sangerseq_viewer Installation and User Manual

sangerseq_viewer is a python package to automatically visualize Sanger sequencing results and the corresponding annotated sequence map.

Despite the fact that Sanger sequencing is one of the indispensable tasks in constructing and editing DNA sequences, there is no open-source software that provides an intuitive and understandable graphical representation of sequencing results. Some commercial GUI software (Snapgene, Geneious prime) fulfills this requirement. However, now that it is common to design and construct dozens or hundreds of DNA sequences, manually processing large numbers of Sanger sequencing results is a tedious and time-consuming task.

Here, I provide sangerseq_viewer that allow us to visulize sanger sequncing result with a simple command.

*sangerseq_viewer is depend on m packages patchworklib and QUEEN. Both packages provide APIs for handling matplotlib subplots and GenBank files, respectivily. If you are interested in them, please see their documents. *

Software dependency

• python 3.8.0 or later

Installation

Plese execute the following commands.

pip install patchworklib
pip install python-queen
pip install sangerseq_viewer --prefix=PREFIX

PREFIX is the executable path of sangerseq_viewer. By specifying --prefix, you can run sangerseq_viewer from your command line.

Example code

Example command 1 sangerseq_viewer -s example_data/puc19_spec_2xu6grna.gb -q example_data/ab1/Spec-2xU6gRNA-1.ab1 -o output/example1.png --dpi 200

Output figure 1

Example command 2 sangerseq_viewer -s example_data/puc19_spec_2xu6grna.gb -q example_data/ab1/Spec-2xU6gRNA-1.ab1 -o output/example2.png -l 200 --dpi 200

Output figure 2

Example command 3 sangerseq_viewer -s example_data/puc19_spec_2xu6grna.gb -q example_data/ab1/Spec-2xU6gRNA-1.ab1 -o output/example3.png-l 200 -rs 1700 -re 2100 --dpi 200

Output figure 3

Example command 4 sangerseq_viewer -s example_data/puc19_spec_2xu6grna.gb -q example_data/ab1/ -o output/example4.png --dpi 200

Output figure 4

Example command 5 sangerseq_viewer -s example_data/puc19_spec_2xu6grna.gb -q example_data/ab1/ -o output/example5.png -l 200 --dpi 200

Output figure 5

Example command 6

sangerseq_viewer -s example_data/puc19_spec_2xu6grna.gb -q example_data/ab1/ -o output/example6.png -l 200 -rs 1700 -re 2100 --dpi 200

Output figure 6

Usage

SYNOPSIS
sangerseq_viewer [-h] [-q QUERY] [-s SUBJECT] [-l LINEBREAK] [-o OUTPUT] [-rs START] [-re END] [-wq {True,False}] [-d DPI]

  -h, --help            
     show this help message and exit
  -q QUERY, --query QUERY
     Abi file path.
  -s SUBJECT, --subject SUBJECT
     Genbank file path.
  -l LINEBREAK, --linebreak LINEBREAK
     Sequence length for line break.
  -o OUTPUT, --output OUTPUT
     Output file path. The output image format can be specified by the filename extension.
  -rs START, --start START
     Start position of the subject sequence region to be visualized. 
  -re END, --end END    
     End position of the subject sequence region to be visualized.
  -wq {True,False}, --quality {True,False}
     If True, display bar plot representing Quality value at each nucleotide position.
  -d DPI, --dpi DPI     
     Resolution of the output image. If output format is pdf, the value is ignored.

If you want to use sanger_seqviewer as python module, please import sangerseq_viewer.sangerseq_viewer and use view_sanger() fucntion. It takes same parameters with sangerseq_viewer command and returns matplotlib.figure object.

sangerseq_viewer.sangerseq_viewer provides other useful functions such as generate_consensusseq() and ab1_to_dict() for handling ab1 file. I will add the document for them later.