Re: [EMBOSS] EMBOSS remote server list?

Ashika Umanga Umagiliya Fri, 10 Oct 2008 01:22:06 -0700

Thanks all for the responses,

As Alan said I changed 'srs7bin' to 'srsbin' and tried executing both offollowing 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) '' 0USA 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 dataconnecting 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&quot;; 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 fileEnd 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

807bb18807c370 <!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&quot;; 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&quot;; 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*



[EMAIL PROTECTED] 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" ]

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
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