Microbesoft

This is the result of our participiation in Copenhacks 2018, created 7th-8th of April, 2018. The team members are:

• Christian
• Hannah
• Rebeca
• Valentijn

The purpose of this script is to make it easier to plot large datasets of gene sequences and add functionalities such as the consensus sequence.

Domain

http://microbesoft.net/

Prerequisites

Download and install the MAFFT alignment tool from source.

Navigate to the correct folder

cd ~/Microbesoft

Install python3 modules: with conda installed:

conda install -r etc/requirements.txt -y

or with pip:

pip install --file etc/requirements.txt

The script

python src/align.py -in input_file -c color_scheme -w char_width

The script takes the following arguments:

• -in --infile: the input fasta file
• -out --outfile [optional]: Outfile name. Default is infile with "align" added.
• -p --plotfile [optional]: Plot outfile name. Default is infile with ending .png.
• -c --colors [optional]: options are "all", "dna", "gbmr4", "sdm12", "hsdm17", "hp2", "murphy10", "alex6", "aromatic2", "hp_vs_aromatic", "cinema". Default is "cinema".
• -w --width [optional]: width in characters of the sequence. Default is 200.
• -same --same_length [optional]: flag to indicate that we try to create plot spanning multiple lines have the same length in each line.

Example

Run the script

python src/align.py  -in data/ebola_virus_reduced.fasta -c cinema -w 100