| name | amino-acid-composition |
| description | Use when counting amino-acid letters in raw protein sequence lines inside simple EDirect text pipelines. |
| disable-model-invocation | true |
| user-invocable | true |
amino-acid-composition
CLI tool from the Entrez Direct (EDirect) package for computing amino acid composition of protein sequences.
Quick Start
- Command:
printf 'ACDE\n' | PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH /home/vimalinx/miniforge3/envs/bio/bin/amino-acid-composition
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/amino-acid-composition
- Full reference: See references/help.md for complete options and examples
When To Use This Tool
- Count amino-acid letters in one raw sequence line at a time.
- Emit a fixed 26-row three-letter abbreviation table for each input line.
- Do quick composition checks in lightweight EDirect or shell pipelines where a full FASTA parser would be overkill.
Common Patterns
printf 'ACDE\n' | \
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
/home/vimalinx/miniforge3/envs/bio/bin/amino-acid-composition
grep -v '^>' proteins.fa | \
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
/home/vimalinx/miniforge3/envs/bio/bin/amino-acid-composition
Recommended Workflow
- Feed only raw sequence lines on stdin.
- Remove FASTA headers and any non-sequence metadata before running the tool.
- Interpret each 26-row block as the composition for one input line.
- Aggregate across lines separately if you need per-file rather than per-line totals.
Guardrails
- This script does not parse FASTA records. A header line such as
>p1 will be treated as sequence text and counted.
- Non-letter characters are stripped, output is case-insensitive, and each input line is processed independently.
- The wrapper depends on the EDirect helper
sort-uniq-count, so keep the bio / EDirect bin directory on PATH.
- Output covers all 26 alphabet letters via three-letter labels (
Ala, Asx, Xle, Pyl, Sec, Xxx, Glx, etc.), not just the canonical 20 amino acids.
