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, 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
AUTHOR
The National Center for Biotechnology Information.