idfetch1

Retrieve biological data from the ncbi id1 server

Usage

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]

Overview

idfetch is a client for NCBI's ID1 server, which contains a large database of annotated biological sequences.

Options

A summary of options is included below.

-: Print usage message

-F str: Add the specified feature types (comma-delimited); allowed values are CDD, SNP, SNP_graph, MGC, HPRD, STS, tRNA, and microRNA.

-G filename: File with list of GIs, (versioned) accessions, FASTA SeqIDs to dump

-Q filename: Generate GI list by Entrez query in filename; requires -dn or -dp.

-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, can be either n for nucleotides or p for proteins).

-e N: Entity number (retrieval number) to dump

-f str: Flattened SeqId. Possible formats:
type([name][,[accession][,[release][,version]]]) as '5(HUMHBB)'
type=accession
type:number
(type is a number indicating the ASN.1 Seq-id subtype.)

-g N: GI id for single Entity to dump

-i N

Type of lookup:

0: get Seq-entry (default)

1: get GI state (output 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

-n: Output only the list of GIs (with -q and -Q).

-o filename: Filename for output (default = stdout)

-q str: Generate gi list by Entrez query. Requires -dn or -dp.

-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

-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

Releases

12 releases since Debian 3.0 (Woody); the text changed 5 times.

-F since Debian 3.1 (Sarge).