GTF/GFF to FASTA conversion

convert the transcript annotation to transcriptome assembly as FASTA file.

Usage

annotation_to_fasta(isoform_annotation, genome_fa, outfile, extract_fn)

Arguments

isoform_annotation

Path to the annotation file (GTF/GFF3)

genome_fa

The file path to genome fasta file.

outfile

The file path to the output FASTA file.

extract_fn

(optional) Function to extract a GRangesList object E.g. function(grl){GenomicFeatures::cdsBy(grl, by="tx")}

Value

This does not return anything. A FASTA file will be created at the specified location.

Examples

fasta <- tempfile()
annotation_to_fasta(system.file("extdata", "rps24.gtf.gz", package = "FLAMES"), system.file("extdata", "rps24.fa.gz", package = "FLAMES"), fasta)
cat(readChar(fasta, 1e3))
#> >ENSMUST00000169826.2
#> CTCTTTTCCTCCTCTCCAGCTCCGGCGCCGTAGCCATCATGAATGACACAGTAACCATCCGGACCAGGAAGTTCATGACC
#> AACCGTCTGCTTCAGAGGAAACAGATGGTCATTGATGTCCTTCATCCTGGGAAGGCAACAGTACCAAAGACAGAAATTCG
#> GGAAAAGCTGGCCAAAATGTACAAAACCACACCAGATGTCATCTTTGTATTTGGATTCAGAACCCACTTCGGTGGTGGCA
#> AGACCACTGGCTTTGGCATGATCTATGATTCTTTAGATTATGCAAAGAAGAATGAGCCTAAACACAGACTGGCAAGACAT
#> GGCCTTTATGAGAAGAAAAAGACCTCCCGAAAACAGCGAAAGGAACGCAAGAACAGAATGAAGAAGGTCAGGGGCACGGC
#> GAAGGCCAATGTTGGTGCTGGCAAAAAGTGAGTGGAGATTGGATACAGCCAAAGGAGTAGATCTGCGGTGACTTGATGTT
#> TTGCTGTGATGTGCAGATTTCTGAGAGGACAAATAAACT
#> >ENSMUST00000223939.1
#> CTCTCCAGCTCCGGCGCCGTAGCCATCATGAATGACACAGTAACCATCCGGACCAGGAAGTTCATGACCAACCGTCTGCT
#> TCAGAGGAAACAGATGGTCATTGATGTCCTTCATCCTGGGAAGGCAACAGTACCAAAGACAGAAATTCGGGAAAAGCTGG
#> CCAAAATGTACAAAACCACACCAGATGTCATCTTTGTATTTGGATTCAGAACCCACTTCGGTGGTGGCAAGACCACTGGC
#> TTTGGCATGATCTATGATTCTTTAGATTATGCAAAGAAGAATGAGCCTAAACACAGACTGGCAAGACATGGCCTTTATGA
#> GAAGAAAAAGACCTCCCGAAAACAGCGAAAGGAACGCAAGAACAGAATGAAGAAGGTCAGGGGCACGGCGAAGGCCAATG
#> TTGGTGCTGGCAAAAAGGTATGGTT