man idfetch (Commandes) - retrieve biological data from the NCBI ID1 server
NAME
idfetch - retrieve biological data from the NCBI ID1 server
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]
DESCRIPTION
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, and STS.
- -G filename
- File with list of GIs, (versioned) accessions, FASTA SeqID's 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
AUTHOR
The National Center for Biotechnology Information.