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.
Path to the FASTA file to be read. The file can remain gzipped.
Logical, whether to get gene names.
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
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.
Whether to display progress.
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:
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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
Biostrings is recommended; after reading the FASTA file into
R, the sequence names can be accessed by the
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
and proceed directly to
EC2gene with the output of this
A data frame with at least 2 columns:
gene for gene ID,
transcript for transcript ID, and optionally
gene_name for gene
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