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 |
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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.)
|
-g N |
GI id for single Entity to dump |
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|
-i N |
Type of lookup: |
0
|
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
|
-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) |
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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 |
AUTHOR
The National Center for Biotechnology Information.