Interleave

Interleave mate-pair FASTQ files
Using: Python, Biopython

Author: Inbar Ofer

  • Access to the GitHub repository may be provided upon request.

Overview

This program takes two mate-pair FASTQ files and interleaves them into a single FASTQ file. It uses the Biopython library to read and write FASTQ and FASTA files. Additionally, the program generates a log file that records the progress of the interleaving process, including a summary of the input arguments. The output file and log file paths can be customized using command line arguments.

Running interleaved.py

This program is run from the command line, but there are multiple ways to do so. Once within the /scripts/ directory, the program can be run in the following ways:

  • ./interleaved.py --pathInputR1 [Left FASTQ file] --pathInputR2 [Right FASTQ file]
  • python3 interleaved.py --pathInputR1 [Left FASTQ file] --pathInputR2 [Right FASTQ file]

Here are some optional arguments:

  • -o and --output specify the output file path (default is ../data/{currentDateTime}.interleaved.fasta)
  • --logFolder specifies the log file path (default is ../results/logs/)
  • --logBase specifies the base name of the log file (default is interleaved.py)
  • -h and --help show a help message with a description of the program and its arguments

Example

For example, running

python3 interleaved.py --pathInputR1 ../data/top24_Aip02.R1.fastq --pathInputR2 ../data/top24_Aip02.R1.fastq -o Aip02.interleaved.fasta

will create a new FASTA file called Aip02.interleaved.fasta in the ../results/interleaved directory. The log file will be created in the ../results/logs/ directory and will be named {currentDateTime}_interleaved.py.log.