[EMBOSS] Impossible t ofetch a sequence from srs internet site with "seqret" command
simon stockes
simonstockes at yahoo.fr
Sat Nov 29 14:29:12 UTC 2003
Hi All,
I'm trying to fetch a sequence from srs site with "seqret" command and
got an error. This error was obtain from
"seqret -debug qasrswww:HSCAD5 HSCAD5.fasta" commande line and the
emboss.default part corresponding is :
DB qasrswww [
type: "N"
format: "embl"
methodquery: "srswww"
dbalias: "EMBL"
fields: "sv des org key"
url: "http://www.infobiogen.fr/srs71bin/cgi-bin/wgetz"
comment: "Remote SRS web server"
]
Config Mac OS 10.2.8, G3 ibook, /usr/local installation (with fink
installation I got the same error).
I suspect there is no proxy between me and the srs server.
The seqret.dbg file (see below) says : it get the sequence file but
there is a problem after ....
Hope tracks,
Simon.
seqret.dbg
=========
Debug file seqret.dbg buffered:No
ajFileNewIn '/usr/local/emboss/share/EMBOSS/acd/seqret.acd'
EOF ajFileGetsL file /usr/local/emboss/share/EMBOSS/acd/seqret.acd
closing file '/usr/local/emboss/share/EMBOSS/acd/seqret.acd'
ajFeatTabInNew 1b1320
ajSeqinClear called
ajFeattabInClear called
++seqUsaProcess 'qasrswww:HSCAD5' 0..0(N) '' 0
USA to test: 'qasrswww:HSCAD5'
format regexp: No list:No
no format specified in USA
...input format not set
dbname dbexp: Yes
found dbname 'qasrswww' level: '<null>' qry->QryString: 'HSCAD5'
seqQueryFieldC usa 'sv' fields 'sv des org key'
seqQueryField test 'sv'
seqQueryField match 'sv'
ajSeqQueryWild id 'HSCAD5' acc 'HSCAD5' sv 'HSCAD5' des '' org '' key ''
wild (has) query Sv 'HSCAD5'
database type: 'N' format 'embl'
use access method 'srswww'
Matched seqAccess[3] 'srswww'
seqAccessSrswww EMBL:HSCAD5
seqHttpUrl http://www.infobiogen.fr/srs71bin/cgi-bin/wgetz
searching with SRS url 'GET
/srs71bin/cgi-bin/wgetz?-e+-ascii+[EMBL-id:HSCAD5]|[EMBL-acc:HSCAD5]'
httpver getValueC '<null>'
httpver after qry '<null>'
host 'www.infobiogen.fr' port 80 get 'GET
/srs71bin/cgi-bin/wgetz?-e+-ascii+[EMBL-id:HSCAD5]|[EMBL-acc:HSCAD5]
HTTP/1.0
'
gethostbyname host 'www.infobiogen.fr' returns 'babbage.infobiogen.fr'
errno 0 hp_addr 193.52.226.5
creating socket
setup socket data
connecting to socket 4
sin sizeof 16
connect status 0 errno 0 msg 'Successful system call (0 - Undefined
error: 0)'
inet_ntoa '193.52.226.5'
sending: 'GET
/srs71bin/cgi-bin/wgetz?-e+-ascii+[EMBL-id:HSCAD5]|[EMBL-acc:HSCAD5]
HTTP/1.0
' status: 82
send for GET errno 0 msg 'Successful system call (0 - Undefined error:
0)'
sending: 'Host: www.infobiogen.fr:80
' status: 27
send for host errno 0 msg 'Successful system call (0 - Undefined error:
0)'
sending: '
' status: 1
send for blankline errno 0 msg 'Successful system call (0 - Undefined
error: 0)'
fdopen errno 0 msg 'Successful system call (0 - Undefined error: 0)'
EOF ajFileGetsL file
End of file - data in buffer - return ajFalse
First line [1] 'HTTP/1.1 200 OK
'
fileBuffLineDel removing line [1], 'HTTP/1.1 200 OK
' len 16
first line gone, new start [1] 1b5e60, '
' len 1
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
first line gone, new start [1] 1b5dd0, 'Date: Sat, 29 Nov 2003 09:46:49
GMT
' len 36
:[1] Date: Sat, 29 Nov 2003 09:46:49 GMT
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line [1] 1b5ea0, 'Server: Apache/1.3.27 (Unix) mod_perl/1.27
PHP/4.3.1
' len 53
:[1] Server: Apache/1.3.27 (Unix) mod_perl/1.27 PHP/4.3.1
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line [1] 1b6010, 'Connection: close
' len 18
:[1] Connection: close
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line [1] 1b60a0, 'Content-Type: text/plain
' len 25
:[1] Content-Type: text/plain
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line [1] 1b6130, '
' len 1
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line [1] 1b6170, '
' len 1
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line [1] 1b61b0, 'ID HSCAD5 standard; mRNA; HUM; 3170
BP.
' len 46
:[1] ID HSCAD5 standard; mRNA; HUM; 3170 BP.
:[1] XX
:[1] AC X59796;
:[1] XX
:[1] SV X59796.1
:[1] XX
:[1] DT 12-FEB-1992 (Rel. 30, Created)
:[1] DT 24-JAN-1995 (Rel. 42, Last updated, Version 6)
:[1] XX
:[1] DE H.sapiens mRNA for cadherin-5
:[1] XX
:[1] KW cadherin.
:[1] XX
:[1] OS Homo sapiens (human)
:[1] OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
Euteleostomi; Mammalia;
:[1] OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
:[1] XX
:[1] RN [1]
:[1] RP 1-3169
:[1] RA Suzuki S.;
:[1] RT ;
:[1] RL Submitted (16-MAY-1991) to the EMBL/GenBank/DDBJ databases.
:[1] RL S. Suzuki, Doheny Eye Institute, 1355 San Pablo St, Los
Angeles, CA 90033,
:[1] RL USA
:[1] XX
:[1] RN [2]
:[1] RP 1-3169
:[1] RX MEDLINE; 91283540.
:[1] RX PUBMED; 2059658.
:[1] RA Suzuki S., Sano K., Tanihara H.;
:[1] RT "Diversity of the cadherin family: evidence for eight new
cadherins in
:[1] RT nervous tissue";
:[1] RL Cell Regul. 2(4):261-270(1991).
:[1] XX
:[1] RN [3]
:[1] RP 1-3170
:[1] RA Suzuki S.;
:[1] RT ;
:[1] RL Submitted (24-JAN-1995) to the EMBL/GenBank/DDBJ databases.
:[1] RL S. Suzuki, Doheny Eye Institute, 1355 San Pablo St, Los
Angeles, CA 90033,
:[1] RL USA
:[1] XX
:[1] DR GOA; P33151.
:[1] DR SWISS-PROT; P33151; CAD5_HUMAN.
:[1] XX
:[1] FH Key Location/Qualifiers
:[1] FH
:[1] FT source 1..3170
:[1] FT /db_xref="taxon:9606"
:[1] FT /mol_type="mRNA"
:[1] FT /organism="Homo sapiens"
:[1] FT /dev_stage="fetus, 15-20 weeks"
:[1] FT /tissue_type="brain"
:[1] FT CDS 104..2446
:[1] FT /db_xref="GOA:P33151"
:[1] FT /db_xref="SWISS-PROT:P33151"
:[1] FT /product="cadherin-5"
:[1] FT /protein_id="CAA42468.1"
:[1] FT
/translation="MMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQKRDW
:[1] FT
IWNQMHIDEEKNTSLPHHVGKIKSSVSRKNAKYLLKGEYVGKVFRVDAETGDVFAIERL
:[1] FT
DRENISEYHLTAVIVDKDTGENLETPSSFTIKVHDVNDNWPVFTHRLFNASVPESSAVG
:[1] FT
TSVISVTAVDADDPTVGDHASVMYQILKGKEYFAIDNSGRIITITKSLDREKQARYEIV
:[1] FT
VEARDAQGLRGDSGTATVLVTLQDINDNFPFFTQTKYTFVVPEDTRVGTSVGSLFVEDP
:[1] FT
DEPQNRMTKYSILRGDYQDAFTIETNPAHNEGIIKPMKPLDYEYIQQYSFIVEATDPTI
:[1] FT
DLRYMSPPAGNRAQVIINITDVDEPPIFQQPFYHFQLKENQKKPLIGTVLAMDPDAARH
:[1] FT
SIGYSIRRTSDKGQFFRVTKKGDIYNEKELDREVYPWYNLTVEAKELDSTGTPTGKESI
:[1] FT
VQVHIEVLDENDNAPEFAKPYQPKVCENAVHGQLVLQISAIDKDITPRNVKFKFILNTE
:[1] FT
NNFTLTDNHDNTANITVKYGQFDREHTKVHFLPVVISDNGMPSRTGTSTLTVAVCKCNE
:[1] FT
QGEFTFCEDMAAQVGVSIQAVVAILLCILTITVITLLIFLRRRLRKQARAHGKSVPEIH
:[1] FT
EQLVTYDEEGGGEMDTTSYDVSVLNSVRRGGAKPPRPALDARPSLYAQVQKPPRHAPGA
:[1] FT
HGGPGEMAAMIEVKKDEADHDGDGPPYDTLHIYGYEGSESIAESLSSLGTDSSDSDVDY
:[1] FT DFLNDWGPRFKMLAELYGSDPREELLY"
:[1] XX
:[1] SQ Sequence 3170 BP; 773 A; 962 C; 844 G; 588 T; 3 other;
:[1] ctccactcac gctcagccct ggacggacag gcagtccaac ggaacagaaa
catccctcag 60
:[1] cccacaggca cgatctgttc ctcctgggaa gatgcagagg ctcatgatgc
tcctcgccac 120
:[1] atcgggcgcc tgcctgggcc tgctggcagt ggcagcagtg gcagcagcag
gtgctaaccc 180
:[1] tgcccaacgg gacacccaca gcctgctgcc cacccaccgg cgccaaaaga
gagattggat 240
:[1] ttggaaccag atgcacattg atgaagagaa aaacacctca cttccccatc
atgtaggcaa 300
:[1] gatcaagtca agcgtgagtc gcaagaatgc caagtacctg ctcaaaggag
aatatgtggg 360
:[1] caaggtcttc cgggtcgatg cagagacagg agacgtgttc gccattgaga
ggctggaccg 420
:[1] ggagaatatc tcagagtacc acctcactgc tgtcattgtg gacaaggaca
ctggcgaaaa 480
:[1] cctggagact ccttccagct tcaccatcaa agttcatgac gtgaacgaca
actggcctgt 540
:[1] gttcacgcat cggttgttca atgcgtccgt gcctgagtcg tcggctgtgg
ggacctcagt 600
:[1] catctctgtg acagcagtgg atgcagacga ccccactgtg ggagaccacg
cctctgtcat 660
:[1] gtaccaaatc ctgaagggga aagagtattt tgccatcgat aattctggac
gtattatcac 720
:[1] aataacgaaa agcttggacc gagagaagca ggccaggtat gagatcgtgg
tggaagcgcg 780
:[1] agatgcccag ggcctccggg gggactcggg cacggccacc gtgctggtca
ctctgcaaga 840
:[1] catcaatgac aacttcccct tcttcaccca gaccaagtac acatttgtcg
tgcctgaaga 900
:[1] cacccgtgtg ggcacctctg tgggctctct gtttgttgag gacccagatg
agccccagaa 960
:[1] ccggatgacc aagtacagca tcttgcgggg cgactaccag gacgctttca
ccattgagac 1020
:[1] aaaccccgcc cacaacgagg gcatcatcaa gcccatgaag cctctggatt
atgaatacat 1080
:[1] ccagcaatac agcttcatag tcgaggccac agaccccacc atcgacctcc
gatacatgag 1140
:[1] ccctcccgcg ggaaacagag cccaggtcat tatcaacatc acagatgtgg
acgagccccc 1200
:[1] cattttccag cagcctttct accacttcca gctgaaggaa aaccagaaga
agcctctgat 1260
:[1] tggcacagtg ctggccatgg accctgatgc ggctaggcat agcattggat
actccatccg 1320
:[1] caggaccagt gacaagggcc agttcttccg agtcacaaaa aagggggaca
tttacaatga 1380
:[1] gaaagaactg gacagagaag tctacccctg gtataacctg actgtggagg
ccaaagaact 1440
:[1] ggattccact ggaaccccca caggaaaaga atccattgtg caagtccaca
ttgaagtttt 1500
:[1] ggatgagaat gacaatgccc cggagtttgc caagccctac cagcccaaag
tgtgtgagaa 1560
:[1] cgctgtccat ggccagctgg tcctgcagat ctccgcaata gacaaggaca
taacaccacg 1620
:[1] aaacgtgaag ttcaaattca tcttgaatac tgagaacaac tttaccctca
cggataatca 1680
:[1] cgataacacg gccaacatca cagtcaagta tgggcagttt gaccgggagc
ataccaaggt 1740
:[1] ccacttccta cccgtggtca tctcagacaa tgggatgcca agtcgcacgg
gcaccagcac 1800
:[1] gctgaccgtg gccgtgtgca agtgcaacga gcagggcgag ttcaccttct
gcgaggatat 1860
:[1] ggccgcccag gtgggcgtga gcatccaggc agtggtagcc atcttactct
gcatcctcac 1920
:[1] catcacagtg atcaccctgc tcatcttcct gcggcggcgg ctccggaagc
aggcccgcgc 1980
:[1] gcacggcaag agcgtgccgg agatccacga gcagctggtc acctacgacg
aggagggcgg 2040
:[1] cggcgagatg gacaccacca gctacgatgt gtcggtgctc aactcggtgc
gccgcggcgg 2100
:[1] ggccaagccc ccgcggcccg cgctggacgc ccggccttcc ctctatgcgc
aggtgcagaa 2160
:[1] gccaccgagg cacgcgcctg gggcacacgg agggcccggg gagatggcag
ccatgatcga 2220
:[1] ggtgaagaag gacgaggcgg accacgacgg cgacggcccc ccctacgaca
cgctgcacat 2280
:[1] ctacggctac gagggctccg agtccatagc cgagtccctc agctccctgg
gcaccgactc 2340
:[1] atccgactct gacgtggatt acgacttcct taacgactgg ggacccaggt
ttaagatgct 2400
:[1] ggctgagctg tacggctcgg acccccggga ggagctgctg tattaggcgg
ccgaggtcac 2460
:[1] tctgggcctg gggacccaaa ccccctgcag cccaggccag tcagactcca
ggcaccacag 2520
:[1] cvncadctcc aaaaatggca gtgactcccc agcccagcac cccttcctcg
tgggtcccag 2580
:[1] agacctcatc agccttggga tagcaaactc caggttcctg aaatatccag
gaatatatgt 2640
:[1] cagtgatgac tattctcaaa tgctggcaaa tccaggctgg tgttctgtct
gggctcagac 2700
:[1] atccacataa ccctgtcacc cacagaccgc cgtctaactc aaagacttcc
tctggctccc 2760
:[1] caaggctgca aagcaaaaca gactgtgttt aactgctgca gggtcttttt
ctagggtccc 2820
:[1] tgaacgccct ggtaaggctg gtgaggtcct ggtgcctatc tgcctggagg
caaaggcctg 2880
:[1] gacagcttga cttgtggggc aggattctct gcagcccatt cccaagggag
actgaccatc 2940
:[1] atgccctctc tcgggagccc tagccctgct ccaactccat actccactcc
aagtgcccca 3000
:[1] ccactcccca acccctctcc aggcctgtca agagggagga aggggcccca
tggcagctcc 3060
:[1] tgaccttggg tcctgaagtg acctcactgg cctgccatgc cagtaactgt
gctgtactga 3120
:[1] gcactgaacc acattcaggg aaatggctta ttaaactttg aagcaactgt
3170
:[1] //
ajRegFree 1b27a0 size regexp 4
ajRegFree 1b2890 size regexp 4
ajRegFree 1b2960 size regexp 4
ajRegFree 1b29e0 size regexp 4
ajRegFree 1b2a80 size regexp 4
ajRegFree 1afa60 size regexp 4
ajRegFree 1afb30 size regexp 4
ajRegFree 1afbc0 size regexp 4
ajRegFree 1afc50 size regexp 4
seqRead: seqin format 3 'embl'
ajFeattableDel 0
seqRead: cleared
seqRead: one format specified
ajFileBuffNoBuff buffsize: 132
++seqRead known format 3
++seqReadFmt format 3 (embl) 'qasrswww:HSCAD5' feat No
seqReadEmbl first line 'Date: Sat, 29 Nov 2003 09:46:49 GMT
'
Format 3 (embl) failed, file buffer reset by seqReadFmt
++seqReadFmt failed - nothing read
seqRead: (b2) seqReadFmt stat == FAIL *failed*
ajFeattableDel 0
seqRead failed - try again with format 3 'embl'
++seqReadFmt format 3 (embl) 'qasrswww:HSCAD5' feat No
seqReadEmbl first line 'Date: Sat, 29 Nov 2003 09:46:49 GMT
'
Format 3 (embl) failed, file buffer reset by seqReadFmt
++seqReadFmt failed - nothing read
seqRead: (b3) seqReadFmt stat == FAIL *failed*
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