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.

./190731FN-022/
├── person1
│   ├── ITS1-F_ITS1-R
│   │   ├── 01_ITS1-F.ab1
│   │   ├── 01_ITS1-F.pdf
│   │   ├── 01_ITS1-F.phd.1
│   │   ├── 01_ITS1-F.txt
│   │   ├── 01_ITS1-R.ab1
│   │   ├── 01_ITS1-R.pdf
│   │   ├── 01_ITS1-R.phd.1
│   │   ├── 01_ITS1-R.txt
├── person2
│   ├── ITS1-F_ITS1-R
│   │   ├── 01_ITS1-F.ab1
│   │   ├── 01_ITS1-F.pdf
│   │   ├── 01_ITS1-F.phd.1
│   │   ├── 01_ITS1-F.txt
│   │   ├── 01_ITS1-R.ab1
│   │   ├── 01_ITS1-R.pdf
│   │   ├── 01_ITS1-R.phd.1
│   │   ├── 01_ITS1-R.txt
...

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