get_prts {surfaltr} | R Documentation

## Create fasta file containing amino acid sequences based on IDs

### Description

This function creates a fasta file with the transcript ID followed by the amino acid sequence for all given alternative transcripts and associated primary transcripts. The file is organized so that all transcripts from a gene are next to each other. The function also returns a final table containing the gene names, transcript IDs, APPRIS annotations, and amino acid sequences for each transcript

### Usage

    get_prts(aa_trans, temp = FALSE)

### Arguments

`aa_trans` | A data frame containing the gene names, transcript IDs, APPRIS annotations, UniProt Swissprot IDs, UniProt Swissprot isoform IDs, and UniProt TREMBL IDs for all transcripts.
`temp` | Boolean indicating if the fasta file should be deleted after the function finishes running or not. Recommended to always be set to FALSE.

### Value

A data frame containing the gene names, transcript IDs, APPRIS annotations, UniProt IDs, and protein sequences for each transcript.

### Note

This function also creates a fasta file containing the transcript IDs and associated amino acid sequences in the root directory.

[Package surfaltr version 1.0.0 Index]