Login or Register to Ask a Question and Join Our Community

Linux and UNIX Man Pages

Linux & Unix Commands - Search Man Pages

idfetch(1) [debian man page]

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 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.

NCBI
								    2011-09-02								IDFETCH(1)

Check Out this Related Man Page

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

NAME

       fastacmd - retrieve FASTA sequences from a BLAST database

SYNOPSIS

       fastacmd [-] [-D N] [-I] [-L start,stop] [-P N] [-S N] [-T] [-a] [-c] [-d str] [-i str] [-l N] [-o filename] [-p type] [-s str] [-t]

DESCRIPTION

       fastacmd retrieves FASTA formatted sequences from a blast(1) database formatted using the `-o' option.  An example fastacmd call would be

								fastacmd -d nr -s p38398

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -D N   Dump the entire database in some format:
	      1      fasta
	      2      GI list
	      3      Accession.version list

       -I     Print database information only (overrides all other options)

       -L start,stop
	      Range of sequence to extract (0 in start is beginning of sequence, 0 in stop is end of sequence, default is whole sequence)

       -P N   Retrieve sequences with Protein Identification Group (PIG) N.

       -S N   Strand on subsequence (nucleotide only):
	      1      top (default)
	      2      bottom

       -T     Print taxonomic information for requested sequence(s)

       -a     Retrieve duplicate accessions

       -c     Use ^A (01) as non-redundant defline separator

       -d str Database (default is nr)

       -i str Input file with GIs/accessions/loci for batch retrieval

       -l N   Line length for sequence (default = 80)

       -o filename
	      Output file (default = stdout)

       -p type
	      Type of file:
	      G      guess (default): look for protein, then nucleotide
	      T      protein
	      F      nucleotide

       -s str Comma-delimited search string(s).  GIs, accessions, loci, or fullSeq-id strings may be used, e.g., 555, AC147927, 'gnl|dbname|tag'

       -t     Definition line should contain target GI only

EXIT STATUS

	      0      Completed successfully.
	      1      An error (other than those below) occurred.
	      2      The BLAST database was not found.
	      3      A search (accession, GI, or taxonomy info) failed.
	      4      No taxonomy database was found.

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       blast(1), /usr/share/doc/blast2/fastacmd.html.

NCBI
								    2005-11-04							       FASTACMD(1)
Man Page