Combine Uid Lists

combine-uid-lists

Quick Start

• Command: combine-uid-lists FILE1 FILE2 ...
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/combine-uid-lists
• Full reference: See references/help.md

When To Use This Tool

• Merge several one-UID-per-line files into a single union list.
• Deduplicate repeated PubMed, PMC, taxonomy, or other Entrez IDs before downstream fetches.
• Normalize multiple EDirect search results into one numerically sorted file.
• Use this when you want a quick set-union step without writing a custom sort | uniq command.

Common Patterns

# 1) Combine two Entrez UID lists into one unique union
combine-uid-lists cohort_a.ids cohort_b.ids > union.ids

# 2) Merge several partial search results before efetch
combine-uid-lists day1.ids day2.ids day3.ids > merged.ids

# 3) Check how many unique IDs remain after the merge
combine-uid-lists a.ids b.ids c.ids | wc -l

Recommended Workflow

1. Save each upstream UID set as one ID per line.
2. Run combine-uid-lists on all source files you want to union.
3. Redirect the result to a new file or pipe it directly into a downstream EDirect step.
4. Check the merged count before using the result in expensive downstream fetches.

Guardrails

• The real implementation is a tiny wrapper around sort -nu "$@"; it always numeric-sorts and deduplicates.
• --help and --version come from GNU sort, not from custom EDirect documentation.
• This command expects file arguments, not two streams on stdin.
• Locale can affect sorting behavior in general sort usage; use LC_ALL=C if you need fully reproducible collation.