Amplicon Suite Aggregator
Description
Aggregates results from AmpliconSuite-pipeline runs.
- Accepts compressed input files (
.tar.gz,.zip) of individual or grouped AmpliconSuite results, or plain directories. - Aggregates and packages results into a new
.tar.gzfile, along with an aggregated.csvand.htmlsummary. - The output
.tar.gzcan be directly uploaded to AmpliconRepository.org. - Supports batch sample renaming via a name map file.
- Can include auxiliary files alongside the upload; place them in a directory containing a file named
AUX_DIR.
Installation
Option 1 — pip
pip install AmpliconSuiteAggregator
Option 2 — Git clone
git clone https://github.com/AmpliconSuite/AmpliconSuiteAggregator.git
cd AmpliconSuiteAggregator
pip install -r requirements.txt
Dependencies
Python packages: pandas, requests
Usage
python src/AmpliconSuiteAggregator.py -flist <input_list.txt> -o <project_name> [options]
input_list.txt is a plain text file with one input path per line (.tar.gz, .zip, or directory).
Aggregation options
| Flag | Description |
|---|---|
-flist FILE |
Text file listing input paths, one per line |
--files PATH [PATH ...] |
Input files or directories directly on the command line |
-o NAME |
Output prefix / project name (required) |
--name_map FILE |
Two-column file: col 1 = current sample name, col 2 = replacement name. Applies a deep rename throughout all output files and tables. |
-c {Yes,No} |
Re-run Amplicon Classifier on inputs (Yes/No) |
--ref GENOME |
Reference genome: hg19, GRCh37, GRCh38, GRCh38_viral, or mm10 |
AmpliconRepository upload options
| Flag | Description |
|---|---|
-u EMAIL |
AmpliconRepository username (email). If provided, triggers upload after aggregation. |
--upload_only {Yes,No} |
Skip aggregation and upload an existing .tar.gz directly |
-s {prod,dev} |
Target server (prod for most users) |
Examples
Aggregate a set of results:
python src/AmpliconSuiteAggregator.py -flist input_list.txt -o MyProject
Aggregate and upload to AmpliconRepository:
python src/AmpliconSuiteAggregator.py -flist input_list.txt -o MyProject -u you@email.com -s prod
Upload an already-aggregated file without re-aggregating:
python src/AmpliconSuiteAggregator.py --files MyProject.tar.gz -o MyProject -u you@email.com --upload_only Yes -s prod
Input files
For a breakdown of which per-sample files make up a classification project — which are essential, which are strongly recommended, and the naming patterns the Aggregator expects — see INPUT_FILES.md.
Authors
- Jens Luebeck (main contact)
- Thorin Tabor
- Edwin Huang
Issues
Bug reports and feature requests: GitHub Issues
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Source Distribution
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