FASTQ Pracitce

A project for practicing OOP in python.

A tool for reading through paired fastq files, compiling various statistics on them, and outputting those statstics in various ways (plots, tables, etc.).

Module Structure

• fastq_reader.py - tools for reading fastq files
• stats_collectors.py - classes for generating stats from fastq records, and tools for aggregating those stats over a whole file.
• stats_output.py - classes for outputting statistics results in different ways.
• run_analysis.py - class for running a whole analysis (read -> stats -> output) and a command line interface for using it.

Example

test/test_data/test_out.csv and test/test_data/test_plot.csv can be generated with:

python -m fastq_stats --seq AG TCC --quality --csv ./test/test_data/test_out.csv --hist ./test/test_data/test_plot.png ./test/test_data/test_R1.fastq ./test/test_data/test_R2.fastq

TODOs

• Figure out how/if to do test for outputs
• Figure out integration/application level testing