From Oliver.Wafzig at sygnis.de  Tue Oct  7 05:41:58 2008
From: Oliver.Wafzig at sygnis.de (Oliver Wafzig)
Date: Tue, 7 Oct 2008 11:41:58 +0200
Subject: [EMBOSS] seqret: warnings with refseq format
Message-ID: <AB3CFB42F4EB57478F6B1947BCDB247C1108F0@mxserver.sygnis.de>

 
Dear emboss users,

Using the following command to convert a 'RefSeq' protein file to fasta,
I get a lot of warnings about "bad Genbank LOCUS line".
	seqret -nofeature -sequence rsnc.0312.2008.gpff  -nofirstonly
-outseq fasta::stdout

I tested it with version 5.0.0 and the current stable 6.0.1 emboss
package.

Is that a known issue?

Kind regards,

Oliver
 
  



From pmr at ebi.ac.uk  Tue Oct  7 06:44:56 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 07 Oct 2008 11:44:56 +0100
Subject: [EMBOSS] seqret: warnings with refseq format
In-Reply-To: <AB3CFB42F4EB57478F6B1947BCDB247C1108F0@mxserver.sygnis.de>
References: <AB3CFB42F4EB57478F6B1947BCDB247C1108F0@mxserver.sygnis.de>
Message-ID: <48EB3DA8.6020007@ebi.ac.uk>

Dear Oliver,

Oliver Wafzig wrote:
> Using the following command to convert a 'RefSeq' protein file to fasta,
> I get a lot of warnings about "bad Genbank LOCUS line".
> 	seqret -nofeature -sequence rsnc.0312.2008.gpff  -nofirstonly
> -outseq fasta::stdout
> 
> I tested it with version 5.0.0 and the current stable 6.0.1 emboss
> package.
> 
> Is that a known issue?


Thanks for pointing it out. It is some time since I looked at refseq and 
nobody has reported this one.

We define refseq as using GenBank format. We need to make a separate 
Refseq parser (copy the GenBank one and fix the messages). Not hard to do.

regards,

Peter Rice

From maoj at helix.nih.gov  Tue Oct  7 11:04:48 2008
From: maoj at helix.nih.gov (Jean Mao)
Date: Tue, 07 Oct 2008 11:04:48 -0400
Subject: [EMBOSS] tfscan upper limit
Message-ID: <48EB7A90.8080602@helix.nih.gov>

Hi,

Could someone tell me what's the upper limit for the input sequence? I 
tried a genomic fragment but failed but a 4500bp fragment is fine. Thanks.

Jean

From aumanga at biggjapan.com  Fri Oct 10 00:49:57 2008
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Fri, 10 Oct 2008 13:49:57 +0900
Subject: [EMBOSS] EMBOSS remote server list?
Message-ID: <48EEDEF5.902@biggjapan.com>

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

From pmr at ebi.ac.uk  Fri Oct 10 03:35:04 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 10 Oct 2008 08:35:04 +0100
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <48EEDEF5.902@biggjapan.com>
References: <48EEDEF5.902@biggjapan.com>
Message-ID: <48EF05A8.9000203@ebi.ac.uk>

Ashika Umanga Umagiliya wrote:
> 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 remote 
> 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" ]

That should be the correct definition. It works for me.

What was the entry you are trying to retrieve? One possible problem is that 
the EMBL database has renamed the older entries (the ones that has useful 
names like PAAMIR).

Unfortunately, EMBOSS can only tell you it failed to find the entry you ask 
for.

If you still have problems, add -debug to the command line and send the 
entret.dbg file to emboss-bug at emboss.open-bio.org and we will try to 
diagnose the problem.

There is a list of other SRS servers at 
http://downloads.biowisdomsrs.com/publicsrs.html

Hope this helps

Peter Rice




From ajb at ebi.ac.uk  Fri Oct 10 03:56:17 2008
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Fri, 10 Oct 2008 08:56:17 +0100 (BST)
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <48EEDEF5.902@biggjapan.com>
References: <48EEDEF5.902@biggjapan.com>
Message-ID: <41499.86.9.126.186.1223625377.squirrel@webmail.ebi.ac.uk>

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
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From gbottu at vub.ac.be  Fri Oct 10 03:52:07 2008
From: gbottu at vub.ac.be (Guy Bottu)
Date: Fri, 10 Oct 2008 09:52:07 +0200
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <48EEDEF5.902@biggjapan.com>
References: <48EEDEF5.902@biggjapan.com>
Message-ID: <48EF09A7.8060100@vub.ac.be>

Ashika Umanga Umagiliya wrote:
> It would be much appreciated if anyway can give me some working remove 
> DB Urls to use with entret.

You could try these :
DB ncbi_nuc [ type: N method: entrez format: genbank
               comment: 'nonredundant nuc. acid db at NCBI (by GI number)'
]

DB ncbi_prot [ type: P method: entrez format: genbank
               comment: 'nonredundant protein db at NCBI (by GI number)'
]

DB cmbi_sw [ type: P comment: 'SwissProt at CMBI'
              method: mrs3 dbalias: sprot format: swiss
              url: 'http://mrs.cmbi.ru.nl/mrs-web/plain.do'
]
(you can only use the entry name as identifier, e.g. cmbi_sw:papa1_carpa ; you 
can figure out what databases besided "sprot" are available at 
http://mrs.cmbi.ru.nl/mrs-web/status.do?method=databanks)

	Hope this helps,
	Guy Bottu,
	Belgian EMBnet Node


From aumanga at biggjapan.com  Fri Oct 10 04:23:16 2008
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Fri, 10 Oct 2008 17:23:16 +0900
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <41499.86.9.126.186.1223625377.squirrel@webmail.ebi.ac.uk>
References: <48EEDEF5.902@biggjapan.com>
	<41499.86.9.126.186.1223625377.squirrel@webmail.ebi.ac.uk>
Message-ID: <48EF10F4.8000304@biggjapan.com>

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&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 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&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*



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" ]
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>   
>> 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
>>
>>     
>
>
>
>   


From pmr at ebi.ac.uk  Fri Oct 10 04:45:20 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 10 Oct 2008 09:45:20 +0100
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <48EF10F4.8000304@biggjapan.com>
References: <48EEDEF5.902@biggjapan.com>	<41499.86.9.126.186.1223625377.squirrel@webmail.ebi.ac.uk>
	<48EF10F4.8000304@biggjapan.com>
Message-ID: <48EF1620.2050102@ebi.ac.uk>

Ashika Umanga Umagiliya wrote:
> 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.


Many thanks. Easy to spot now.

In all your definitions, like this one:

>>>
>>> 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" ]

There is an extra ';' character at the end of the URL.

Unfortunately this breaks the parsing of quotes. it loses the "dbalias"
definition, and also gives an invalid URL.

You should be able to retrieve from all the databases with the ';' removed.

regards,

Peter Rice

From aumanga at biggjapan.com  Fri Oct 10 05:20:08 2008
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Fri, 10 Oct 2008 18:20:08 +0900
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <48EF1620.2050102@ebi.ac.uk>
References: <48EEDEF5.902@biggjapan.com>	<41499.86.9.126.186.1223625377.squirrel@webmail.ebi.ac.uk>
	<48EF10F4.8000304@biggjapan.com> <48EF1620.2050102@ebi.ac.uk>
Message-ID: <48EF1E48.4060709@biggjapan.com>

Thank you very much peter ,
now the following queries working well:
entret em:ab000131
entret uni:opsd_human

But my query
entret genbank:AB019441

does not work well.My entry for 'genbank' database is as :

DB genbank [ type: N method: srswww format: genbank release: "NCBI"
url: "http://www.infobiogen.fr/srsbin/cgi-bin/wgetz"
comment: "GenBank from Infobiogen" ]

I checked the URL http://www.infobiogen.fr and it says the service is 
down (or something like that ,cuz i dont speak french ).

Any ideas ?

Best Regards
umanga


Following is the debug log for command 'entret genbank:AB019441'

-------------------------------------------------------
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 'genbank:AB019441' 0..0(N) '' 0
USA to test: 'genbank:AB019441'

format regexp: No list:No
no format specified in USA

...input format not set
dbname dbexp: Yes
found dbname 'genbank' level: '<null>' qry->QryString: 'AB019441'
seqQueryFieldC usa 'sv' fields '<null>'
ajSeqQueryWild id 'AB019441' acc 'AB019441' sv '' gi '' des '' org '' key ''
no wildcard in stored qry
database type: 'N' format 'genbank'
use access method 'srswww'
Matched seqAccess[9] 'srswww'
seqAccessSrswww genbank:AB019441
seqHttpUrl db: 'genbank' url: 
'http://www.infobiogen.fr/srsbin/cgi-bin/wgetz'
searching with SRS url 'GET 
/srsbin/cgi-bin/wgetz?-e+-ascii+[genbank-id:AB019441]|[genbank-acc:AB019441]'
httpver getValueC '<null>'
httpver after qry '<null>'
host 'www.infobiogen.fr' port 80 get 'GET 
/srsbin/cgi-bin/wgetz?-e+-ascii+[genbank-id:AB019441]|[genbank-acc:AB019441] 
HTTP/1.1
'
seqHttpGet db: 'genbank' host 'www.infobiogen.fr' get: 'GET 
/srsbin/cgi-bin/wgetz?-e+-ascii+[genbank-id:AB019441]|[genbank-acc:AB019441] 
HTTP/1.1
'
gethostbyname host 'www.infobiogen.fr' returns 'lovelace.infobiogen.fr' 
errno 1 hp_addr 194.57.183.13
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 '194.57.183.13'
sending: 'GET 
/srsbin/cgi-bin/wgetz?-e+-ascii+[genbank-id:AB019441]|[genbank-acc:AB019441] 
HTTP/1.1
' status: 0
send for GET errno 0 msg 'Successful system call (0 - Success)'
sending: 'Host: www.infobiogen.fr: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: <Date: Fri, 10 Oct 2008 09:11:37 GMT
 >
read: <Server: Apache/1.3.29 (Unix) PHP/4.3.6 mod_ssl/2.8.16 OpenSSL/0.9.6l
 >
read: <Last-Modified: Wed, 26 Jul 2006 18:30:45 GMT
 >
read: <ETag: "76f3e-16b-44c7b4d5;44b62a93"
 >
read: <Accept-Ranges: bytes
 >
read: <Content-Length: 363
 >
read: <Content-Type: text/html
 >
read: <
 >
read: <<html>
 >
read: <<head>
 >
read: <<title>Infobiogen est ferm? - Infobiogen is closed</title>
 >
read: <</head>
 >
read: <<body background="/ibgbg.png" >
 >
read: <<center>
 >
read: <<a href="https://lovelace.infobiogen.fr/"><font size=+2 
style="color:red;background-color:white">==> Acc?s au webmail <== 
</font></a>
 >
read: <<br>
 >
read: <<br>
 >
read: <<img src="/ibg.png" ALT="Infobiogen est ferm? - Infobiogen is 
closed">
 >
read: <</center>
 >
read: <</body>
 >
read: <</html>
 >
EOF ajFileGetsL file
End of file - data in buffer - return ajFalse
read: <>
=== File Buffer: Before ajFileBuffStripHtml ===
* 8076b98 HTTP/1.1 404 Not Found
80786a0 Date: Fri, 10 Oct 2008 09:11:37 GMT
8077038 Server: Apache/1.3.29 (Unix) PHP/4.3.6 mod_ssl/2.8.16 OpenSSL/0.9.6l
80785a0 Last-Modified: Wed, 26 Jul 2006 18:30:45 GMT
80785d0 ETag: "76f3e-16b-44c7b4d5;44b62a93"
807b910 Accept-Ranges: bytes
807c168 Content-Length: 363
807c9c0 Content-Type: text/html
807d218
807da70 <html>
807e2c8 <head>
807eb20 <title>Infobiogen est ferm? - Infobiogen is closed</title>
807f378 </head>
807fbd0 <body background="/ibgbg.png" >
8080428 <center>
8080c80 <a href="https://lovelace.infobiogen.fr/"><font size=+2 
style="color:red;background-color:white">==> Acc?s au webmail <== 
</font></a>
80814d8 <br>
8081d30 <br>
8082588 <img src="/ibg.png" ALT="Infobiogen est ferm? - Infobiogen is 
closed">
8082de0 </center>
8083638 </body>
8083e90 </html>
=== end of file, free list 1 lines ===
First line [1] 'HTTP/1.1 404 Not Found
'
fileBuffLineDel removing line [0/22], 'HTTP/1.1 404 Not Found
' len 24
fileBuffLineDel removing line [0/21], 'Date: Fri, 10 Oct 2008 09:11:37 GMT
' len 37
fileBuffLineDel removing line [0/20], 'Server: Apache/1.3.29 (Unix) 
PHP/4.3.6 mod_ssl/2.8.16 OpenSSL/0.9.6l
' len 70
fileBuffLineDel removing line [0/19], 'Last-Modified: Wed, 26 Jul 2006 
18:30:45 GMT
' len 46
fileBuffLineDel removing line [0/18], 'ETag: "76f3e-16b-44c7b4d5;44b62a93"
' len 37
fileBuffLineDel removing line [0/17], 'Accept-Ranges: bytes
' len 22
fileBuffLineDel removing line [0/16], 'Content-Length: 363
' len 21
fileBuffLineDel removing line [0/15], 'Content-Type: text/html
' len 25
fileBuffLineDel removing line [0/14], '
' len 2
=== File Buffer: About to preprocess ===
* 807da70 <html>
807e2c8 <head>
807eb20 <title>Infobiogen est ferm? - Infobiogen is closed</title>
807f378 </head>
807fbd0 <body background="/ibgbg.png" >
8080428 <center>
8080c80 <a href="https://lovelace.infobiogen.fr/"><font size=+2 
style="color:red;background-color:white">==> Acc?s au webmail <== 
</font></a>
80814d8 <br>
8081d30 <br>
8082588 <img src="/ibg.png" ALT="Infobiogen est ferm? - Infobiogen is 
closed">
8082de0 </center>
8083638 </body>
8083e90 </html>
=== end of file, free list 1 lines ===
ajFileBuffStripHtmlPre testing for <pre> line(s)
fileBuffLineDel removing line [0/13], '' len 0
fileBuffLineDel removing line [0/12], '' len 0
fileBuffLineDel removing line [0/11], '' len 0
fileBuffLineDel removing line [0/10], '' len 0
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 [0/5], '' len 0
fileBuffLineDel removing line [0/4], '' len 0
fileBuffLineDel removing line [0/3], '' len 0
fileBuffLineDel removing line [0/2], '' len 0
fileBuffLineDel removing line [0/1], '' len 0
=== File Buffer: After ajFileBuffStripHtml ===
=== end of file, free list 1 lines ===
seqRead: cleared
seqRead: seqin format 16 'genbank'
seqRead: one format specified
ajFileBuffNobuff buffsize: 0
++seqRead known format 16
++seqReadFmt format 16 (genbank) 'genbank:AB019441' feat No
seqReadGenbank
at EOF: File already read to end
ajFileReopenNext for non-list file
End of file - no new file to read - return ajFalse
Testing input buffer: IsBuff: No Eof: Yes
seqRead: (d2) seqReadFmt stat == EOF *try again*
seqRead failed - try again with format 16 'genbank'
ajFileBuffEmpty Size: 0 Pos: 0 End: Y Handle: 6 Fp: 80786b8 List; 0
Search:Yes Data:0 ajFileBuffEmpty:Yes
ajFileBuffEmpty Size: 0 Pos: 0 End: Y Handle: 6 Fp: 80786b8 List; 0
seqRead: *failed* to read sequence genbank:AB019441 using format genbank



Peter Rice wrote:
> Ashika Umanga Umagiliya wrote:
>> 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.
>
>
> Many thanks. Easy to spot now.
>
> In all your definitions, like this one:
>
>>>>
>>>> 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" ]
>
> There is an extra ';' character at the end of the URL.
>
> Unfortunately this breaks the parsing of quotes. it loses the "dbalias"
> definition, and also gives an invalid URL.
>
> You should be able to retrieve from all the databases with the ';' 
> removed.
>
> regards,
>
> Peter Rice
>


From aumanga at biggjapan.com  Fri Oct 10 05:38:14 2008
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Fri, 10 Oct 2008 18:38:14 +0900
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <ABFBFB70E2124E2F89C51DD2EB616AA2@class23>
References: <48EEDEF5.902@biggjapan.com>	<41499.86.9.126.186.1223625377.squirrel@webmail.ebi.ac.uk><48EF10F4.8000304@biggjapan.com>
	<48EF1620.2050102@ebi.ac.uk> <48EF1E48.4060709@biggjapan.com>
	<ABFBFB70E2124E2F89C51DD2EB616AA2@class23>
Message-ID: <48EF2286.2040909@biggjapan.com>

Thank toy Sergei and all other guys..
Now everything works fine...

thanks again
Sergei Spirin wrote:
>>
>> But my query
>> entret genbank:AB019441
>>
>> does not work well.My entry for 'genbank' database is as :
>>
>> DB genbank [ type: N method: srswww format: genbank release: "NCBI"
>> url: "http://www.infobiogen.fr/srsbin/cgi-bin/wgetz"
>> comment: "GenBank from Infobiogen" ]
>>
>> I checked the URL http://www.infobiogen.fr and it says the service is 
>> down (or something like that ,cuz i dont speak french ).
>>
>> Any ideas ?
>>
>
> Add the following to emboss.default:
>
> DB genbank [
>   type: N
>   method: url
>   format: genbank
>   url: "http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=genbank_release&id=%s"
>   comment: "GenBank from MRS on CMBI" ]
>
> Sergei
>


From rls at ebi.ac.uk  Fri Oct 10 06:00:54 2008
From: rls at ebi.ac.uk (Rodrigo Lopez)
Date: Fri, 10 Oct 2008 11:00:54 +0100
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <48EF2286.2040909@biggjapan.com>
References: <48EEDEF5.902@biggjapan.com>	<41499.86.9.126.186.1223625377.squirrel@webmail.ebi.ac.uk><48EF10F4.8000304@biggjapan.com>	<48EF1620.2050102@ebi.ac.uk>
	<48EF1E48.4060709@biggjapan.com>	<ABFBFB70E2124E2F89C51DD2EB616AA2@class23>
	<48EF2286.2040909@biggjapan.com>
Message-ID: <48EF27D6.9080102@ebi.ac.uk>

Probably worth noting that the Genbank, Embl and Ddbj are part of the 
INSDC (International Nucleotide Sequence Database Collaboration). The 
three databases store and exchange data on a daily basis and have 
equivalent content. The only difference being the format in which the 
data is distributed. The accession numbers for genebank are the same as 
for embl and ddbj - so you should be able to get to these data using the 
  same method you have defined for embl.

Hope this helps,

R:)

Ashika Umanga Umagiliya wrote:
> Thank toy Sergei and all other guys..
> Now everything works fine...
> 
> thanks again
> Sergei Spirin wrote:
>>>
>>> But my query
>>> entret genbank:AB019441
>>>
>>> does not work well.My entry for 'genbank' database is as :
>>>
>>> DB genbank [ type: N method: srswww format: genbank release: "NCBI"
>>> url: "http://www.infobiogen.fr/srsbin/cgi-bin/wgetz"
>>> comment: "GenBank from Infobiogen" ]
>>>
>>> I checked the URL http://www.infobiogen.fr and it says the service is 
>>> down (or something like that ,cuz i dont speak french ).
>>>
>>> Any ideas ?
>>>
>>
>> Add the following to emboss.default:
>>
>> DB genbank [
>>   type: N
>>   method: url
>>   format: genbank
>>   url: "http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=genbank_release&id=%s"
>>   comment: "GenBank from MRS on CMBI" ]
>>
>> Sergei
>>
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss

From gbottu at vub.ac.be  Fri Oct 10 05:54:34 2008
From: gbottu at vub.ac.be (Guy Bottu)
Date: Fri, 10 Oct 2008 11:54:34 +0200
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <48EF1E48.4060709@biggjapan.com>
References: <48EEDEF5.902@biggjapan.com>	<41499.86.9.126.186.1223625377.squirrel@webmail.ebi.ac.uk>	<48EF10F4.8000304@biggjapan.com>
	<48EF1620.2050102@ebi.ac.uk> <48EF1E48.4060709@biggjapan.com>
Message-ID: <48EF265A.8060802@vub.ac.be>

Ashika Umanga Umagiliya wrote:
> I checked the URL http://www.infobiogen.fr and it says the service is 
> down (or something like that ,cuz i dont speak french ).

Yes, Infobiogen has been closed down because of cutting of its financing.
You can find a list of SRS servers at http://downloads.lionbio.co.uk/publicsrs.html

	Guy Bottu

From michael.watson at bbsrc.ac.uk  Fri Oct 10 08:28:30 2008
From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C))
Date: Fri, 10 Oct 2008 13:28:30 +0100
Subject: [EMBOSS] EMBOSS An error in ajfile.c at line 1276:
Message-ID: <8975119BCD0AC5419D61A9CF1A923E9506D87DFE@iahce2ksrv1.iah.bbsrc.ac.uk>

Hi

I'm running EMBOSS 5.0, I think, and running needle on some very short
sequences.

I get the error:

   EMBOSS An error in ajfile.c at line 1276:

Any clues?

Mick

Head of Informatics
Institute for Animal Health
Compton
Berks
RG20 7NN
01635 578411 

http://www.iah.ac.uk/research/bioinformatics/bioinf.shtml

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From pmr at ebi.ac.uk  Fri Oct 10 10:02:52 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 10 Oct 2008 15:02:52 +0100
Subject: [EMBOSS] EMBOSS An error in ajfile.c at line 1276:
In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9506D87DFE@iahce2ksrv1.iah.bbsrc.ac.uk>
References: <8975119BCD0AC5419D61A9CF1A923E9506D87DFE@iahce2ksrv1.iah.bbsrc.ac.uk>
Message-ID: <48EF608C.9020506@ebi.ac.uk>

michael watson (IAH-C) wrote:
> Hi
> 
> I'm running EMBOSS 5.0, I think, and running needle on some very short
> sequences.
> 
> I get the error:
> 
>    EMBOSS An error in ajfile.c at line 1276:
> 
> Any clues?

That message indicates an error code from closing a file.

Unfortunately it does not say what the error was. if you run with -debug
on the command line the last message in the needle.dbg file should be
"closing file 'filename'" so you can find out which file has the problem.

Hope that helps.

Peter

From maoj at helix.nih.gov  Fri Oct 10 11:39:59 2008
From: maoj at helix.nih.gov (Jean Mao)
Date: Fri, 10 Oct 2008 11:39:59 -0400
Subject: [EMBOSS] tfscan error received
Message-ID: <48EF774F.8030904@helix.nih.gov>

Hi,

I ran tfscan using a fragment about 200 mega bp and successfully created a 2gb output file without error. But recently the same job failed (with the same transfac datafile). The error I got is:

Uncaught exception:  Allocation failed, insufficient memory available, raised at embpat.c:1475

The command I used was 

tfscan -menu O -mismatch 0 -minlength 4 -sequence inseq -outfile outseq

The output file was indeed created but only about 20mb.

I tried to run the same job several times and got 1 successful run and got 2gb of output file as well. The binary, the database and the computer node I ran on have all stay the same. Is there any reasonable explanation about this?

Thanks.

Jean


From pmr at ebi.ac.uk  Fri Oct 10 11:57:31 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 10 Oct 2008 16:57:31 +0100
Subject: [EMBOSS] tfscan error received
In-Reply-To: <48EF774F.8030904@helix.nih.gov>
References: <48EF774F.8030904@helix.nih.gov>
Message-ID: <48EF7B6B.7040504@ebi.ac.uk>

Jean Mao wrote:
> Hi,
> 
> I ran tfscan using a fragment about 200 mega bp and successfully created 
> a 2gb output file without error. But recently the same job failed (with 
> the same transfac datafile). The error I got is:
> 
> Uncaught exception:  Allocation failed, insufficient memory available, 
> raised at embpat.c:1475

What version of EMBOSS are you using?
 From the line number in embpat.c it seems to be 4.0.0

It is only allocating a small data object at that point, so if this is
related to system overload from other jobs I would expect to see it fail
at some other point sometimes.

You could try updating to 6.0.1 and see if the error persists.

Hope this helps,

Peter

From aumanga at biggjapan.com  Tue Oct 14 04:28:39 2008
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 14 Oct 2008 17:28:39 +0900
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <48EF2286.2040909@biggjapan.com>
References: <48EEDEF5.902@biggjapan.com>	<41499.86.9.126.186.1223625377.squirrel@webmail.ebi.ac.uk><48EF10F4.8000304@biggjapan.com>	<48EF1620.2050102@ebi.ac.uk>
	<48EF1E48.4060709@biggjapan.com>	<ABFBFB70E2124E2F89C51DD2EB616AA2@class23>
	<48EF2286.2040909@biggjapan.com>
Message-ID: <48F45837.4040309@biggjapan.com>

Hi all,

I used :

DB genbank [
  type: N
  method: url
  format: genbank
  url: "http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=genbank_release&id=%s"
  comment: "GenBank from MRS on CMBI" ]

as my GenBank DB ,but some sequence id does not exist in DB.Such as:

Error: Failed to read sequence 'genbank:AJ972404'
upError: Failed to read sequence 'genbank:AJ972403'
Error: Failed to read sequence 'genbank:CAAA01078923'
Error: Failed to read sequence 'genbank:CAAA01073483'


Error: Failed to read sequence 'genbank:10129688'
Error: Failed to read sequence 'genbank:1054739'
Error: Failed to read sequence 'genbank:112004011'
Error: Failed to read sequence 'genbank:1136277'

I tried some other servers in 
http://downloads.lionbio.co.uk/publicsrs.html  and most of the servers 
didnt give results to the latter ids (10129688-113627).
Where can i find a server which has all this data?


best regards









Ashika Umanga Umagiliya wrote:
> Thank toy Sergei and all other guys..
> Now everything works fine...
>
> thanks again
> Sergei Spirin wrote:
>>>
>>> But my query
>>> entret genbank:AB019441
>>>
>>> does not work well.My entry for 'genbank' database is as :
>>>
>>> DB genbank [ type: N method: srswww format: genbank release: "NCBI"
>>> url: "http://www.infobiogen.fr/srsbin/cgi-bin/wgetz"
>>> comment: "GenBank from Infobiogen" ]
>>>
>>> I checked the URL http://www.infobiogen.fr and it says the service 
>>> is down (or something like that ,cuz i dont speak french ).
>>>
>>> Any ideas ?
>>>
>>
>> Add the following to emboss.default:
>>
>> DB genbank [
>>   type: N
>>   method: url
>>   format: genbank
>>   url: "http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=genbank_release&id=%s"
>>   comment: "GenBank from MRS on CMBI" ]
>>
>> Sergei
>>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>


From aumanga at biggjapan.com  Tue Oct 14 04:38:25 2008
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 14 Oct 2008 17:38:25 +0900
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <48F45837.4040309@biggjapan.com>
References: <48EEDEF5.902@biggjapan.com>	<41499.86.9.126.186.1223625377.squirrel@webmail.ebi.ac.uk><48EF10F4.8000304@biggjapan.com>	<48EF1620.2050102@ebi.ac.uk>
	<48EF1E48.4060709@biggjapan.com>	<ABFBFB70E2124E2F89C51DD2EB616AA2@class23>
	<48EF2286.2040909@biggjapan.com> <48F45837.4040309@biggjapan.com>
Message-ID: <48F45A81.8050601@biggjapan.com>

Hi again guys,

I found that 'http://srs.embl.de/srs' has almost all the GenBank IDs  i 
want.
What is the URL i should add in emboss.default ?

regards
umanga


Ashika Umanga Umagiliya wrote:
> Hi all,
>
> I used :
>
> DB genbank [
>  type: N
>  method: url
>  format: genbank
>  url: "http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=genbank_release&id=%s"
>  comment: "GenBank from MRS on CMBI" ]
>
> as my GenBank DB ,but some sequence id does not exist in DB.Such as:
>
> Error: Failed to read sequence 'genbank:AJ972404'
> upError: Failed to read sequence 'genbank:AJ972403'
> Error: Failed to read sequence 'genbank:CAAA01078923'
> Error: Failed to read sequence 'genbank:CAAA01073483'
>
>
> Error: Failed to read sequence 'genbank:10129688'
> Error: Failed to read sequence 'genbank:1054739'
> Error: Failed to read sequence 'genbank:112004011'
> Error: Failed to read sequence 'genbank:1136277'
>
> I tried some other servers in 
> http://downloads.lionbio.co.uk/publicsrs.html  and most of the servers 
> didnt give results to the latter ids (10129688-113627).
> Where can i find a server which has all this data?
>
>
> best regards
>
>
>
>
>
>
>
>
>
> Ashika Umanga Umagiliya wrote:
>> Thank toy Sergei and all other guys..
>> Now everything works fine...
>>
>> thanks again
>> Sergei Spirin wrote:
>>>>
>>>> But my query
>>>> entret genbank:AB019441
>>>>
>>>> does not work well.My entry for 'genbank' database is as :
>>>>
>>>> DB genbank [ type: N method: srswww format: genbank release: "NCBI"
>>>> url: "http://www.infobiogen.fr/srsbin/cgi-bin/wgetz"
>>>> comment: "GenBank from Infobiogen" ]
>>>>
>>>> I checked the URL http://www.infobiogen.fr and it says the service 
>>>> is down (or something like that ,cuz i dont speak french ).
>>>>
>>>> Any ideas ?
>>>>
>>>
>>> Add the following to emboss.default:
>>>
>>> DB genbank [
>>>   type: N
>>>   method: url
>>>   format: genbank
>>>   url: 
>>> "http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=genbank_release&id=%s"
>>>   comment: "GenBank from MRS on CMBI" ]
>>>
>>> Sergei
>>>
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
>


From pmr at ebi.ac.uk  Tue Oct 14 05:34:53 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 14 Oct 2008 10:34:53 +0100
Subject: [EMBOSS] EMBOSS remote server list?
In-Reply-To: <48F45837.4040309@biggjapan.com>
References: <48EEDEF5.902@biggjapan.com>	<41499.86.9.126.186.1223625377.squirrel@webmail.ebi.ac.uk><48EF10F4.8000304@biggjapan.com>	<48EF1620.2050102@ebi.ac.uk>	<48EF1E48.4060709@biggjapan.com>	<ABFBFB70E2124E2F89C51DD2EB616AA2@class23>	<48EF2286.2040909@biggjapan.com>
	<48F45837.4040309@biggjapan.com>
Message-ID: <48F467BD.8040301@ebi.ac.uk>

Hi Ashika,

>  url: "http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=genbank_release&id=%s"
>
> Error: Failed to read sequence 'genbank:AJ972404'
> Error: Failed to read sequence 'genbank:AJ972403'
> Error: Failed to read sequence 'genbank:CAAA01078923'
> Error: Failed to read sequence 'genbank:CAAA01073483'
> 
> Error: Failed to read sequence 'genbank:10129688'
> Error: Failed to read sequence 'genbank:1054739'
> Error: Failed to read sequence 'genbank:112004011'
> Error: Failed to read sequence 'genbank:1136277'
> 
> Where can i find a server which has all this data?

Those look like NCBI "GI numbers" to me. These are only in Genbank, not
in the EMBL versions of the same entries.

Although MRS can search by GI number in the web interface, we need a URL
that can query by GI number and return the entry.

A further issue is that MRS servers are changing to MRS version 4 so
their interfaces could change.

The URLs for all these database servers can change. Here is one for
Entrez at NCBI that worked today:

DB gigenbank [ type: N method: url format: genbank
    url: 
"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=%s&cmd=text"
    comment: "Genbank GIs" ]

This will retrieve the entries you listed.

> I tried some other servers in 
> http://downloads.lionbio.co.uk/publicsrs.html  and most of the 
> servers didnt give results to the latter ids (10129688-113627).

That is an SRS 8 server. We are waiting for information from SRS8
support on a good URL to use to get ASCII (normal text format) entries.
meanwhile we support SRS 7 servers especially the srs.ebi.ac.uk server.

Does anyone have suggestions for SRS8 server access?

regards,

Peter


From sduslh at tom.com  Tue Oct 14 20:31:28 2008
From: sduslh at tom.com (=?gb2312?B?TGlodWEgU29uZw==?=)
Date: Wed, 15 Oct 2008 08:31:28 +0800 (CST)
Subject: [EMBOSS] =?gb2312?B?dW5kZXNjcmliZQ==?=
Message-ID: <48F539E0.000046.06278@bjapp23>

please undescribe email for me. 



From jeedward at yahoo.com  Sun Oct 19 13:07:26 2008
From: jeedward at yahoo.com (John Edward)
Date: Sun, 19 Oct 2008 10:07:26 -0700 (PDT)
Subject: [EMBOSS] BCBGC-09 call for papers
Message-ID: <601012.23286.qm@web45909.mail.sp1.yahoo.com>



BCBGC-09 call for papers
?
The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include:
????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) 
????????? International Conference on Automation, Robotics and Control Systems (ARCS-09)
????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09)
????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) 
????????? International Conference on Information Security and Privacy (ISP-09)
????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09)
????????? International Conference on Software Engineering Theory and Practice (SETP-09) 
????????? International Conference on Theory and Applications of Computational Science (TACS-09)
????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09)
?
The website www.PromoteResearch.org contains more details.
?
Sincerely
John Edward
Publicity committee
?
?

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

From Sebastien.Moretti at unil.ch  Wed Oct 22 10:27:56 2008
From: Sebastien.Moretti at unil.ch (Sebastien Moretti)
Date: Wed, 22 Oct 2008 16:27:56 +0200
Subject: [EMBOSS] density
Message-ID: <48FF386C.6030507@unil.ch>

Hi,

According to the ACD file, the density application seems to use the 
'graph' qualifier.

When used, I get this error message:
Unknown qualifier -graph=colourps


graph seems to have been replaced by ggraph and dgraph.
And colourps seems to be cps now.


How to fix it in the source ?
Thanks

-- 
S?bastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

From ajb at ebi.ac.uk  Wed Oct 22 17:09:15 2008
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 22 Oct 2008 22:09:15 +0100 (BST)
Subject: [EMBOSS] density
In-Reply-To: <48FF386C.6030507@unil.ch>
References: <48FF386C.6030507@unil.ch>
Message-ID: <41313.86.9.126.186.1224709755.squirrel@webmail.ebi.ac.uk>

Hi,

colourps and cps are synonymous so you should be able to use either.
If you want to specify the output type from the command line
you could type:

  density -quad -qgraph=colourps inputsequence

for a quad graph (qgraph, not ggraph in your email) or, for a dual graph

  density -dual -dgraph=cps inputsequence

or am I misunderstanding your question?

HTH

Alan


> Hi,
>
> According to the ACD file, the density application seems to use the
> 'graph' qualifier.
>
> When used, I get this error message:
> Unknown qualifier -graph=colourps
>
>
> graph seems to have been replaced by ggraph and dgraph.
> And colourps seems to be cps now.
>
>
> How to fix it in the source ?
> Thanks
>
> --
> S??bastien Moretti
> SIB EMBnet, Quartier Sorge - Genopode
> CH-1015 Lausanne, Switzerland
> Tel.: +41 (21) 692 4056/4221
> http://ch.embnet.org/  http://myhits.vital-it.ch/
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From Sebastien.Moretti at unil.ch  Thu Oct 23 03:43:20 2008
From: Sebastien.Moretti at unil.ch (Sebastien Moretti)
Date: Thu, 23 Oct 2008 09:43:20 +0200
Subject: [EMBOSS] density
In-Reply-To: <41313.86.9.126.186.1224709755.squirrel@webmail.ebi.ac.uk>
References: <48FF386C.6030507@unil.ch>
	<41313.86.9.126.186.1224709755.squirrel@webmail.ebi.ac.uk>
Message-ID: <49002B18.8020103@unil.ch>

Sorry,
the service, which provides EMBOSS tools as web interface, fails to 
interprets properly the density ACD file.

Everything is fine in the ACD.

> Hi,
> 
> colourps and cps are synonymous so you should be able to use either.
> If you want to specify the output type from the command line
> you could type:
> 
>   density -quad -qgraph=colourps inputsequence
> 
> for a quad graph (qgraph, not ggraph in your email) or, for a dual graph
> 
>   density -dual -dgraph=cps inputsequence
> 
> or am I misunderstanding your question?
> 
> HTH
> 
> Alan
> 
> 
>> Hi,
>>
>> According to the ACD file, the density application seems to use the
>> 'graph' qualifier.
>>
>> When used, I get this error message:
>> Unknown qualifier -graph=colourps
>>
>>
>> graph seems to have been replaced by ggraph and dgraph.
>> And colourps seems to be cps now.
>>
>>
>> How to fix it in the source ?
>> Thanks

-- 
S?bastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

From ajb at ebi.ac.uk  Thu Oct 23 05:09:05 2008
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Thu, 23 Oct 2008 10:09:05 +0100 (BST)
Subject: [EMBOSS] density
In-Reply-To: <49002B18.8020103@unil.ch>
References: <48FF386C.6030507@unil.ch>
	<41313.86.9.126.186.1224709755.squirrel@webmail.ebi.ac.uk>
	<49002B18.8020103@unil.ch>
Message-ID: <50739.86.9.126.186.1224752945.squirrel@webmail.ebi.ac.uk>

Hi,

So it's a limitation of the web interface which requires
all graphs to be called 'graph' ?

If I've understood you correctly then, attached, are two new
versions of density.c and density.acd that only use one
graph (called 'graph') with the -dual and -quad qualifiers
working as before. I'll consider adding this to CVS. It
is, of course, currently not tested that well. Please let
me know how it behaves.

HTH

Alan


> Sorry,
> the service, which provides EMBOSS tools as web interface, fails to
> interprets properly the density ACD file.
>
> Everything is fine in the ACD.
>
>> Hi,
>>
>> colourps and cps are synonymous so you should be able to use either.
>> If you want to specify the output type from the command line
>> you could type:
>>
>>   density -quad -qgraph=colourps inputsequence
>>
>> for a quad graph (qgraph, not ggraph in your email) or, for a dual graph
>>
>>   density -dual -dgraph=cps inputsequence
>>
>> or am I misunderstanding your question?
>>
>> HTH
>>
>> Alan
>>
>>
>>> Hi,
>>>
>>> According to the ACD file, the density application seems to use the
>>> 'graph' qualifier.
>>>
>>> When used, I get this error message:
>>> Unknown qualifier -graph=colourps
>>>
>>>
>>> graph seems to have been replaced by ggraph and dgraph.
>>> And colourps seems to be cps now.
>>>
>>>
>>> How to fix it in the source ?
>>> Thanks
>
> --
> S?bastien Moretti
> SIB EMBnet, Quartier Sorge - Genopode
> CH-1015 Lausanne, Switzerland
> Tel.: +41 (21) 692 4056/4221
> http://ch.embnet.org/  http://myhits.vital-it.ch/
>
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From uludag at ebi.ac.uk  Thu Oct 23 06:39:42 2008
From: uludag at ebi.ac.uk (Mahmut Uludag)
Date: Thu, 23 Oct 2008 11:39:42 +0100
Subject: [EMBOSS] density
In-Reply-To: <50739.86.9.126.186.1224752945.squirrel@webmail.ebi.ac.uk>
References: <48FF386C.6030507@unil.ch>
	<41313.86.9.126.186.1224709755.squirrel@webmail.ebi.ac.uk>
	<49002B18.8020103@unil.ch>
	<50739.86.9.126.186.1224752945.squirrel@webmail.ebi.ac.uk>
Message-ID: <1224758382.2610.479.camel@emboss2.ebi.ac.uk>

Hi Alan,

> So it's a limitation of the web interface which requires
> all graphs to be called 'graph' ?

Yes this is a limitation in Soaplab dictated by the legacy acd2xml
parser.

> If I've understood you correctly then, attached, are two new
> versions of density.c and density.acd that only use one
> graph (called 'graph') with the -dual and -quad qualifiers
> working as before. I'll consider adding this to CVS. It
> is, of course, currently not tested that well. Please let
> me know how it behaves.

Modified density.c and density.acd files solved the problem in my local
Soaplab installation. One possible change would be to set a positive
default value either for the quad or the dual option.

I have noticed that dotmatcher and dottup programs also have two graphic
outputs. One of them called xygraph in both applications is not
recognised by Soaplab due to the same limitation.

Regards,
Mahmut
 
> HTH
> 
> Alan
> 
> 
> > Sorry,
> > the service, which provides EMBOSS tools as web interface, fails to
> > interprets properly the density ACD file.
> >
> > Everything is fine in the ACD.
> >
> >> Hi,
> >>
> >> colourps and cps are synonymous so you should be able to use either.
> >> If you want to specify the output type from the command line
> >> you could type:
> >>
> >>   density -quad -qgraph=colourps inputsequence
> >>
> >> for a quad graph (qgraph, not ggraph in your email) or, for a dual graph
> >>
> >>   density -dual -dgraph=cps inputsequence
> >>
> >> or am I misunderstanding your question?
> >>
> >> HTH
> >>
> >> Alan
> >>
> >>
> >>> Hi,
> >>>
> >>> According to the ACD file, the density application seems to use the
> >>> 'graph' qualifier.
> >>>
> >>> When used, I get this error message:
> >>> Unknown qualifier -graph=colourps
> >>>
> >>>
> >>> graph seems to have been replaced by ggraph and dgraph.
> >>> And colourps seems to be cps now.
> >>>
> >>>
> >>> How to fix it in the source ?
> >>> Thanks
> >
> > --
> > S?bastien Moretti
> > SIB EMBnet, Quartier Sorge - Genopode
> > CH-1015 Lausanne, Switzerland
> > Tel.: +41 (21) 692 4056/4221
> > http://ch.embnet.org/  http://myhits.vital-it.ch/
> >
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss


From Sebastien.Moretti at unil.ch  Thu Oct 23 07:05:36 2008
From: Sebastien.Moretti at unil.ch (Sebastien Moretti)
Date: Thu, 23 Oct 2008 13:05:36 +0200
Subject: [EMBOSS] density
In-Reply-To: <1224758382.2610.479.camel@emboss2.ebi.ac.uk>
References: <48FF386C.6030507@unil.ch>	
	<41313.86.9.126.186.1224709755.squirrel@webmail.ebi.ac.uk>	
	<49002B18.8020103@unil.ch>	
	<50739.86.9.126.186.1224752945.squirrel@webmail.ebi.ac.uk>
	<1224758382.2610.479.camel@emboss2.ebi.ac.uk>
Message-ID: <49005A80.1020500@unil.ch>

> Hi Alan,
> 
>> So it's a limitation of the web interface which requires
>> all graphs to be called 'graph' ?
> 
> Yes this is a limitation in Soaplab dictated by the legacy acd2xml
> parser.
> 
>> If I've understood you correctly then, attached, are two new
>> versions of density.c and density.acd that only use one
>> graph (called 'graph') with the -dual and -quad qualifiers
>> working as before. I'll consider adding this to CVS. It
>> is, of course, currently not tested that well. Please let
>> me know how it behaves.
> 
> Modified density.c and density.acd files solved the problem in my local
> Soaplab installation. One possible change would be to set a positive
> default value either for the quad or the dual option.
> 
> I have noticed that dotmatcher and dottup programs also have two graphic
> outputs. One of them called xygraph in both applications is not
> recognised by Soaplab due to the same limitation.
> 
> Regards,
> Mahmut

Following Mahmut' tests, it seems to work with your modifications.
Thanks

>> HTH
>>
>> Alan
>>
>>
>>> Sorry,
>>> the service, which provides EMBOSS tools as web interface, fails to
>>> interprets properly the density ACD file.
>>>
>>> Everything is fine in the ACD.
>>>
>>>> Hi,
>>>>
>>>> colourps and cps are synonymous so you should be able to use either.
>>>> If you want to specify the output type from the command line
>>>> you could type:
>>>>
>>>>   density -quad -qgraph=colourps inputsequence
>>>>
>>>> for a quad graph (qgraph, not ggraph in your email) or, for a dual graph
>>>>
>>>>   density -dual -dgraph=cps inputsequence
>>>>
>>>> or am I misunderstanding your question?
>>>>
>>>> HTH
>>>>
>>>> Alan
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> According to the ACD file, the density application seems to use the
>>>>> 'graph' qualifier.
>>>>>
>>>>> When used, I get this error message:
>>>>> Unknown qualifier -graph=colourps
>>>>>
>>>>>
>>>>> graph seems to have been replaced by ggraph and dgraph.
>>>>> And colourps seems to be cps now.
>>>>>
>>>>>
>>>>> How to fix it in the source ?
>>>>> Thanks

-- 
S?bastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

From gbottu at vub.ac.be  Fri Oct 24 11:26:15 2008
From: gbottu at vub.ac.be (Guy Bottu)
Date: Fri, 24 Oct 2008 17:26:15 +0200
Subject: [EMBOSS] question about delimiter in infoseq
Message-ID: <4901E917.80901@vub.ac.be>

	Dear Peter, dear Alan,

The ACD file of the program infoseq contains a parameter "delimiter" with 
default value "|". My attention was drawn on it because it causes an error when 
you try to run the program infoseq under Staden spin. But is this parameter used 
at all ? I failed to obtain an output file that contains the "|".

	Guy Bottu,
	BEN


From ajb at ebi.ac.uk  Fri Oct 24 12:10:14 2008
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Fri, 24 Oct 2008 17:10:14 +0100 (BST)
Subject: [EMBOSS] question about delimiter in infoseq
In-Reply-To: <4901E917.80901@vub.ac.be>
References: <4901E917.80901@vub.ac.be>
Message-ID: <49713.86.9.126.186.1224864614.squirrel@webmail.ebi.ac.uk>

Hi Guy,

The delimiter is used if you specify -nocolumns on the command line.

HTH

Alan


> 	Dear Peter, dear Alan,
>
> The ACD file of the program infoseq contains a parameter "delimiter" with
> default value "|". My attention was drawn on it because it causes an error
> when
> you try to run the program infoseq under Staden spin. But is this
> parameter used
> at all ? I failed to obtain an output file that contains the "|".
>
> 	Guy Bottu,
> 	BEN
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>