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MiniBioKit

A mini Biochemistry toolkit developed in Python 3 with some degree of Python 2 compatibility.

Originally developed to provide some aid in primer design, it provide more functionalities that may eventually become a general purpose library.

Currently under active development.

Major modules:

  • BioChemTool: Collection of utilities to deal with different file formats

  • commonUtil: Utilities to define some data types for easier processing through other utils.

  • BioChemData:

  • Nucleotide: Provide functionalities for nucleotide sequence processing

  • Protein: Provide functionalities for peptide sequence processing

File Format Compatibility

The most commonly used format in this library is the so-called "PSV" file.

PSV file is a dialect of CSV that use Pipe "|" as the separator. As the pipe symbol does not commonly appear in data, it can save a lot of hassle when dealing with quotations and escape sequences.

The special point regarding the PSV processor here is that it would treat all lines starting with a pound/hash "#" symbol as comment. This design would allow users to include some comments as well as headers to the data without messing up with data.