degap: Remove all gaps from a fasta file

In rgyoung6/MDOP: Molecular Data Organization for Publication Tools

Remove all gaps from a fasta file

Description

This function removes gaps from all sequences in the selected fasta file.

Usage

degap( target_dir, Seq_file)

Arguments

target_dir	A string with a path for a target file folder. ie. "C:/A_file"
Seq_file	A srting with the pat for the target file. ie. "C:/seqfile.fas"

Details

The function will operate with or without an argument in a Windows or Apple OS environment.

Value

There are no values returned and results of degap are printed to screen and are evident through the creation of a fasta file with no gaps.

Note

This function was created and tested using Ver. 3.5.1; R Core Team 2018 It was tested on the operating systems Windows 7 and 10, Mac OS Mojave Version 10.14.6 Aside from base functions for this R version no other packages were utilizied

Author(s)

Written by Rob Young and Jiaojia Yu at the University of Guelph in Ontario Canada, October 2019

References

https://github.com/HannerLab Young, R. G., Yu, J., Cote, Young, R. G., Yu, J., Cote, M. J., Hanner, R. H. (Submitted January 2020). The Molecular Data Organization for Publication (MDOP) R package to aid the upload of data to shared databases. Biodiversity Data Journal.

See Also

target_file_list() recursive_copy() max_packs() copy_by_list() degap() rank_seq() head_derep() seq_derep() multi_to_single_fasta()

rgyoung6/MDOP documentation built on March 14, 2024, 5:23 p.m.