Package: sangerseq-viewer
sangerseq_viewer Installation and User Manualsangerseq_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 packagespatchworklibandQUEEN. Both packages provide APIs for handling matplotlib subplots and GenBank files, respectivily. If you are interested in them, please see their documents. *Software dependencypython 3.8.0 or laterInstallationPlese execute the following commands.pip install patchworklib
pip install python-queen
pip install sangerseq_viewer --prefix=PREFIXPREFIXis the executable path of sangerseq_viewer.
By specifying--prefix, you can runsangerseq_viewerfrom your command line.Example codeExample command 1sangerseq_viewer -s example_data/puc19_spec_2xu6grna.gb -q example_data/ab1/Spec-2xU6gRNA-1.ab1 -o output/example1.png --dpi 200Output figure 1Example command 2sangerseq_viewer -s example_data/puc19_spec_2xu6grna.gb -q example_data/ab1/Spec-2xU6gRNA-1.ab1 -o output/example2.png -l 200 --dpi 200Output figure 2Example command 3sangerseq_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 200Output figure 3Example command 4sangerseq_viewer -s example_data/puc19_spec_2xu6grna.gb -q example_data/ab1/ -o output/example4.png --dpi 200Output figure 4Example command 5sangerseq_viewer -s example_data/puc19_spec_2xu6grna.gb -q example_data/ab1/ -o output/example5.png -l 200 --dpi 200Output figure 5Example command 6sangerseq_viewer -s example_data/puc19_spec_2xu6grna.gb -q example_data/ab1/ -o output/example6.png -l 200 -rs 1700 -re 2100 --dpi 200Output figure 6UsageSYNOPSIS
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 usesanger_seqvieweras python module, please importsangerseq_viewer.sangerseq_viewerand useview_sanger()fucntion. It takes same parameters withsangerseq_viewercommand and returnsmatplotlib.figureobject.sangerseq_viewer.sangerseq_viewerprovides other useful functions such asgenerate_consensusseq()andab1_to_dict()for  handling ab1 file. I will add the document for them later.