---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Wrangling - Rename Pgenerosa_v074 Files and Scaffolds
date: '2019-11-05 09:03'
tags:
  - jupyter notebook
  - Panopea generosa
  - geoduck
  - Pgenerosa_v074
categories:
  - 2019
  - Geoduck Genome Sequencing
---
Continuing to organizing files for a manuscript dealing with the geoduck genome assembly/annotation we've done, we decided to rename the files as well as rename the scaffolds, to make the naming consistent and a bit easier to read (both for humans and computers).

Currently, most of the GFF and BED files are named something like:

- Panopea-generosa-vv0.74.a4.rRNA.gff3

A couple of other files (like the assembly FastA) have names like this:

- Pgenerosa_v074.fa

The scaffolds within each of the files are named like so:

- PGA_scaffold18__69_contigs__length_27737463


We want the filenames to look like this:

- Panopea-generosa-v1.0

We want the scaffold names to look like this:

- Scaffold_01

I processed all of the necessary files and documented in the following Jupyter Notebook (GitHub):

- [20191105_swoose_pgen_v074_renaming.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20191105_swoose_pgen_v074_renaming.ipynb)

---

# RESULTS

Output folder:

- [20191105_swoose_pgen_v074_renaming/](https://gannet.fish.washington.edu/Atumefaciens/20191105_swoose_pgen_v074_renaming/)

Uploaded files to Gannet folder (linked above) and to the [Open Science Foundation repository for this project](https://osf.io/yem8n/).