get_prts: Create fasta file containing amino acid sequences based on...

In EliLillyCo/surfaltr: Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

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.

EliLillyCo/surfaltr documentation built on May 3, 2022, 10:12 a.m.