Metadata-Version: 2.1
Name: demort
Version: 0.2.4
Summary: DEmultiplexing MOnitoring Report Tool
Home-page: https://github.com/Grelot/demort
Author: Pierre-Edouard GUERIN
Author-email: pierre-edouard.guerin@cefe.cnrs.fr
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
Requires-Dist: argparse
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: biopython
Requires-Dist: joblib

`demort` evaluates demultiplexed fastq files by computing various metrics.

# DEPENDENCIES

You need to install [python 3.7](https://www.python.org/download/releases/3.0/) and depencies. Check version by typing on:
```
python3 --version
```
**python3 depencies :**
* [joblib](https://joblib.readthedocs.io/en/latest/installing.html)
* [biopython](https://github.com/biopython/biopython)
* [matplotlib](https://matplotlib.org/3.1.1/faq/installing_faq.html)


# USAGE

`demort` check fastq files into specified folder(s) then count number of reads for each fastq files for each folder and finally return a summary `csv` table and a `pdf` boxplot picture.

(process a list of folder as a strings)
```
demort.py -d folder/folder1,folder/folder2,folder/folder3 \
 -t 8 \
 -p results.pdf \
 -o results.csv
```
(process a list of folder into a file)
```
demort.py -d example/folder_to_process.txt \
 -t 8 \
 -p results.pdf \
 -o results.csv
```

# COMMAND-LINE ARGUMENTS

| complete flag argument | short flag |Default value | Summary |
| --- | --- | --- | --- |
| `--inputFolder` | `-d` | NA |  a string of folderpath separated by coma `,` OR a file containing a list |
| `--threads` | `-t` | 1 | Number of available cores |
| `--output_pdf` | `-p` | NA | path of the file where to write a `pdf` boxplot picture |
| `--output_csv` | `-o` | NA | path of the file where to write a `csv` table |


# INPUT

```
folder/
├── folder1
│   ├── fqfileA.fq.gz
│   ├── fqfileB.fq.gz
│   └── fqfileC.fq.gz
├── folder2
│   ├── fqfileD.fq.gz
│   └── fqfileE.fq.gz
└── folder3
    ├── fqfileF.fq.gz
    ├── fqfileG.fq.gz
    └── fqfileH.fq.gz
```

# OUTPUTS

* summary `csv` table [foldername, filename, number of reads]
* `pdf` boxplot picture

# SYSTEM REQUIREMENTS

Linux (64-bit and 32-bit with slightly limited functionality) and macOS (OS X) are supported.


