FastQ Mock Generator

This script generates a FastQ file with mock sequences assembled from a template sequence and an upstream sequence. It will need a FASTA file with the target sequence. It can be used with the parameters set up as commands or by pointing to a parameters.json file as shown in the example scripts. It will output a FastQ-like file with Phred scores attached.

The chosen template sequence comes from an RSV fusion inhibitor peptide derived from a 20-amino acid segment from HR2 (positions 497-516) ¹. The function that generates the Phred scores will create a smoothed noisy curve based on a center of maximal Phred score using the ASCII 33-126 offset.².

Figure 1: Smooth noisy Phred scores of a sample sequence with 500 bases. The value on the Y-axis represents the Phred score, and the X-axis denotes the position of the sequence (Index). Phred scores outside of the thresholds were clipped and substituted with their limit values.

Usage

Install requirements.txt using python>3.0. You can run the script using the following command:

python fastq_generator.py [OPTIONS]

Options

• --output_file: The output file. Default is output.fastq.
• --template_sequence: The template sequence in fasta format. If not provided, a default sequence is used.
• --with_parameters: Flag to indicate if parameters should be used. If not passed, default parameters are used.
• --upstream_sequence: The upstream sequence. Default is "GCCGGCCATGGCG".
• --left_margin: The left margin. Default is 15.
• --total_length: The total length. Default is 500.
• --number_of_sequences: The number of sequences. Default is 10.
• --center: The center. Default is 150.
• --min_val: The minimum value. Default is 40.
• --max_val: The maximum value. Default is 73.
• --std_dev: The standard deviation. Default is 75.
• --noise_level: The noise level. Default is 0.1.

Example

See the other example in the examples folder. Permissions are needed to run the scripts (chmod u+x).

python fastq_generator.py --output_file output.fastq --template_sequence template.fasta --with_parameters --upstream_sequence GCCGGCCATGGCG --left_margin 15 --total_length 500 --number_of_sequences 10 --center 150 --min_val 40 --max_val 73 --std_dev 75 --noise_level 0.1

References

Footnotes

1. Gaillard V, Galloux M, Garcin D, Eléouët JF, Le Goffic R, Larcher T, Rameix-Welti MA, Boukadiri A, Héritier J, Segura JM, Baechler E. A short double-stapled peptide inhibits respiratory syncytial virus entry and spreading. Antimicrobial agents and chemotherapy. 2017 Apr;61(4):10-128. DOI: 10.1128/AAC.02241-16 ↩

2. Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic acids research. 2010 Apr 1;38(6):1767-71. DOI: 10.1093/nar/gkp1137 ↩