Print Columns

print-columns

Quick Start

• Command: print-columns 'awk_print_expression'
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/print-columns
• I/O shape: reads tab-delimited stdin and emits the requested fields on stdout

When To Use This Tool

• Project or reorder tab-delimited columns without writing a full awk command each time.
• Add lightweight arithmetic or string transforms inside an EDirect shell pipeline.
• Stamp output with the current year (YR) or date (DT) via the wrapper's built-in variables.
• Quickly quote or lowercase specific fields before piping into another shell utility.

Common Patterns

# 1) Reorder columns and add arithmetic
printf '1\t2\t3\n' | print-columns '$1, $2+1, YR, DT'

# 2) Quote a selected field
printf 'geneA\t42\n' | print-columns '$1, "\"" $2 "\""'

# 3) Lowercase and keep selected columns from an upstream extractor
xtract -pattern DocumentSummary -element Name,Status,CreateDate |
print-columns '$1, tolower($2), $3'

Recommended Workflow

1. Make sure the incoming stream is tab-delimited, because the wrapper hard-codes -F '\t'.
2. Write the desired awk print expression and wrap it in single quotes so the shell does not expand $1, $2, and friends.
3. Pipe stdin into print-columns and verify that the transformed columns still line up with downstream expectations.
4. Use the built-in YR and DT variables when you need run-date metadata without calling date yourself.

Guardrails

• The expression is injected directly into awk "{print ...}"; if you forget shell quoting, $1 and similar fields will be expanded by the shell and the command can break with an awk syntax error.
• There is no real option parsing or built-in help path; print-columns --help with no stdin produces no useful output.
• The wrapper is stdin-oriented and does not support separate filenames or flags in the usual awk style.
• Field splitting is always tab-based, not whitespace-generic.
• The wrapper defines YR as the current year and DT as the current YYYY-MM-DD date for use inside the print expression.