| name | refseq-nm-cds |
| description | Use when retrieving RefSeq NM coding sequences for supported species (cow, frog, human, mouse, pig, rat, zebrafish) via the entrez-direct toolkit. |
| disable-model-invocation | true |
| user-invocable | true |
refseq-nm-cds
Operational EDirect workflow for downloading RefSeq mRNA GenBank flatfiles by species and extracting NM_* CDS intervals/sequences into <species>_cds.txt.
Quick Start
- Command:
refseq-nm-cds <species>
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/refseq-nm-cds
- Supported species/aliases:
human|man, mouse|mice, rat, pig, cow, frog, fish|zebrafish, or all
When To Use This Tool
Retrieving NCBI RefSeq NM (mRNA) coding sequences for model organisms. Accepts species name as the sole argument and outputs CDS records. Installed as part of the bioconda entrez-direct package.
Common Patterns
refseq-nm-cds human
refseq-nm-cds man
refseq-nm-cds zebrafish
refseq-nm-cds all
Recommended Workflow
- Pick one species first to estimate runtime, disk growth, and network behavior.
- Let the script finish both its download and processing phases.
- Collect the resulting
<species>_cds.txt files and inspect a few rows before downstream use.
- Only then scale out to
all if you really need every supported species.
Guardrails
- This script is not a light query helper. By default it both downloads many
*.rna.gbff.gz files and processes them.
- If no species is supplied, source inspection shows it defaults to
human.
- Unsupported arguments such as
--help or --version are treated as species names. In local testing that path also emitted a shell error from a stray break before printing the species warning.
- The workflow depends on many sibling tools being on
PATH, including nquire, skip-if-file-exists, gbf2xml, and xtract.
- Output is written to files such as
human_cds.txt, mouse_cds.txt, and zebrafish_cds.txt; it is not primarily a stdout-streaming tool.
