Join Into Groups Of

join-into-groups-of

CLI tool from the entrez-direct bioconda package that groups input lines into batches of a specified size using xargs.

Quick Start

• Command: join-into-groups-of <group_size>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/join-into-groups-of
• Reference: See references/help.md for detailed usage

When To Use This Tool

• Batch large ID lists into comma-separated chunks.
• Respect API or wrapper limits by controlling how many IDs appear in each emitted group.
• Prepare EDirect-friendly comma-joined ID batches from one-record-per-line input.

Common Patterns

# 1) Group IDs into batches of 200
cat ids.txt | \
  /home/vimalinx/miniforge3/envs/bio/bin/join-into-groups-of 200

# 2) Use the default batch size (10000)
cat ids.txt | \
  /home/vimalinx/miniforge3/envs/bio/bin/join-into-groups-of

a,b,c

Recommended Workflow

1. Start from a newline-separated list with no embedded whitespace inside individual IDs.
2. Pick a group size that matches the downstream tool or API limit.
3. Pipe each emitted comma-joined line into the next query step.
4. Keep the final short batch; the tool does not pad or discard remainders.

Guardrails

• With no positional argument, the default batch size is 10000.
• Output groups are comma-separated, not space-separated.
• The implementation uses xargs, so embedded spaces or tabs inside records will be tokenized and destroyed.
• There is no dedicated help or version mode; unsupported flags are forwarded into the xargs -n code path rather than handled cleanly.