tooluniverse-data-wrangling

name	tooluniverse-data-wrangling
description	Universal data access patterns for downloading and parsing scientific data when ToolUniverse tools don't cover the source, only return metadata, or you need bulk records. Use for VCF/h5ad/BAM/SDF/GCT parsing, multi-step API workflows (search to filter to download to parse), thousands of records at once, or sources with no dedicated tool. Write Python code via Bash for every step.

Data Wrangling: Universal Access Patterns

Reference for downloading and parsing scientific data from any source. Write and run Python code via Bash for every step.

When to Use

• ToolUniverse tool returned metadata/search results but you need raw or bulk data
• Data is in a format tools don't parse (VCF, h5ad, BAM, SDF, GCT)
• You need a multi-step API workflow (search -> filter -> download -> parse)
• The data source has no ToolUniverse tool at all
• You need thousands of records, not the 10-100 a tool returns

Decision: Tool vs Code

Situation	Use
Single record lookup, simple search, <100 results	ToolUniverse tool (execute_tool)
Bulk download, custom filtering, format conversion	Write Python code
Tool exists but returns truncated results	Write code using the same API the tool wraps
No tool exists for this source	Write code directly

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Section A: Format Cookbook

Tabular

import pandas as pd, io

df = pd.read_csv("data.csv")                                
df = pd.read_csv(, sep=)                      
df = pd.read_sas(io.BytesIO(content), =)       
df = pd.read_sas(, =)        
df = pd.read_stata()                               
df = pd.read_parquet()                         
df = pd.read_excel()                              
df = pd.read_spss()                                
df = pd.read_fwf()