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IDFETCH(1)		   NCBI	Tools User's Manual		    IDFETCH(1)

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 data-
       base 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  val-
	      ues 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 in-
		     terest
	      3	     get the minimal nuc-prot containing the bioseq of	inter-
		     est
	      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.

NCBI				  2016-09-01			    IDFETCH(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR

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