expand-cols

name	expand-cols
description	Use when you need to expand comma-separated values in file columns into individual lines, replicating each line for every value in the specified columns.
disable-model-invocation	true
user-invocable	true

expand-cols

Quick Start

• Command: expandCols -i <input> -c <cols>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/expandCols
• Full reference: references/help.md

When To Use This Tool

• Expand comma-separated values in one or more columns into one row per element.
• Normalize bedtools or annotation outputs where a single field stores multiple values.
• Convert compact list-like cells into row-wise tabular form for downstream joins, filters, or summaries.
• Expand multiple columns in parallel when their comma-separated entries are aligned by position.

Common Patterns

# 1) Expand one comma-separated column into multiple rows
expandCols \
  -i test.txt \
  -c 5

# 2) Expand two aligned comma-separated columns in lockstep
expandCols \
  -i test.txt \
  -c 4,5

# 3) Read from stdin and expand a list-valued annotation column
cat annotations.tsv | expandCols \
  -c 7

Recommended Workflow

1. Identify which 1-based columns contain comma-separated payloads that should be expanded.
2. If expanding more than one column, confirm the comma-separated lists are aligned positionally within each row.
3. Run expandCols on the file or stdin and redirect the normalized output into downstream processing.
4. Spot-check a few rows to confirm the replicated row count matches the number of values you expected to unpack.

Guardrails

• -c is required.
• If multiple columns are expanded together, they should have the same number of comma-separated values per row.
• Non-expanded columns are simply replicated across the emitted rows.
• If -i is omitted, input is read from stdin.
• Prefer -h for help; GNU-style --help and --version emit wrapper errors before usage text.