filter-columns

name	filter-columns
description	Use when filtering or manipulating columns in tabular data files from bioinformatics workflows.
disable-model-invocation	true
user-invocable	true

filter-columns

Quick Start

• Command: filter-columns 'awk_expression' < input.tsv
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/filter-columns
• Full reference: See references/help.md

When To Use This Tool

• Filter tab-delimited streams with an inline awk condition over $1, $2, and so on.
• Keep or discard rows from lightweight EDirect or bioinformatics tables without opening a spreadsheet.
• Apply simple numeric/date/string predicates inside a shell pipeline.

Common Patterns

# 1) Keep rows whose second column is between 10 and 20
filter-columns '10 <= $2 && $2 <= 20' < input.tsv

# 2) Keep only protein-coding rows with high score
filter-columns '$3 == "protein_coding" && $5 >= 0.95' < annotations.tsv

Recommended Workflow

1. Confirm the stream is tab-delimited.
2. Write the predicate as a single quoted awk expression.
3. Run filter-columns in a pipe or with stdin redirection.
4. Spot-check the retained rows before continuing downstream.

Guardrails

• The expression must be quoted as one shell argument, or the shell will split and reinterpret it before awk sees it.
• This wrapper hard-codes tab as the field separator; it is not a CSV-aware filter.
• --help and --version do not provide real documentation in this build.
• The wrapper injects YR and DT awk variables with the current year and date, so avoid accidental name collisions.