Linux GUI app to codon optimize a directory with fasta files using taxonomy ids imported as a 1-column txt file (1 taxonomy id for each file)

Related tags

GUI Developmentcodon_optimize_cds_paired_with_taxids_singlefastas_gui
Overview

codon optimize cds paired with taxids singlefastas gui DOI

Linux GUI app to codon optimize a directory with fasta files using taxonomy ids imported as a 1-column txt file (1 taxonomy id for each file)

Depedences

  1. linux OS (tested on ubuntu 20.04 LTS)
  2. python 3.8.2 or later
  3. anaconda or miniconda
  4. Gooey conda install -c conda-forge gooey(if you get errors during installation or runtime try installing gtk sudo apt-get install libgtk-3-dev)
  5. biopython pip install biopython
  6. pandas pip install pandas
  7. dnachisel pip install dnachisel

linux desktop app installation

  1. open a linux text editor and edit in the python file the shebang line (to find where python is type in the terminal which python3)
  2. convert to executable with chmod +x codon_optimize_cds_paired_with_taxids_singlefastas_gui.py
  3. open a linux text editor and edit the PATHs in the .desktop file
  4. move the file to /usr/share/applications
  5. reboot your machine

Output

The output single-fasta files will have the same prefix as the input ones and as suffix the taxonomy id of the organism they are codon optimized for

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Releases(v2.0)

  • v2.0(Jan 13, 2022)

  • v1.0(Jan 9, 2022)

    Linux GUI app to codon optimize a directory with fasta files using taxonomy ids imported as a 1-column txt file (1 taxonomy id for each file). The output single-fasta files will have the same prefix as the input ones and as suffix the taxonomy id of the organism they are codon optimized for.

    Source code(tar.gz)
    Source code(zip)
Owner
Olga Tsiouri
Biochemist & Biotechnologist. PhD candidate at @plant_env, @uth.gr #bioinformatics, plant-fungal omics
Olga Tsiouri
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