Hi Steve, NCBI added an extra line in their entrez output. We put a patch file on the ftp server a while ago that should fix this.
ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/ If it doesn't then if you add '-debug' to any EMBOSS application you'll get an 'applicationname'.dbg file which gives verbose information on the workings (or not) of the application. HTH Alan > > 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 > > However, if I try > > http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=ACA69081&uids=&dopt=fasta&dispmax=5&sendto=t&from=begin&to=end > > I get > >>gi|169751563|gb|ACA69081.1| glycoside hydrolase family 1 [Yersinia >> pseudotuberculosis YPIII] > MSYQQLPKDFLWGGAVAAHQVEGGWDKGGKGVSIADVLSGGSHGVDRVMTDGVLEGYRYPNHEAVDFYSH > YKEDIALFAEMGFKCFRTSIAWTRIFPHGDEQQPNEAGLQFYDDMFDELLKYGIEPVITLSHFEMPWHLV > KEYGGWKNRKVVDFFVKFSEVVMARYKSKVKYWMTFNEINNQRNWKYPLFGYCCSGVVFTEQENPEETLY > QVLHHQFVASAKVVKLGHAINPEFKIGCMVAMVPLYPFSCHPDDMMYSVEAMRERYLFGDVHMRGYYPSY > ILQEWARRGFNIHMEEGDLETLRDGCADYMGLSYYMSNAVSAINPGSGNSLSGFEGSVPNPHVKASDWGW > QIDPVGLRYSLSVLYERYQKPLFIVENGFGAIDKVAADGMVHDDYRIAYLKAHIEQMKKAVFEDGVDLMG > YTPWGCIDCVSFTTGEYSKRYGFIYVDKNDDGTGTMARSRKLSFDWYKKVIASNGEVL > > > Any ideas why or is there a way I can get more verbose information about > what is going on? > > Thanks, > > Steve > > _______________________________________________ > 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
