Hi Peter/Alan,
Thanks - I changed to entrez to sviewer and it all works fine now.
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
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