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idfetch - Online in the Cloud

Run idfetch in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command idfetch that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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