[EMBOSS] EMBOSS remote server list?
Ashika Umanga Umagiliya
aumanga at biggjapan.com
Fri Oct 10 08:23:16 UTC 2008
Thanks all for the responses,
As Alan said I changed 'srs7bin' to 'srsbin' and tried executing both of
following queries:
entret em:ab000131
entret uni:opsd_human
And gave the following debug log.Original IDs I wanted to query were something like follows:
genbank:AB019441
genbank:AB019440
genbank:AB019439
genbank:AB019438
genbank:AB019437
genbank:M99673
genbank:X92210
genbank:M99638
genbank:M99640
genbank:M99641
genbank:X60503
genbank:X07448
Debug log for command 'entret em:ab000131'
Debug file entret.dbg buffered:No
ajAcdInitP pgm 'entret' package ''
ajFileNewInNameS '/usr/local/share/EMBOSS/acd/entret.acd'
EOF ajFileGetsL file /usr/local/share/EMBOSS/acd/entret.acd
closing file '/usr/local/share/EMBOSS/acd/entret.acd'
ajFileNewInNameS '/usr/local/share/EMBOSS/acd/codes.english'
EOF ajFileGetsL file /usr/local/share/EMBOSS/acd/codes.english
closing file '/usr/local/share/EMBOSS/acd/codes.english'
ajTableNewFunctionLen hint 25 size 251
ajTableNewFunctionLen hint 25 size 251
ajTableNewFunctionLen hint 25 size 251
ajFileNewInNameS '/usr/local/share/EMBOSS/acd/knowntypes.standard'
EOF ajFileGetsL file /usr/local/share/EMBOSS/acd/knowntypes.standard
closing file '/usr/local/share/EMBOSS/acd/knowntypes.standard'
Set acdprotein value '$(sequence.protein)'
ajSeqinClear called
++seqUsaProcess 'em:ab000131' 0..0(N) '' 0
USA to test: 'em:ab000131'
format regexp: No list:No
no format specified in USA
...input format not set
dbname dbexp: Yes
found dbname 'em' level: '<null>' qry->QryString: 'ab000131'
seqQueryFieldC usa 'sv' fields '<null>'
ajSeqQueryWild id 'ab000131' acc 'ab000131' sv '' gi '' des '' org '' key ''
no wildcard in stored qry
database type: 'N' format 'embl'
use access method 'srswww'
Matched seqAccess[9] 'srswww'
seqAccessSrswww em:ab000131
seqHttpUrl db: 'em' url: 'http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"; dbalias: "EMBL'
searching with SRS url 'GET /srsbin/cgi-bin/wgetz"; dbalias: "EMBL?-e+-ascii+[em-id:ab000131]|[em-acc:ab000131]'
httpver getValueC '<null>'
httpver after qry '<null>'
host 'srs.ebi.ac.uk' port 80 get 'GET /srsbin/cgi-bin/wgetz"; dbalias: "EMBL?-e+-ascii+[em-id:ab000131]|[em-acc:ab000131] HTTP/1.1
'
seqHttpGet db: 'em' host 'srs.ebi.ac.uk' get: 'GET /srsbin/cgi-bin/wgetz"; dbalias: "EMBL?-e+-ascii+[em-id:ab000131]|[em-acc:ab000131] HTTP/1.1
'
gethostbyname host 'srs.ebi.ac.uk' returns 'www5.ebi.ac.uk' errno 1 hp_addr 193.62.197.19
creating socket
setup socket data
connecting to socket 4
sin sizeof 16
connect status 0 errno 0 msg 'Successful system call (0 - Success)'
inet_ntoa '193.62.197.19'
sending: 'GET /srsbin/cgi-bin/wgetz"; dbalias: "EMBL?-e+-ascii+[em-id:ab000131]|[em-acc:ab000131] HTTP/1.1
' status: 0
send for GET errno 0 msg 'Successful system call (0 - Success)'
sending: 'Host: srs.ebi.ac.uk:80
' status: 0
send for host errno 0 msg 'Successful system call (0 - Success)'
sending: '
' status: 0
send for blankline errno 0 msg 'Successful system call (0 - Success)'
fdopen errno 29 msg 'Something wrong with a system call (29 - Illegal seek)'
read: <HTTP/1.1 404 Not Found
>
read: <Content-Length: 304
>
read: <Date: Fri, 10 Oct 2008 08:03:49 GMT
>
read: <Connection: Keep-Alive
>
read: <Server: Apache/2.0.52 (CentOS)
>
read: <Content-Type: text/html; charset=iso-8859-1
>
read: <
>
read: <<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
>
read: <<html><head>
>
read: <<title>404 Not Found</title>
>
read: <</head><body>
>
read: <<h1>Not Found</h1>
>
read: <<p>The requested URL /srsbin/cgi-bin/wgetz"; was not found on this server.</p>
>
read: <<hr>
>
read: <<address>Apache/2.0.52 (CentOS) Server at srs.ebi.ac.uk Port 80</address>
>
read: <</body></html>
>
EOF ajFileGetsL file
End of file - data in buffer - return ajFalse
read: <>
=== File Buffer: Before ajFileBuffStripHtml ===
* 8076550 HTTP/1.1 404 Not Found
8078050 Content-Length: 304
8076a00 Date: Fri, 10 Oct 2008 08:03:49 GMT
8077f50 Connection: Keep-Alive
8077f80 Server: Apache/2.0.52 (CentOS)
807b2c0 Content-Type: text/html; charset=iso-8859-1
807bb18
807c370 <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
807cbc8 <html><head>
807d420 <title>404 Not Found</title>
807dc78 </head><body>
807e4d0 <h1>Not Found</h1>
807ed28 <p>The requested URL /srsbin/cgi-bin/wgetz"; was not found on this server.</p>
807f580 <hr>
807fdd8 <address>Apache/2.0.52 (CentOS) Server at srs.ebi.ac.uk Port 80</address>
8080630 </body></html>
=== end of file, free list 1 lines ===
First line [1] 'HTTP/1.1 404 Not Found
'
fileBuffLineDel removing line [0/16], 'HTTP/1.1 404 Not Found
' len 24
fileBuffLineDel removing line [0/15], 'Content-Length: 304
' len 21
fileBuffLineDel removing line [0/14], 'Date: Fri, 10 Oct 2008 08:03:49 GMT
' len 37
fileBuffLineDel removing line [0/13], 'Connection: Keep-Alive
' len 24
fileBuffLineDel removing line [0/12], 'Server: Apache/2.0.52 (CentOS)
' len 32
fileBuffLineDel removing line [0/11], 'Content-Type: text/html; charset=iso-8859-1
' len 45
fileBuffLineDel removing line [0/10], '
' len 2
=== File Buffer: About to preprocess ===
* 807c370 <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
807cbc8 <html><head>
807d420 <title>404 Not Found</title>
807dc78 </head><body>
807e4d0 <h1>Not Found</h1>
807ed28 <p>The requested URL /srsbin/cgi-bin/wgetz"; was not found on this server.</p>
807f580 <hr>
807fdd8 <address>Apache/2.0.52 (CentOS) Server at srs.ebi.ac.uk Port 80</address>
8080630 </body></html>
=== end of file, free list 1 lines ===
ajFileBuffStripHtmlPre testing for <pre> line(s)
fileBuffLineDel removing line [0/9], '' len 0
fileBuffLineDel removing line [0/8], '' len 0
fileBuffLineDel removing line [0/7], '' len 0
fileBuffLineDel removing line [0/6], '' len 0
fileBuffLineDel removing line [1/5], '' len 0
fileBuffLineDel removing line [1/4], '' len 0
fileBuffLineDel removing line [1/3], '' len 0
fileBuffLineDel removing line [1/2], '' len 0
=== File Buffer: After ajFileBuffStripHtml ===
* 807e4d0 Not Found
=== end of file, free list 1 lines ===
seqRead: cleared
seqRead: seqin format 3 'embl'
seqRead: one format specified
ajFileBuffNobuff buffsize: 1
++seqRead known format 3
++seqReadFmt format 3 (embl) 'em:ab000131' feat No
ajBuffreadLineStore: 'Not Found'seqReadEmbl first line 'Not Found'
Testing input buffer: IsBuff: No Eof: Yes
seqRead: (d2) seqReadFmt stat == EOF *try again*
seqRead failed - try again with format 3 'embl'
ajFileBuffEmpty Size: 1 Pos: 0 End: Y Handle: 6 Fp: 8078068 List; 0
Search:Yes Data:0 ajFileBuffEmpty:No
ajFileBuffEmpty Size: 1 Pos: 0 End: Y Handle: 6 Fp: 8078068 List; 0
++seqReadFmt format 3 (embl) 'em:ab000131' feat No
ajBuffreadLineStore: 'Not Found'seqReadEmbl first line 'Not Found'
Testing input buffer: IsBuff: No Eof: Yes
seqRead: (d3) seqReadFmt stat == EOF *failed*
ajb at ebi.ac.uk wrote:
> To add to Peter's email, though the 'srs7bin' style of SRS
> DB definition may well work it is better to use 'srsbin'
> definitions instead. The following should all work with
> emboss 6.0.1 e.g.
>
> entret em:ab000131
> entret uni:opsd_human
>
> ATB
>
> Alan
>
>
> DB emblebi [ type: N method: srswww format: embl release: "EBI"
> dbalias: "embl"
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> comment: "EMBL from the EBI" ]
>
> DB em [ type: N method: srswww format: embl release: "EBI"
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> dbalias: "EMBL"
> comment: "EMBL from the EBI" ]
>
> DB swissprot [ type: P method: srswww format: swiss release: "EBI"
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> comment: "SWISSPROT from the EBI" ]
>
> DB sw [ type: P method: srswww format: swiss release: "EBI"
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> dbalias: "SWISSPROT"
> comment: "SWISSPROT from the EBI" ]
>
> DB uniprot [ type: P method: srswww format: swiss release: "EBI"
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> comment: "UNIPROT from the EBI" ]
>
> DB uni [ type: P method: srswww format: swiss release: EBI
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> dbalias: "UNIPROT"
> comment: "UNIPROT from the EBI" ]
>
> DB pir [ type: P method: srswww format: nbrf release: "EBI"
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> comment: "PIR from the EBI" ]
>
>
> DB gb [ type: N
> methodentry: mrs3 format: genbank
> dbalias: "genbank_release"
> url: "http://mrs.cmbi.ru.nl/mrs-3/plain.do"
> comment: "GenBank IDs via MRS"
> ]
>
> DB genbank [ type: N
> methodentry: mrs3 format: genbank
> dbalias: "genbank_release"
> url: "http://mrs.cmbi.ru.nl/mrs-3/plain.do"
> comment: "GenBank IDs via MRS"
> ]
>
> DB refseq [ type: N method: srswww format: genbank release: "NCBI"
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> comment: "REFSEQ from EBI" ]
>
>
>
>
>
>
>
>
>
>
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>
>
>
>
>
>
>
>
>> hi all,
>>
>> I am new to EMBOSS and I want to use entret but, seems the default
>> remote DBs are inactive.
>> It would be much appreciated if anyway can give me some working remove
>> DB Urls to use with entret.
>>
>> I used following list also ,but no use:
>>
>> DB embl [ type: N method: srswww format: embl release: "EBI"
>> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz";
>> comment: "EMBL from the EBI" ]
>>
>> DB em [ type: N method: srswww format: embl release: "EBI"
>> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz";
>> dbalias: "EMBL"
>> comment: "EMBL from the EBI" ]
>>
>> DB swissprot [ type: P method: srswww format: swiss release: "EBI"
>> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz";
>> comment: "SWISSPROT from the EBI" ]
>>
>> DB sw [ type: P method: srswww format: swiss release: "EBI"
>> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz";
>> dbalias: "SWISSPROT"
>> comment: "SWISSPROT from the EBI" ]
>>
>> DB uniprot [ type: P method: srswww format: swiss release: "EBI"
>> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz";
>> comment: "UNIPROT from the EBI" ]
>>
>> DB uni [ type: P method: srswww format: swiss release: EBI
>> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz";
>> dbalias: "UNIPROT"
>> comment: "UNIPROT from the EBI" ]
>>
>> DB pir [ type: P method: srswww format: nbrf release: "EBI"
>> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz";
>> comment: "PIR from the EBI" ]
>>
>> DB genbank [ type: N method: srswww format: genbank release: "NCBI"
>> url: "http://www.infobiogen.fr/srs7bin/cgi-bin/wgetz";
>> comment: "GenBank from Infobiogen" ]
>>
>> DB gb [ type: N method: srswww format: genbank release: "NCBI"
>> url: "http://www.infobiogen.fr/srs7bin/cgi-bin/wgetz";
>> dbalias: "GENBANK"
>> comment: "GenBank from Infobiogen" ]
>>
>> DB refseq [ type: N method: srswww format: genbank release: "NCBI"
>> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz";
>> comment: "REFSEQ from EBI" ]
>>
>>
>> thanks in advance
>>
>> umanga
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>>
>
>
>
>
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