[EMBOSS] Seqret fetch by URL

[Steve Taylor]

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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>>
> 
>