retrieveseq
RetrieveSeq is a GUI application that performs batch download of how many gene sequences you wish from Ensembl database. Mind you: this application is still under development. Our goal is to increase its functions, as well as provide more database options.
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (9.7%) to scientific vocabulary
Repository
RetrieveSeq is a GUI application that performs batch download of how many gene sequences you wish from Ensembl database. Mind you: this application is still under development. Our goal is to increase its functions, as well as provide more database options.
Basic Info
Statistics
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
RetrieveSeq (beta) 1.1.1
RetrieveSeq is a GUI application that performs batch download of how many gene sequences you wish from Ensembl database. Mind you: this application is still under development. Our goal is to increase its functions, as well as provide more database options.
Dependencies
In order to properly run RetrieveSeq BETA, you need to have the following tools installed in your device: - Python3 - Pillow (Python3 library). To install Pillow, open the terminal and type:
$ sudo pip3 install Pillow
Running RetrieveSeq
Open the terminal in the application folder and type the following:
$ python3 main.py
Ps.: you might need to change permission before running:
$ chmod a+x main.py
Using RetrieveSeq
- Type or paste the gene symbols or gene ID separated by comma (anything else won't work) in the genes entry box.
- RetrieveSeq BETA only works with gene symbol or gene ID!
- In the next page, configure your output file(s).
- When downloading data via gene symbol, you can download selected genes for one species or more, just paste or type species separated by comma in the entry box. If you want to download genes for all species in the database, type "all" in the species entry box.
- A log file will be saved in the same directory you choose to save the genes. While running, RetrieveSeq BETA saves useful information in the log file (ex.: why determined gene can't be downloaded).
Cite this application
APA: Mello, A. C., & Matte, U. (2021). RetrieveSeq (Version v1.1.1-beta) [Computer software]. https://github.com/anamello/RetrieveSeq
BibTex: @software{AnaCarolinaRetrieveSeq_2021, author = {Mello, Ana Carolina and Matte, Ursula}, month = {12}, title = {{RetrieveSeq}}, url = {https://github.com/anamello/RetrieveSeq}, version = {v1.1.1-beta}, year = {2021} }
Owner
- Name: Ana Mello
- Login: anamello
- Kind: user
- Repositories: 1
- Profile: https://github.com/anamello
Hello! I've got a major in bioinformatics and I'm currently a phD student. I'll be posting some codes that are useful for me and maybe for you!
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Mello" given-names: "Ana Carolina" orcid: "https://orcid.org/0000-0002-5028-7682" - family-names: "Matte" given-names: "Ursula" orcid: "https://orcid.org/0000-0003-4977-6662" title: "RetrieveSeq" version: v1.1.1-beta date-released: 2021-12-14 url: "https://github.com/anamello/RetrieveSeq"