PlamidInsertChecker

Code for SWbioDTP Data Science and Machine Learning module

This is an installable python package that can be used to interrogate DNA sequences for restriction enzyme cutting sites. It can produce:
i. a table of cut sites with useful information on the number of cut sites, the cut site locations, the enzyme cut overhang, and the commercial suppliers
ii. a figure showing the cut locations on a plasmid or linear section of DNA

Installation

Create a virtual environment using your favourite tool, clone the repsotiory to obtain the data and install the package using pip

virtualenv env_plasmidin
source env_plasmidin/bin/activate
git clone git@github.com:bmm514/PlamidInsertChecker.git
pip install plasmidin

Basic useage

1. Import required plasmidin Classes

from plasmidin.plasmidin import RSInserter
from plasmidin.plasmid_diagrams import PlasmidDrawer

2. Input fasta file or bio python Seq() for plasmid and insert

plasmid_seq = 'path/to/plasmid_fasta.fa'
plasmid_linear = False
insert_seq = 'path/to/insert_fasta.fa'
insert_linear = True
remove_ambiguous_enzymes = True

3. Run analysis on these to find restriction enzyme cut sites and show the enzymes of interest i.e. single cut enzymes

rsinserter = RSInserter(plasmid_seq, plasmid_linear, insert_seq, insert_linear, remove_ambiguous_enzymes)

rsinserter_XbaI_BamHI.shared_single_enzymes

4. Select from the list appropriate restriction enzymes to cut

plasmid_cut_enzymes = ('EnzymeA', 'EnzymeB')
insert_cut_enzymes = ('EnzymeA', 'EnzymeB')

5. Integrate insert sequence into plasmid sequence

rsinserter.integrate_seq(plasmid_cut_enzymes, insert_cut_enzymes)

6. Analyse the output restriction sites and save a table of the restriction sites present

integrated_table = '/path/to/restriction_enzymes.csv'

rsinserter.integrated_rsfinder.save_enzyme_table(integrated_table, delimiter = ',')

7. Create plasmid map for the integrated sequence

input_seq = rsinserter.integrated_rsfinder.input_seq
feature_info = rsinserter.integrated_rsfinder.feature_info
integrated_figure = '/path/to/integrated_restriction_map.pdf'

plasmid_drawer = PlasmidDrawer(input_seq, 'IntegratedSeq', feature_info)
plasmid_drawer.draw_gd_diagram(integrated_figure, 'circular', {'pagesize' : 'A4', 'circle_core' : 0.5, 'track_size' : 0.1})

Examples

See plasmidin_example.py for code to run and produce output from PlasmidInsertChecker:

python3 scripts/plasmidin_examples.py

This will use the example fasta files in data/ directory and produce output into plasmidin_output