parse_imgt_fasta: Extract gene names from a reference FASTA
In TCRconvertR: Convert TCR Gene Names
parse_imgt_fasta R Documentation
Extract gene names from a reference FASTA
Description
parse_imgt_fasta() extracts the second element from a "|"-delimited FASTA
header, which will be the gene name for IMGT reference FASTAs.
Usage
parse_imgt_fasta(infile)
Arguments
infile
A string, the path to FASTA file.
Value
A character vector of gene names.
Examples
# Given a FASTA file containing this header:
# >SomeText|TRBV29-1*01|MoreText|
# >SomeText|TRBV29-1*02|MoreText|
# >SomeText|TRBV29/OR9-2*01|MoreText|
fasta <- get_example_path("fasta_dir/test_trbv.fa")
parse_imgt_fasta(fasta)
TCRconvertR documentation built on June 8, 2025, 10:43 a.m.
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| parse_imgt_fasta | R Documentation |
Extract gene names from a reference FASTA
Description
parse_imgt_fasta() extracts the second element from a "|"-delimited FASTA
header, which will be the gene name for IMGT reference FASTAs.
Usage
parse_imgt_fasta(infile)
Arguments
infile |
A string, the path to FASTA file. |
Value
A character vector of gene names.
Examples
# Given a FASTA file containing this header:
# >SomeText|TRBV29-1*01|MoreText|
# >SomeText|TRBV29-1*02|MoreText|
# >SomeText|TRBV29/OR9-2*01|MoreText|
fasta <- get_example_path("fasta_dir/test_trbv.fa")
parse_imgt_fasta(fasta)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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