Results for “python”

Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).

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Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.

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Build publication-quality figures with matplotlib using the object-oriented Figure/Axes API, constrained_layout, rcParams customization, TrueType (Type-42) font embedding for journal submission, and CVD-safe palettes. Covers seaborn integration, common chart types, axis formatting, and the small gotchas that distinguish reproducible matplotlib from notebook scratch. Use when producing publication figures in Python — RNA-seq scatter, single-cell embeddings, generic biological plotting.

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Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency correction, custom alphabets, and multi-logo stacking. Use when visualizing motif PWMs (TF binding, splice sites, CRISPR spacers), aligned-position composition, or comparing two motif sets.

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Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when finding expression datasets, navigating SuperSeries vs SubSeries, choosing between series-matrix (submitter-normalized) and raw supplementary files, downloading via GEOparse (Python) or GEOquery (R/Bioconductor), linking GEO to SRA for raw reads, or distinguishing GSE/GSM/GPL/GDS record types. Encodes the SuperSeries trap, the series-matrix normalization-trust caveat, GEOmetadb deprecation, ArrayExpress migration to BioStudies, and processed-vs-raw decision matrix.

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Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures (Python) including shared axes/legends/guides collection, panel labels in Nature/Cell convention, and journal-spec sizing. Covers patchwork ≥1.2.0 axes='collect' feature, Type-42 font embedding, and the cairo_pdf save path. Use when composing 2+ subpanels into a single figure for journal submission.

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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CTCF-only/DNase-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

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Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Design error handling strategies for TypeScript and Python applications — exception hierarchies, Result/Either types, retry patterns, error boundaries, and structured error logging. Use when designing error handling architecture, choosing between exceptions and Result types, implementing retry logic, or building error recovery flows. Activate on "error handling", "exception hierarchy", "Result type", "retry pattern", "circuit breaker", "error boundary", "Pokemon exception". NOT for debugging specific runtime errors, logging infrastructure setup, or monitoring/alerting configuration.

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Use when running analytical SQL over Parquet/CSV/JSON without a warehouse, replacing pandas for data wrangling, joining S3 data in-place, building local data marts, or embedding OLAP into an app. Triggers: read_parquet/read_csv setup, partitioned dataset queries, hive partitioning, glob patterns for S3, COPY TO export, attach Postgres/MySQL, UDFs in Python/R, MotherDuck cloud sync, columnar performance vs row stores. NOT for OLTP workloads (concurrent writes), distributed analytics at petabyte scale (use Spark/Trino), or vector search (use pgvector/Lance).

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Chooses and designs developer surfaces for an agentic product: SDK, CLI, MCP, GUI, API, webhooks, and pd tube-style listener/sender workflows. Use when deciding why a user belongs in an SDK versus CLI/MCP/GUI, planning Python SDK parity, or making agent invocation easy across languages. NOT for implementing the full SDK, generic API docs, or UI visual design.

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Send and receive transactional emails with Cloudflare Email Service (Email Sending + Email Routing). Use when building email sending (Workers binding or REST API), email routing, Agents SDK email handling, or integrating email into any app — Workers, Node.js, Python, Go, etc. Also use for email deliverability, SPF/DKIM/DMARC, wrangler email setup, MCP email tools, or when a coding agent needs to send emails. Even for simple requests like "add email to my Worker" — this skill has critical config details.

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Expert bot developer specializing in Discord, Telegram, Slack automation with deep knowledge of rate limiting, state machines, event sourcing, moderation systems, and conversational AI integration. Activate on 'Discord bot', 'Telegram bot', 'Slack bot', 'chat automation', 'moderation system'. NOT for web APIs (use backend-architect), general automation scripts (use python-pro), or frontend chat widgets (use frontend-developer).

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Convert an existing find-XXXX SKILL.md into a preprocessor Python script, updating configs/<GAMEVER>.yaml and removing the old SKILL.md. Covers xref-string-based and LLM_DECOMPILE-based discovery patterns.

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Create a new find-XXXX preprocessor Python script from scratch (no existing SKILL.md), add configs/<GAMEVER>.yaml skill and symbol entries. Covers xref-string-based and LLM_DECOMPILE-based discovery patterns. Use when a GitHub issue or user instruction specifies a new function to find.

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Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).

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Perform language and framework specific security best-practice reviews and suggest improvements. Use when the user explicitly requests security best practices guidance, a security review/report, or secure-by-default coding help. Trigger only for supported languages (python, javascript/typescript, go), and not for general debugging or non-security tasks.

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Build a LiveAvatar integration end-to-end — assesses the user's existing stack, recommends the optimal path, and guides implementation. Use when: (1) Building a new LiveAvatar integration, (2) Adding a real-time avatar to an app or site, (3) Connecting LiveAvatar to an existing AI pipeline, (4) User mentions LiveAvatar, real-time avatar, interactive avatar, conversational avatar, or lip-sync avatar, (5) Deciding between Embed, FULL Mode, and LITE Mode, (6) Migrating from HeyGen Interactive Avatar to LiveAvatar.

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Build voice AI agents with LiveKit Cloud and the Agents SDK. Use when the user asks to "build a voice agent", "create a LiveKit agent", "add voice AI", "implement handoffs", "structure agent workflows", or is working with LiveKit Agents SDK. Provides opinionated guidance for the recommended path: LiveKit Cloud + LiveKit Inference. REQUIRES writing tests for all implementations.

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Troubleshoot and debug LiveAvatar integration issues. Use when the user's LiveAvatar integration isn't working, the avatar is silent, audio is garbled, sessions fail to start, events aren't received, or they're getting API errors.

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