*ë tE_:csdZdkZdkZdklZ!dd„Z1eedd„ZDedd„ZWd d „Z lhd d „Z dS( sNCBI.py Provides code to access NCBI over the WWW. The main Entrez web page is available at: http://www.ncbi.nlm.nih.gov/Entrez/ A list of the Entrez utilities is available at: http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html The main Blast web page is available at: http://www.ncbi.nlm.nih.gov/BLAST/ Functions: query Query Entrez. pmfetch Retrieve results using a unique identifier. pmqty Search PubMed. pmneighbor Return a list of related articles for a PubMed entry. _open N(sFiles-http://www.ncbi.nlm.nih.gov/entrez/query.fcgic sE!,-h|d<|d<}.|i|ƒ/t||ƒSdS(s]query(cmd, db, cgi='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi', **keywds) -> handle Query Entrez and return a handle to the results. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html Raises an IOError exception if there's a network error. scmdsdbN(scmdsdbs variablessupdateskeywdss_openscgi(scmdsdbscgiskeywdss variables((s%/mit/seven/lib/python/Bio/WWW/NCBI.pysquery!s s5http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgicsw1<=h|d<|d<}>|tj o?||d handle Query PmQty and return a handle to the results. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty_help.html Raises an IOError exception if there's a network error. sdbstermsdoptN( sdbsterms variablessdoptsNonesupdateskeywdss_openscgi(sdbstermsdoptscgiskeywdss variables((s%/mit/seven/lib/python/Bio/WWW/NCBI.pyspmqtyDs  s8http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgics-Wbid|||f}jt|ƒSdS(svpmneighbor(pmid, display, cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi') -> handle Query PMNeighbor and return a handle to the results. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor_help.html Raises an IOError exception if there's a network error. s %s?pmid=%s&%sN(scgispmidsdisplaysfullcgis_open(spmidsdisplayscgisfullcgi((s%/mit/seven/lib/python/Bio/WWW/NCBI.pys pmneighborWs ic sĘltvti|ƒ}w|o@x|} y|ozd||f} n{ti| ƒ}n}ti||ƒ}€t i |ƒ}„g}…x/t dƒd…r}†|i|iƒƒqĪW‡x5t dd d ƒd‡r}ˆ|i||ƒqáW‰ti|dƒ}‹ti|dƒdjotd‚n}Žti|d ƒdjotd ‚nQti|d ƒdjo‘td ‚n%’|d d jo•td‚n—|SdS(sP_open(cgi, params={}, get=1) -> UndoHandle Open a handle to Entrez. cgi is the URL for the cgi script to access. params is a dictionary with the options to pass to it. get is a boolean that describes whether a GET should be used. Does some simple error checking, and will raise an IOError if it encounters one. s%s?%siiiiss500 Proxy Errors500 Proxy Error (NCBI busy?)s502 Proxy Errors502 Proxy Error (NCBI busy?)sWWW Error 500 Diagnostics%WWW Error 500 Diagnostic (NCBI busy?)sERRORs)ERROR, possibly because id not available?N(surllibs urlencodesparamssoptionssgetscgisfullcgisurlopenshandlesFiles UndoHandlesuhandleslinessrangesisappendsreadlinessavelinesstringsjoinsdatasfindsIOError( scgisparamssgetsoptionssuhandlesdataslinessishandlesfullcgi((s%/mit/seven/lib/python/Bio/WWW/NCBI.pys_openls4      ( s__doc__sstringsurllibsBiosFilesquerysNonespmfetchspmqtys pmneighbors_open(surllibspmfetchsqueryspmqtysFilesstrings_opens pmneighbor((s%/mit/seven/lib/python/Bio/WWW/NCBI.pys?s