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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 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 2016-09-01 IDFETCH(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR
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