Write Sequences - Usage Guide

Overview

This skill enables AI agents to help you write biological sequence data to files (FASTA, FASTQ, GenBank, EMBL) using Biopython. The recurring theme is that what survives a write depends on which SeqRecord fields are populated before the call, since each format reads only the fields it understands.

Prerequisites

pip install biopython

Quick Start

Tell your AI agent what you want to do:

• "Create a FASTA file with these sequences"
• "Save the modified sequences to a new file"
• "Convert these records to GenBank format with organism annotation"
• "Write FASTQ output with quality scores"
• "Append this new sequence to my existing FASTA file"

Example Prompts

Basic Writing

"Create a FASTA file with sequences for gene1, gene2, and gene3"

Modifying and Saving

"Read input.fasta, uppercase all sequences, and save to output.fasta"

Format-Specific

"Write these reads to FASTQ with a constant quality of Q40"

"Write these sequences to GenBank format with molecule_type and organism set"

Appending

"Add this new sequence to my existing FASTA file without overwriting it"

What the Agent Will Do

1. Import Bio.SeqIO and build SeqRecord objects with the required fields
2. Set format-specific fields: letter_annotations['phred_quality'] for FASTQ, annotations['molecule_type'] for GenBank/EMBL
3. Make the FASTA description start with the id so the header is not mangled
4. Write records with SeqIO.write() (filename or open handle, 'a' mode to append)
5. Confirm the record count returned matches what was expected

Tips

• FASTA writes > + record.description, not record.id. If you set both, make the description start with the id plus a space, or the id is dropped from the header.
• The FASTA writer wraps sequence lines at 60 characters by default.
• FASTQ requires a quality score per base. letter_annotations is length-locked to the sequence, so set the sequence first, then a quality list of matching length.
• GenBank and EMBL require annotations['molecule_type'] (the alphabet that carried this was removed in BioPython 1.78); writing without it raises.
• When both Phred and Solexa qualities are present, the writer uses Phred. Writing 'fastq-solexa' from a Phred-only record is lossy and warns at high quality; prefer plain 'fastq' for modern data.
• Use a file handle in 'a' mode to append records to an existing file.

Related Skills

• read-sequences - Read sequences before modifying and writing
• format-conversion - Direct format conversion without intermediate processing
• filter-sequences - Filter sequences before writing a subset
• fastq-quality - Phred/Solexa encodings and quality-score handling
• sequence-manipulation/seq-objects - Create SeqRecord objects to write
• alignment-files/sam-bam-basics - For SAM/BAM output, use samtools/pysam