DEmultiplexing MOnitoring Report Tool
Project description
demort
evaluates demultiplexed fastq files by computing various metrics.
demort
is a python3 program.
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
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 |
--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.
For the main pipeline:
- Python3 (3.7 or higher)
- zlib development files
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