Man page - idfetch(1)

Packages contains this manual

Package:  ncbi-tools-bin
apt-get install ncbi-tools-bin

Manuals in package:
• asn2ff(1)
• asn2gb(1)
• asntool(1)
• vecscreen(1)
• sortbyquote(1)
• trna2tbl(1)
• asn2xml(1)
• getpub(1)
• gil2bin(1)
• gene2xml(1)
• asn2all(1)
• checksub(1)
• subfuse(1)
• getmesh(1)
• taxblast(1)
• asn2asn(1)
• spidey(1)
• tbl2asn(1)
• asnval(1)
• asnmacro(1)
• idfetch(1)
• asndhuff(1)
• insdseqget(1)
• nps2gps(1)
• indexpub(1)
• findspl(1)
• asn2fsa(1)
• gbseqget(1)
• errhdr(1)
• asn2idx(1)
• trna2sap(1)
• cleanasn(1)
• asndisc(1)
• makeset(1)
• fa2htgs(1)
• debruijn(1)
Documentations in package:
• ncbi-tools-bin

Manual

IDFETCH

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR

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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.

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