DEMORT
DEmultiplexing MOnitoring Report Tool. DEMORT evaluates demultiplexing fastq files by computing various metrics.
demort evaluates demultiplexed fastq files by computing various metrics.
demort is a python3 program.
INSTALLATION
First, install dependencies, then you can perform a basic installation or PyPI installation.
Dependencies
You need to install python 3.7 and depencies. Check version by typing on:
python3 --version
python3 depencies :
- argparse
- os
- gzip
- csv
- multiprocessing
- joblib
- biopython
- matplotlib
see INSTALL.sh for details about installation of python3 dependencies
Basic installation
Simply download the python script
wget https://raw.githubusercontent.com/Grelot/demort/master/src/demort.py
then execute it
python3 demort.py -h
PyPI installation
Install demort on your system using :
pip3 install demort
check installation :
demort.py -h
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
(process folders into a folder)
demort.py -d <(ls folder) \
-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 (e.g. folder_to_process.txt) |
--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
csvtable [foldername, filename, number of reads]
folder1,fqfileA,2686166
folder1,fqfileB,1223937
folder1,fqfileC,934242
folder2,fqfileD,1947607
folder2,fqfileE,1658147
folder3,fqfileF,1699691
folder3,fqfileG,1293436
folder3,fqfileH,1470963
-
pdfboxplot picture
SYSTEM REQUIREMENTS
Linux (64-bit and 32-bit with slightly limited functionality) and macOS (OS X) are supported.
For the main pipeline:
- Python3 (3.7 or higher)
- zlib development files
