ab1_organizer

Goal

Organize AB1 files by researches and primer-pairs.

Instalation

For command line usage, simpleously use pip way:

pip install ab1_organizer

Usage

ab1_organizer receive two arguments on initialization: the results file from Macrogen sequencing (-f, --file argument) and the modified order table (-t, --table argument). The sequencing file consists of the raw zipfile (file-name.zip) containing all .ab1, .pdf, phd.1, and .txt files. The order file consists of a simple excel table containing Macrogen order specifications and containing standardized headers (see next section).

Standardized headers

Your table would contain almost four columns, named respectively:

• sampleName: The unique identifier of sample;
• primerName: The primer name. e.g. "CO3 F", or "ITS1 R";
• personInCharge: The name of a person or a project responsible for the sample processing;
• primerCombination: Underscore separated complementary primer names. As example, if some region are sequenced using the "ITS1-F" and "ITS1-R", the primerCombination would be "ITS1-F_ITS1-R".

At the terminal, run the code:

ab1_organizer.py -f ./path/to/zip/file -t ./path/to/order/table.xlsx

A new folder with the same name of the zip file will be created and all files will be organized by author and genomic marker respectively.

Feel free to add new features and contribute through pull requests. Be happy!!