{"id":51866014,"url":"https://github.com/eben-vranken/protein-aa-counter","last_synced_at":"2026-07-24T16:02:35.553Z","repository":{"id":372021939,"uuid":"1304811819","full_name":"eben-vranken/protein-aa-counter","owner":"eben-vranken","description":"🧫 Zero-dependency Python CLI to count amino acid frequencies in protein sequences from raw strings or FASTA files, with plain and verbose table output formats.","archived":false,"fork":false,"pushed_at":"2026-07-18T11:34:39.000Z","size":10,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-07-18T12:19:02.769Z","etag":null,"topics":["amino-acids","bioinformatics","cli","fasta-parser","proteomics","python"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/eben-vranken.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-07-18T10:31:06.000Z","updated_at":"2026-07-18T11:34:43.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/eben-vranken/protein-aa-counter","commit_stats":null,"previous_names":["eben-vranken/protein-aa-counter"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/eben-vranken/protein-aa-counter","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eben-vranken%2Fprotein-aa-counter","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eben-vranken%2Fprotein-aa-counter/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eben-vranken%2Fprotein-aa-counter/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eben-vranken%2Fprotein-aa-counter/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/eben-vranken","download_url":"https://codeload.github.com/eben-vranken/protein-aa-counter/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eben-vranken%2Fprotein-aa-counter/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35847531,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-07-20T02:08:10.276Z","status":"online","status_checked_at":"2026-07-24T02:00:07.870Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["amino-acids","bioinformatics","cli","fasta-parser","proteomics","python"],"created_at":"2026-07-24T16:02:34.769Z","updated_at":"2026-07-24T16:02:35.542Z","avatar_url":"https://github.com/eben-vranken.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003ch1 align=\"center\"\u003e🧫 Protein Amino Acid Counter\u003c/h1\u003e\n\n\u003cp align=\"center\"\u003e\n    A command-line utility to count amino acid frequencies in a protein sequence.\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n    \u003ca href=\"LICENSE\"\u003e\u003cimg src=\"https://img.shields.io/badge/License-MIT-yellow.svg\" alt=\"MIT License\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\nA modular, zero-dependency Python CLI built to analyze protein sequences. It takes a raw sequence or a FASTA file, validates it against the 20-letter amino acid alphabet, tallies how often each amino acid occurs, and reports the result as plain output or a formatted table.\n\n## Install\n\nClone the repository directly:\n```bash\ngit clone https://github.com/eben-vranken/protein-aa-counter.git\ncd protein-aa-counter\n```\n\n## Usage\n\nPass a raw protein sequence with `-s`, or a FASTA file with `-f`. Exactly one of the two is required. The tool counts every amino acid in the sequence and can print the result as a plain list or as a table, with optional full amino acid names.\n\n```bash\npython amino-acid-counter.py -s MTEYKLVVVGAGGVGKSALTIQ --table --verbose\n```\n\n### Short Flags\n\nThe same arguments are available in short form:\n\n```bash\npython amino-acid-counter.py -s MTEYKLVVVGAGGVGKSALTIQ -t -v\n```\n\n### FASTA Input\n\n```bash\npython amino-acid-counter.py -f data/human_protein.fasta -t\n```\n\n### Example Output\n```\n| Amino         | Count |\n-------------------------\n| Alanine       | 23    |\n| Arginine      | 7     |\n| Asparagine    | 10    |\n| Aspartic acid | 21    |\n| Cysteine      | 13    |\n| Glutamic acid | 36    |\n| Glutamine     | 13    |\n| Glycine       | 15    |\n| Histidine     | 8     |\n| Isoleucine    | 8     |\n| Leucine       | 22    |\n| Lysine        | 12    |\n| Methionine    | 8     |\n| Phenylalanine | 7     |\n| Proline       | 14    |\n| Serine        | 10    |\n| Threonine     | 15    |\n| Tryptophan    | 6     |\n| Tyrosine      | 6     |\n| Valine        | 21    |\n```\n\n## Configuration Matrix\n\n| Argument | Option / Choices | Default | Description |\n| --- | --- | --- | --- |\n| `-s`, `--sequence` | *Protein sequence string* | *None* | Raw protein sequence to count (e.g. `MTEYK`). Required unless `-f` is used. |\n| `-f`, `--file` | *File path* | *None* | Path to a FASTA protein file. Required unless `-s` is used. |\n| `-t`, `--table` | *Flag* | `False` | Print the frequencies as a formatted table instead of a plain list. |\n| `-v`, `--verbose` | *Flag* | `False` | Print full amino acid names (e.g. `Alanine`) instead of single-letter codes. |\n\n## Feature Set\n\n* **Sequence Parsing:** Reads a raw sequence directly, or extracts and concatenates the sequence lines from a FASTA file, skipping header lines.\n* **Input Validation:** Rejects any character outside the 20-letter amino acid alphabet and requires exactly one of `-s` or `-f`.\n* **Frequency Counting:** Tallies occurrences of all 20 amino acids across the sequence, including ones with zero occurrences.\n* **Plain Output:** Prints each amino acid and its count on its own line.\n* **Table Rendering:** Prints a clean, column-aligned table of counts, with column widths sized to fit the longest label.\n* **Verbose Labels:** Swaps single-letter codes for full amino acid names in either output mode.\n\n## License\n\nMIT","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Feben-vranken%2Fprotein-aa-counter","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Feben-vranken%2Fprotein-aa-counter","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Feben-vranken%2Fprotein-aa-counter/lists"}