idfetch (1)

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\|]

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

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

The National Center for Biotechnology Information.