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name: tabix-fasta description: "Guides agents using pysam for tabix compression, tabix indexing, indexed table fetches, BED/GTF/GFF/VCF row parser proxies, BGZF iteration, FASTA random access, FASTQ streaming, and parser or encoding data-format issues." disable-model-invocation: true metadata: disco-role: operating license: MIT

tabix-fasta

Use this sub-skill when a task involves pysam.TabixFile, tabix_compress, tabix_index, tabix_iterator, asTuple, asBed, asGTF, asGFF3, asVCF, FastaFile, legacy Fastafile, FastxFile, FastxRecord, or FASTQ quality streaming.

Read First

• references/api-reference.md for constructor signatures, fetch/index APIs, parser proxy contracts, and FASTA/FASTQ entry points.
• references/data-formats.md for tabix coordinate columns, BED/GTF/GFF/VCF parser fields, BGZF/index files, encodings, and FASTA/FASTQ assumptions.
• references/workflows.md for compression/index/fetch recipes, parser usage, BGZF iteration, FASTA random access, and FASTQ streaming patterns.
• references/troubleshooting.md for unsorted input, stale indexes, wrong presets or columns, coordinate confusion, plain gzip, parser/encoding failures, overwrite protection, and missing FASTA indexes.
• scripts/tabix_fasta_smoke.py for a source-free smoke helper that creates tiny BED, FASTA, and FASTQ fixtures and prints JSON assertions.

Scope

This sub-skill owns tabix-indexed tabular files and sequence-file helpers: compressing and indexing tabular genomic rows, random-access TabixFile.fetch(), row parser proxies, sequential tabix_iterator(), FastaFile.fetch(), and FastxFile iteration.

Use sibling sub-skills instead for object-oriented VariantFile VCF/BCF workflows, SAM/BAM/CRAM alignment I/O, or invoking samtools/bcftools dispatcher commands.

Defaults that prevent common mistakes

• Use BGZF output from pysam.tabix_compress() or pysam.tabix_index(); plain gzip files are not interchangeable with tabix-indexed BGZF files.
• Keep tabix input sorted by contig and start coordinate before indexing; pysam does not sort rows for you.
• Prefer preset="bed", "gff", "sam", or "vcf" when the file matches a standard format; otherwise pass explicit 0-based column numbers.
• Treat integer fetch(reference, start, end) arguments as 0-based, half-open intervals; region strings such as "chr1:101-200" use samtools-style coordinates.
• For BED, pass zerobased=True when using explicit columns, or use preset="bed"; GFF/GTF/VCF/SAM presets handle their own conventional coordinates.
• Use encoding="utf-8" on TabixFile and parser objects when rows can contain non-ASCII text.
• Prefer with pysam.TabixFile(...), with pysam.FastaFile(...), and with pysam.FastxFile(...) so C-backed handles close promptly.