https://github.com/sgelias/abiorganizer
Extract and distribute ab1 files from Sanger DNA sequencing to folders of their respective owners.
https://github.com/sgelias/abiorganizer
ab1-organizer primer sanger-chromatograms sanger-sequencing
Last synced: about 1 year ago
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Extract and distribute ab1 files from Sanger DNA sequencing to folders of their respective owners.
- Host: GitHub
- URL: https://github.com/sgelias/abiorganizer
- Owner: sgelias
- Created: 2020-02-16T22:52:01.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-07-12T21:34:11.000Z (almost 6 years ago)
- Last Synced: 2025-03-14T04:21:54.175Z (about 1 year ago)
- Topics: ab1-organizer, primer, sanger-chromatograms, sanger-sequencing
- Language: Python
- Homepage:
- Size: 5.86 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# ab1_organizer
## Goal
Organize AB1 files by researches and primer-pairs.
## Instalation
For command line usage, simpleously use pip way:
```bash
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:
```bash
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.
```bash
./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!!