Steve Taylor wrote: > > Hi, > > I am trying to fetch a sequence using seqret. In my EMBOSS defaults I > have the following entry set up. I am using EMBOSS 6.0.1 both on Linux > and Solaris. > > DB NCBI_prot [ method: url format: fasta type: P > url: > "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=%s&uids=&dopt=fasta&dispmax=5&sendto=t&fr > > om=begin&to=end" > comment: "NCBI protein - FASTA seqs only" > ] > > If I try: > > seqret NCBI_prot:ACA69081 > > I get: > Reads and writes (returns) sequences > Error: Unable to read sequence 'NCBI_prot:ACA69081' > Died: seqret terminated: Bad value for '-sequence' and no prompt
They have gone away .... but not very far. seqret -debug gives the actual HTML returned in the seqret.dbg file > === File Buffer: Before ajFileBuffStripHtml === > * 952daa0 HTTP/1.1 301 Moved permanently > 951b540 Date: Wed, 24 Jun 2009 11:07:02 GMT > 951b570 Server: Apache > 951b358 Location: > /sviewer/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=AC > A69081&uids=&dopt=fasta&dispmax=5&sendto=t&fr > 951b388 Content-Type: text/plain > 952fd10 Vary: Accept-Encoding > 952fd40 Content-Length: 0 > 952fd70 Connection: close > 951c2e8 If you change /entrez to /sviewer in your URL it should work. Your web browser is able to follow these HTML redirects, EMBOSS is a little more basic. We gave up on trying to interpret HTML error messages in the very early days when one site responded to failed requests with a nice picture of a flower (for those new to the net ... it was EBI :-) Thanks for letting us know, Peter _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
