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.
