reorder-columns

name	reorder-columns
description	Use when you need to reorder columns in tabular bioinformatics data files while preserving row content.
disable-model-invocation	true
user-invocable	true

reorder-columns

Tiny EDirect shell helper that rewrites tab-delimited stdin through awk, printing the requested column order. It is a field selector, not a schema-aware table transformer.

Quick Start

• Command: reorder-columns
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/reorder-columns
• Actual contract: pass 1-based column numbers as positional arguments and feed data on stdin

When To Use This Tool

• Reordering columns in tab-delimited data files
• Preparing output formats for downstream bioinformatics tools
• Adjusting column order from entrez-direct pipeline outputs

Common Patterns

# 1) Move column 3 to the front
printf 'a\tb\tc\n1\t2\t3\n' | reorder-columns 3 1 2

# 2) Keep only a subset of fields
cat table.tsv | reorder-columns 1 4 7

# 3) Duplicate a field intentionally
cat table.tsv | reorder-columns 2 2 1

Recommended Workflow

1. Confirm the input is actually tab-delimited.
2. Decide the 1-based field order you need.
3. Pipe the table through reorder-columns and write the result to a new file.
4. Spot-check the first few rows before using the reordered table downstream.

Guardrails

• reorder-columns -h is silent; there is no real help or version path.
• Source inspection shows the script hard-codes awk -F '\t', so space-delimited data will not behave correctly.
• Column indices are positional and 1-based because the script emits $1, $2, and so on.
• Duplicate indices are allowed and repeat the same source column in the output.
• Missing indices beyond the end of a row follow plain awk behavior and expand to empty fields.