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.TH IDFETCH 1 2005-06-24 NCBI "NCBI Tools User's Manual"
.SH NAME
idfetch \- retrieve biological data from the NCBI ID1 server
.SH SYNOPSIS
.B idfetch
[\|\fB\-\fP\|]
[\|\fB\-F\fP\ \fIstr\fP\|]
[\|\fB\-G\fP\ \fIfilename\fP\|]
[\|\fB\-Q\fP\ \fIfilename\fP\|]
[\|\fB\-c\fP\ \fIN\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-e\fP\ \fIN\fP\|]
[\|\fB\-f\fP\ \fIstr\fP\|]
[\|\fB\-g\fP\ \fIN\fP\|]
[\|\fB\-i\fP\ \fIN\fP\|]
[\|\fB\-l\fP\ \fIfilename\fP\|]
[\|\fB\-n\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-q\fP\ \fIstr\fP\|]
[\|\fB\-s\fP\ \fIstr\fP\|]
[\|\fB\-t\fP\ \fIN\fP\|]
.SH DESCRIPTION
\fBidfetch\fP is a client for NCBI's ID1 server, which contains a
large database of annotated biological sequences.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-F\fP\ \fIstr\fP
Add the specified feature types (comma-delimited); allowed values are
CDD, SNP, SNP_graph, MGC, HPRD, and STS.
.TP
\fB\-G\fP\ \fIfilename\fP
File with list of GIs, (versioned) accessions, FASTA SeqID's to dump
.TP
\fB\-Q\fP\ \fIfilename\fP
Generate GI list by Entrez query in \fIfilename\fP; requires \fB\-dn\fP
or \fB\-dp\fP.
.TP
\fB\-c\fP\ \fIN\fP
Max complexity:
.RS
.PD 0
.IP 0
get the whole blob (default)
.IP 1
get the bioseq of interest
.IP 2
get the minimal bioseq-set containing the bioseq of interest
.IP 3
get the minimal nuc-prot containing the bioseq of interest
.IP 4
get the minimal pub-set containing the bioseq of interest
.PD
.RE
.TP
\fB\-d\fP\ \fIstr\fP
Database to use (with \fB\-q\fP, can be either \fBn\fP for nucleotides
or \fBp\fP for proteins).
.TP
\fB\-e\fP\ \fIN\fP
Entity number (retrieval number) to dump
.TP
\fB\-f\fP\ \fIstr\fP
Flattened SeqId. Possible formats:
.br
\fItype\fP([\fIname\fP][,[\fIaccession\fP][,[\fIrelease\fP][,\fIversion\fP]]])
as '5(HUMHBB)'
.br
\fItype\fP=\fIaccession\fP
.br
\fItype\fP:\fInumber\fP
.br
(\fItype\fP is a number indicating the ASN.1 Seq-id subtype.)
.TP
\fB\-g\fP\ \fIN\fP
GI id for single Entity to dump
.TP
\fB\-i\fP\ \fIN\fP
Type of lookup:
.RS
.PD 0
.IP 0
get Seq-entry (default)
.IP 1
get GI state (output to stderr)
.IP 2
get SeqIds
.IP 3
get GI history (sequence change only)
.IP 4
get revision history (any change to ASN.1)
.PD
.RE
.TP
\fB\-l\fP\ \fIfilename\fP
Log file
.TP
\fB\-n\fP
Output only the list of GIs (with \fB\-q\fP and \fB\-Q\fP).
.TP
\fB\-o\fP\ \fIfilename\fP
Filename for output (default = \fBstdout\fP)
.TP
\fB\-q\fP\ \fIstr\fP
Generate gi list by Entrez query. Requires \fB\-dn\fP or \fB\-dp\fP.
.TP
\fB\-s\fP\ \fIstr\fP
FASTA style SeqId ENCLOSED IN QUOTES. Formats:
.br
.BI lcl| "int or str"
.br
.BI bbs| int
.br
.BI bbm| int
.br
.BI gb| acc | loc
.br
.BI emb| acc | loc
.br
.BI pir| acc | name
.br
.BI sp| acc | name
.br
.BI pat| country | patent | seq
.br
.BI gi| int
.br
.BI dbj| acc | loc
.br
.BI prf| acc | name
.br
.BI pdb| entry | chain
.TP
\fB\-t\fP\ \fIN\fP
Output type:
.RS
.PD 0
.IP 1
text ASN.1 (default)
.IP 2
binary ASN.1
.IP 3
GenBank (Seq-entry only)
.IP 4
GenPept (Seq-entry only)
.IP 5
FASTA (table for history)
.IP 6
quality scores (Seq-entry only)
.IP 7
Entrez DocSums
.PD
.RE
.SH AUTHOR
The National Center for Biotechnology Information.
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