Configuration¶

gs2txt provides flexible configuration options for gene filtering, pathway filtering, and LLM settings.

Gene Filtering Parameters¶

Parameter	Default	Description
`max_gene_num`	60	Maximum number of genes to include
`pvalue_threshold`	0.05	P-value cutoff (genes with pvalue <= threshold)
`log2fc_threshold`	1.0	Log2FC cutoff (genes with \|log2FC\| >= threshold)

Example¶

result = annotator.annotate(
    deg_df,
    max_gene_num=100,
    pvalue_threshold=0.01,
    log2fc_threshold=1.5
)

Pathway Filtering Parameters¶

Parameter	Default	Description
`max_pathway_num`	10	Maximum number of pathways to include
`compute_enrichment`	True	Whether to run enrichment analysis

Example¶

result = annotator.annotate(
    deg_df,
    max_pathway_num=15,
    compute_enrichment=True
)

LLM Provider Configuration¶

OpenAI¶

from gs2txt.llm import OpenAIProvider

provider = OpenAIProvider(
    api_key="sk-xxx",
    model_id="gpt-4",           # or "gpt-4-turbo", "gpt-3.5-turbo"
    temperature=0.0,            # 0.0 = deterministic, 1.0 = creative
    base_url=None               # Optional: custom endpoint
)

Anthropic¶

from gs2txt.llm import AnthropicProvider

provider = AnthropicProvider(
    api_key="sk-ant-xxx",
    model_id="claude-sonnet-4-20250514",
    temperature=0.0
)

LiteLLM (Recommended)¶

from gs2txt.llm import LiteLLMProvider

provider = LiteLLMProvider(
    api_key="your-api-key",
    model_id="gpt-4",
    temperature=0.0,
    base_url="https://your-litellm-server.com/"
)

YAML Configuration (Two-Stage Pipeline)¶

For the two-stage pipeline, use a YAML configuration file:

# config.yaml

# Input paths (for batch mode)
input:
  deg_dir: "./data/deg/"
  pathway_dirs:
    - "./data/GO/"
    - "./data/KEGG/"
    - "./data/Reactome/"

# Gene filtering
gene_filter:
  pvalue_threshold: 0.05
  log2fc_threshold: 1.0
  pvalue_column: "pvalue"
  log2fc_column: "logFC"
  max_gene_num: 60

# Pathway filtering
pathway_filter:
  pvalue_threshold: 0.05
  pvalue_column: "Adjusted P-value"
  term_column: "Term"
  max_pathway_num: 10

# LLM configuration
llm:
  provider: "litellm"
  model_id: "gpt-4"
  temperature: 0.0
  base_url: "https://your-litellm-server.com/"
  api_key_env: "LITELLM_API_KEY"  # Read from environment variable

Using YAML Config¶

from gs2txt.pipeline import TwoStagePipeline

# Stage 1: Preprocess
TwoStagePipeline.preprocess_batch(
    config_file="config.yaml",
    output_file="intermediate.csv"
)

# Stage 2: Annotate
TwoStagePipeline.annotate(
    intermediate_file="intermediate.csv",
    output_file="final_output.csv",
    config_file="config.yaml"
)

Environment Variables¶

Variable	Description
`GS2TXT_API_KEY`	Default API key for CLI
`GS2TXT_PROVIDER`	Default LLM provider
`GS2TXT_MODEL`	Default model ID
`OPENAI_API_KEY`	OpenAI API key
`ANTHROPIC_API_KEY`	Anthropic API key
`LITELLM_API_KEY`	LiteLLM API key

Column Name Mapping¶

gs2txt supports common column name variations:

Gene Columns¶

gene, Gene, GENE, symbol, Symbol

P-value Columns¶

pvalue, p_value, p-value, PValue, padj, FDR

Log2FC Columns¶

logFC, log2FC, log2FoldChange, Log2FC

Pathway Term Columns¶

Term, term, Pathway, pathway, Name, name