python for molecular biology and bioinformatics

Open Source Free Python CGI Scripts for Molecular Biology and Bioinformatics

The Bio-Web >  Python CGI Scripts

Here are some Python and Biopython related scripts and resouces - Free, Open Source Python CGI Scripts

The Bio-Web Python CGI Scripts

The source code of most projects is freely available. If you use significant parts of this code for your own projects please give proper credit.

  • The OLIGO LOCALIZER
    Localizes an oligonucleotide on a DNA sequence. Supports IUPAC ambiguous DNA alphabet.
    Source code

  • High-Throughput Interaction Data Handler
    A multi-tools utility to handle data matrices, with a focus on high throughput protein-protein interaction data. Can of be used with any kind of data matrix, provided the File Format specification are met. Includes the GRAPHER tool, that draws a customizable visual representation of input matrices. The data handler is under development and should be regarded as beta software.

  • DNA/Protein sequence cleaner
    Allows the easy cleaning (removal of unwanted spaces, slashes, numbers etc..) of sequences. Tipically useful when retrieving sequences from online databases. Also allows custom numbering of the input sequence.
    Source code

  • The DNA/Protein sequence randomizer
    Basically this is an interface to the Python "random" module. Custom number of iterations allowed. Optionally cleans the input sequence with the sequence cleaner before randomization. Optionally formats the output sequence.
    Source code

  • The DNA sequence Reverse Complement Tool
    You can reverse, complement or reverse-complement your sequence. The sequence is cleaned by default from non-GATC characters. Support for ambiguous DNA characters (IUPAC) is forthcoming.
    Source code

  • A Simple Python GuestBook script
    A basic python cgi script that can turn any html page in a guestbook where visitors can leave their own comments.
    Python GuestBook Source Code
    Download the Python GuestBook, sample html file and instructions as a zip file

    (Bio)Python Links

    The Python Official Home Page

    The BioPython Official Home Page

    Instant Hacking: A simple "Getting Started" Python Tutorial by Magnus Lie Hetland

    Writing CGI Programs in Python, by Preston Landers

    Introduction to Programming using Python by the Pasteur Institute in Paris Mainly designed for Biologists. Teaches programming from scratch, aimed at non programmers.

    Regular Expression HOWTO This document is an introductory tutorial to using regular expressions in Python with the re module. It provides a gentler introduction than the corresponding section in the official Python Library Reference.

    ug's HTML & Python CGI pages: Forms Very handy reference for writing forms for python scripts

    Introduction to Event-Driven Programming A short, general and clear introduction to events-driven programming

    Thinking in Tkinter Excellent basic tutorial for Tkinter, a module that allows the construction of grafical interfaces for your python scripts

    P-c Regex Builder A nice web-based tool for building regular expressions. Although it is a Perl tool, it can be handy for writing python expressions aswell. A software written by Mohd Yunus bin Sharum

    An introduction to style sheets Most important aspects covered from scratch