https://github.com/pblischak/trim_nds
Trim N's and ?'s from the ends of nucleotide sequences
https://github.com/pblischak/trim_nds
Last synced: 26 days ago
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Trim N's and ?'s from the ends of nucleotide sequences
- Host: GitHub
- URL: https://github.com/pblischak/trim_nds
- Owner: pblischak
- Created: 2016-04-11T21:24:19.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2016-04-13T14:11:53.000Z (about 9 years ago)
- Last Synced: 2025-02-17T07:44:48.526Z (4 months ago)
- Language: R
- Size: 6.84 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# `trim_Nds`
**NOTE: I'm still testing this out, so use with caution. If you try it and it does not work, please consider filing and issue and I'll do my best to address it.**
`trim_Nds` is a simple R script for trimming N's and ?'s off the ends (but not the middle) of nucleotide sequences.
The input is a file of DNA sequences in FASTA format.
The script can be sourced into an R session to run the main function: `trim_Nds`. The method is not case sensitive, and prints all output in upper case letters.
## Installing dependencies
The script relies on the R package [**ape**](https://cran.r-project.org/web/packages/ape/index.html). You can install it using the normal `install.packages` function: `install.packages("ape")`.
## Running the script
The script can be used in an R session by simply calling `source` on the `trim_Nds.R` file. You can then use the `trim_Nds` function, which takes two arguments:
- **in_fasta_file**: the name of the input FASTA file with sequences to trim.
- **out_fasta_file**: the name of the FASTA file that trimmed sequences will be written to.
Running the following bit of code from within R should get the job done. I've also provided an example FASTA file that you can use to test the code ('input.fasta').
```r
# Source the file into an R session
source("trim_Nds.R")
# Then just run the `trim_Nds` function (don't forget quotes)
trim_Nds("input.fasta", "output.fasta")
```
You can also try a one-liner from the command line like this:
```bash
Rscript -e 'source("trim_Nds.R"); trim_Nds("input.fasta", "output.fasta")'
```