Last Change: 2018-09-07, 16:50
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idfetch − retrieve biological data from the NCBI ID1 server
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.
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− |
Print usage message |
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−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.
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−c N |
Max complexity: |
0
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get the whole blob (default) |
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1 |
get the bioseq of interest |
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2 |
get the minimal bioseq-set containing the bioseq of interest |
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3 |
get the minimal nuc-prot containing the bioseq of interest |
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4 |
get the minimal pub-set containing the bioseq of interest |
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−d str |
Database to use (with −q, can be either n for nucleotides or p for proteins).
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−e N |
Entity number (retrieval number) to dump |
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−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.)
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−g N |
GI id for single Entity to dump |
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−i N |
Type of lookup: |
0
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get Seq-entry (default) |
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1 |
get GI state (output to stderr) |
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2 |
get SeqIds |
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3 |
get GI history (sequence change only) |
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4 |
get revision history (any change to ASN.1) |
−l filename
Log file
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−n |
Output only the list of GIs (with −q and −Q). |
−o filename
Filename for output (default = stdout)
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−q str |
Generate gi list by Entrez query. Requires −dn or −dp. |
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−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
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−t N |
Output type: |
1
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text ASN.1 (default) |
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2 |
binary ASN.1 |
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3 |
GenBank (Seq-entry only) |
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4 |
GenPept (Seq-entry only) |
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5 |
FASTA (table for history) |
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6 |
quality scores (Seq-entry only) |
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7 |
Entrez DocSums |
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8 |
FASTA reverse complement |
The National Center for Biotechnology Information.