IDFETCH(1)

💖 idfetch — a whole manual, but make it cute 💖

okay bestie, welcome to IDFETCH(1) from the NCBI Tools User's Manual — yes, that's the manual name, and yes, it's giving "I know things you don't." pull up a chair. 🫶

✨ NAME ✨

idfetch — go grab biological data from the NCBI ID1 server. that's it, that's the job. 🌸

🎀 SYNOPSIS 🎀

idfetch [-] [-F str] [-G filename] [-Q filename] [-c N] [-d str] [-e N]
[-f str] [-g N] [-i N] [-l filename] [-n] [-o filename] [-q str]
[-s str] [-t N]

look at all those little flags. so many options, so little time. iconic honestly. 💅

🦋 DESCRIPTION 🦋

so idfetch is a client for NCBI's ID1 server, and that server is holding a big database of annotated biological sequences. like, annotated. like, the whole vibe. you ask, it fetches. periodt. ✨

👑 OPTIONS 👑

here's the rundown, bestie. a summary of options is included below — literally all of them, i'm not skipping a single one. 💖

• - — print the usage message. that's it. a little help, as a treat. 🙈
• -F str — add the specified feature types, and they're comma-delimited. allowed values are CDD, SNP, SNP_graph, MGC, HPRD, STS, tRNA, and microRNA. yes those are exact, don't freestyle. 💅
• -G filename — file with a list of GIs, (versioned) accessions, and FASTA SeqIDs to dump. give it a list, it dumps. 🍓
• -Q filename — generate a GI list by Entrez query in filename. requires -dn or -dp — don't come for me, that's the rule. 🔥
• -c N — max complexity:
  • 0 — get the whole blob (default)
  • 1 — get the bioseq of interest
  • 2 — get the minimal bioseq-set containing the bioseq of interest
  • 3 — get the minimal nuc-prot containing the bioseq of interest
  • 4 — get the minimal pub-set containing the bioseq of interest
• -d str — database to use. (with -q, it can be either n for nucleotides or p for proteins.) pick your fighter. 🧚
• -e N — entity number (that's the retrieval number) to dump. ✨
• -f str — flattened SeqId. possible formats:
  • type([name][,[accession][,[release][,version]]]) as '5(HUMHBB)'
  • type=accession
  • type:number

and btw, type is a number indicating the ASN.1 Seq-id subtype. iykyk. 💜

• -g N — GI id for a single Entity to dump. 🎀
• -i N — type of lookup:
  • 0 — get Seq-entry (default)
  • 1 — get GI state (output goes to stderr)
  • 2 — get SeqIds
  • 3 — get GI history (sequence change only)
  • 4 — get revision history (any change to ASN.1)
• -l filename — log file. keep the receipts. 💀
• -n — output only the list of GIs (works with -q and -Q). minimalism, but make it data. 🦋
• -o filename — filename for output (default = stdout). where the goods go. 💖
• -q str — generate gi list by Entrez query. requires -dn or -dp. same energy as -Q, different outfit. 🌸
• -s str — FASTA style SeqId ENCLOSED IN QUOTES. formats:
  • lcl|int or str
  • bbs|int
  • bbm|int
  • gb|acc|loc
  • emb|acc|loc
  • pir|acc|name
  • sp|acc|name
  • pat|country|patent|seq
  • gi|int
  • dbj|acc|loc
  • prf|acc|name
  • pdb|entry|chain

bestie the QUOTES are not optional, the manpage literally yells it in caps, so like… quote it. 😭

• -t N — output type:
  • 1 — text ASN.1 (default)
  • 2 — binary ASN.1
  • 3 — GenBank (Seq-entry only)
  • 4 — GenPept (Seq-entry only)
  • 5 — FASTA (table for history)
  • 6 — quality scores (Seq-entry only)
  • 7 — Entrez DocSums
  • 8 — FASTA reverse complement

🌈 AUTHOR 🌈

written by The National Center for Biotechnology Information. absolute main character energy from the NCBI, no cap. 👑

and that's the whole thing, bestie! this page is from the NCBI, dated 2016-09-01, and it's IDFETCH(1) — go fetch something gorgeous. mwah. 💅✨🫶