "databases",
## >     "gencode",
## >     "Gencode_human",
## >     "release_32",
## >     "gencode.v32.transcripts.fa.gz",
## >     protocol = "ftp"
## > )
## > t2g <- makeTxToGeneFromFasta(file)
## > print(t2g)
##
## GRCh37:
## > file <- AcidBase::pasteUrl(
## >     "ftp.ebi.ac.uk",
## >     "pub",
## >     "databases",
## >     "gencode",
## >     "Gencode_human",
## >     "release_44",
## >     "GRCh37_mapping",
## >     "gencode.v44lift37.transcripts.fa.gz",
## >     protocol = "ftp"
## > )
## > t2g <- makeTxToGeneFromFasta(file)
## > print(t2g)

## FlyBase ====
## > file <- AcidBase::pasteUrl(
## >     "ftp.flybase.net",
## >     "releases",
## >     "FB2019_05",
## >     "dmel_r6.30",
## >     "fasta",
## >     "dmel-all-transcript-r6.30.fasta.gz",
## >     protocol = "ftp"
## > )
## > t2g <- makeTxToGeneFromFasta(file)
## > print(t2g)

## WormBase ====
## > file <- AcidBase::pasteUrl(
## >     "ftp.wormbase.org",
## >     "pub",
## >     "wormbase",
## >     "releases",
## >     "WS272",
## >     "species",
## >     "c_elegans",
## >     "PRJNA13758",
## >     "c_elegans.PRJNA13758.WS272.mRNA_transcripts.fa.gz",
## >     protocol = "ftp"
## > )
## > t2g <- makeTxToGeneFromFasta(file)
## > print(t2g)