ANN: NCBI EUtils client

[Andrew Dalke]

We have developed a client-side interface to NCBI's "EUtils" server,
which is a web service for querying their Entrez databases, including
GenBank and PubMed.

It is available from http://www.dalkescientific.com/EUtils/
and distributed under the Biopython license,
   http://www.biopython.org/License.shtml

Example:
     Get all protein sequences related to protein GI:4579714

 >>> import EUtils
 >>> from EUtils import HistoryClient
 >>> client = HistoryClient.HistoryClient()
 >>> result = client.post(EUtils.DBIds("protein", "4579714"))
 >>> related = result.neighbor_links("protein")
 >>> related_dbids = related.linksetdbs["protein_protein"].dbids
 >>> proteins = client.post(related_dbids)
 >>> len(proteins)
223
 >>> infile = proteins.efetch(retmode = "text", rettype = "fasta")
 >>>
 >>> fasta = infile.read()
 >>> print fasta[:788]
 >gi|27450749|gb|AAO14677.1|AF508258_1 rhodopsin [Pyrocystis lunula]
MAPIPDGFTYGQWSLVYNSLSFGIAGMGCATIFFWLQLPNVSKSYRTALTITGLVTAIATYHYVRIFNSW
VDAFKVVNVNGGDYTVTLLGAPFNDAYRYVDWLLTVPLLLIELILVMKLPKAETVKLSWNLGVASAVMVA
LGYPGEIQDDLLVRWFWWAMAMIPFYYVVVTLVNGLSDATAKQPDSVKSLVVTARYLTVISWLTYPGVYI
IKSMGLAGNIATTYEQVGYSVADVVAKAVFGVLIWAIAAGKSDEEEKNGLLG

 >gi|6319528|ref|NP_009610.1| Homolog to HSP30 heat shock protein Yro1p; 
Yro2p [Saccharomyces cerevisiae]
MSDYVELLKRGGNEAIKINPPTGADFHITSRGSDWLFTVFCVNLLFGVILVPLMFRKPVKDRFVYYTAIA
PNLFMSIAYFTMASNLGWIPVRAKYNHVQTSTQKEHPGYRQIFYARYVGWFLAFPWPIIQMSLLGGTPLW
QIAFNVGMTEIFTVCWLIAACVHSTYKWGYYTIGIGAAIVVCISLMTTTFNLVKARGKDVSNVFITFMSV
IMFLWLIAYPTCFGITDGGNVLQPDSATIFYGIIDLLILSILPVLFMPLANYLGIERLGLIFDEEPAEHV
GPVAEKKMPSPASFKSSDSDSSIKEKLKLKKKHKKDKKKAKKAKKAKKAKKAQEEEEDVATDSE
 >>>


				Andrew Dalke
				dalke@dalkescientific.com
-- 
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