Amino Acid Composition

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

# 1) Count amino acids in a single raw sequence line
printf 'ACDE\n' | \
  PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/amino-acid-composition

# 2) Strip FASTA headers first if your input came from a FASTA file
grep -v '^>' proteins.fa | \
  PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/amino-acid-composition

Recommended Workflow

1. Feed only raw sequence lines on stdin.
2. Remove FASTA headers and any non-sequence metadata before running the tool.
3. Interpret each 26-row block as the composition for one input line.
4. 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.