If you want to parse Swissprot files which you get from entret, you could have a look at Swissknife, which is "An object-oriented Perl library to handle Swiss-Prot entries":
http://swissknife.sourceforge.net/docs/ This can be used to access all header information in sprot files, also the information in the special format CC lines. David. [EMAIL PROTECTED] schrieb am 31/10/2006 19:53:00: > Hi Richard, > > Richard Rothery wrote: > > I am interested in using entret to retrieve single field entries from > > swissprot or sptrembl. Specifically, I would like to feed entret a list > > of accessions and have it return a file with the species names and/or > > taxonomies. I intend to use this information to compare with my > > phylogeny analyses of clustalw alignments. > > EMBOSS stores the full text in entret without parsing. > > We could try to extract specific fields but it is not easy to definethem for > all formats. > > You can do this with SRS. Try the EBI server for example: > > Go to the library page > > Select UniProtKB/SwissProt (or UniProtKB/TrEMBL) > > Select "standard query form" > > Enter your query in the top part (e.g. accession number) > > In the "create a view" section click the "list" button to egt the original > lines. Select anything taxonomic from the pull down list (control-click to > select more than one) > > Press "search". > > refine your query. You will see the URL at the top that can be used > to retrieve > data when you are happy. > > Failing that, you could just parse out the ID and O* lines from > entret using a > simple perl script. > > Hope that helps, > > Peter > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
