pyfastx

pyfastx provides memory-efficient random access to sequences in plain and gzip-compressed FASTA and FASTQ files, enabling on-disk index construction and direct subsequence retrieval without loading entire datasets into memory.

Key Features:

• Random Sequence Access: Retrieves full sequences and subsequences from plain and gzip-compressed FASTA and FASTQ files without prior decompression.
• Memory-efficient Indexing: Builds on-disk indices for large FASTA and FASTQ files without loading complete indices or datasets into memory.
• Compressed File Support: Performs random access into gzip-compressed FASTA and FASTQ files.
• Large-scale Dataset Handling: Handles FASTA and FASTQ files containing hundreds of millions of sequences.

Scientific Applications:

• Next-Generation Sequencing Data Processing: Enables rapid retrieval and subsequence extraction from large-scale genomic datasets stored in FASTA and FASTQ formats.

Methodology:

Implements a Python C extension to construct on-disk indices and perform direct byte-level random access within plain and gzip-compressed FASTA and FASTQ files, avoiding full dataset loading and minimizing memory usage during sequence retrieval.