[EMBOSS] Seqret fetch by URL

[ajb at ebi.ac.uk]

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
>
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