Functional test
This is a test of the CONSENSUS of protein secondary structure prediction (CNRS IBCP) service.
Test filesDownload the files for this test
Test runRun test now
Support reference#273-285
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view log 2 weeks agoPASSED
Test began: 2012-01-23 12:29:47 Test ended: 2012-01-23 12:30:03 Result : Test passed ------ stderr and stdout follow ------ waiting waiting waiting waiting waiting running done 0Download this log...
view log 2 weeks agoPASSED
Test began: 2012-01-21 16:59:50 Test ended: 2012-01-21 16:59:55 Result : Test passed ------ stderr and stdout follow ------ waiting done 0Download this log...
view log 4 weeks agoPASSED
Test began: 2012-01-10 01:26:09 Test ended: 2012-01-10 01:26:19 Result : Test passed ------ stderr and stdout follow ------ waiting waiting running done 0Download this log...
view log 4 weeks agoPASSED
Test began: 2012-01-09 12:52:48 Test ended: 2012-01-09 12:52:53 Result : Test passed ------ stderr and stdout follow ------ running done 0Download this log...
view log 4 weeks agoPASSED
Test began: 2012-01-08 18:46:57 Test ended: 2012-01-08 18:47:06 Result : Test passed ------ stderr and stdout follow ------ waiting waiting running done 0Download this log...
view log 4 weeks agoFAILED
Test began: 2012-01-07 19:53:28 Test ended: 2012-01-07 20:23:25 Result : Test failure ------ stderr and stdout follow ------ waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting 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waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting waiting Traceback (most recent call last): File "./gbiowstest-secons.py", line 92, inDownload this log...resp = port.checkStatusConsensus(req) File "/Library/WebServer.embraceregistry/Documents/sites/all/modules/ws_registry/registry/273/285/package/Consensus_Service_client.py", line 49, in checkStatusConsensus self.binding.Send(None, None, request, soapaction="urn:ConsensusWS.wsdl#checkStatusConsensus", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw) File "build/bdist.macosx-10.5-i386/egg/ZSI/client.py", line 291, in Send File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/httplib.py", line 679, in connect raise socket.error, msg socket.error: (60, 'Operation timed out')
view log 4 weeks agoPASSED
Test began: 2012-01-07 17:10:09 Test ended: 2012-01-07 17:10:16 Result : Test passed ------ stderr and stdout follow ------ waiting waiting done 0Download this log...
view log 1 month agoPASSED
Test began: 2012-01-05 18:03:43 Test ended: 2012-01-05 18:03:55 Result : Test passed ------ stderr and stdout follow ------ waiting waiting waiting running done 0Download this log...
view log 1 month agoPASSED
Test began: 2012-01-01 16:05:40 Test ended: 2012-01-01 16:05:47 Result : Test passed ------ stderr and stdout follow ------ waiting waiting done 0Download this log...
view log 1 month agoPASSED
Test began: 2011-12-29 19:27:03 Test ended: 2011-12-29 19:27:16 Result : Test passed ------ stderr and stdout follow ------ waiting waiting waiting waiting running done 0Download this log...
This test consists of the following files:
__MACOSX/
._gbiowstest-secons.py (binary file)
benchy_seq001.seq
>Unknow sequence for GBIO Web Services test ( C Blanchet, 14 jan 2009) MKKITIYDLAELSGVSASAVSAILNGNWKKRRISAKLAEKVTRIAEEQGYAINRQASMLR SKKSHVIGMIIPKYDNRYFGSIAERFEEMARERGLLPIITCTRRRPELEIEAVKAMLSWQ VDWVVATGATNPDKISALCQQAGVPTVNLDLPGSLSPSVISDNYGGAKALTHKILANSAR RRGELAPLTFIGGRRATITPASVYAASTMRIASWGLACRRRIFWLPAIRKATLRTACRSG LAARRRCCRGYLLTRRYPWKGLCAGCRRWV
Consensus_Service_client.py
##################################################
# file: Consensus_Service_client.py
#
# client stubs generated by "ZSI.generate.wsdl2python.WriteServiceModule"
# /usr/local/bin/wsdl2py http://gbio-pbil.ibcp.fr/ws/ConsensusWS.wsdl
#
##################################################
import urlparse, types
from ZSI.TCcompound import ComplexType, Struct
from ZSI import client
from ZSI.schema import GED, GTD
import ZSI
# Locator
class Consensus_ServiceLocator:
ConsensusPort_address = "http://gbio.ibcp.fr:8090/Consensus_Service"
def getConsensusPortAddress(self):
return Consensus_ServiceLocator.ConsensusPort_address
def getConsensusPort(self, url=None, **kw):
return ConsensusBindingSOAP(url or Consensus_ServiceLocator.ConsensusPort_address, **kw)
# Methods
class ConsensusBindingSOAP:
def __init__(self, url, **kw):
kw.setdefault("readerclass", None)
kw.setdefault("writerclass", None)
# no resource properties
self.binding = client.Binding(url=url, **kw)
# no ws-addressing
# op: submitConsensus
def submitConsensus(self, request, **kw):
if isinstance(request, submitConsensusRequest) is False:
raise TypeError, "%s incorrect request type" % (request.__class__)
# no input wsaction
self.binding.Send(None, None, request, soapaction="urn:ConsensusWS.wsdl#submitConsensus", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
# no output wsaction
typecode = Struct(pname=None, ofwhat=submitConsensusResponse.typecode.ofwhat, pyclass=submitConsensusResponse.typecode.pyclass)
response = self.binding.Receive(typecode)
return response
# op: checkStatusConsensus
def checkStatusConsensus(self, request, **kw):
if isinstance(request, checkStatusConsensusRequest) is False:
raise TypeError, "%s incorrect request type" % (request.__class__)
# no input wsaction
self.binding.Send(None, None, request, soapaction="urn:ConsensusWS.wsdl#checkStatusConsensus", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
# no output wsaction
typecode = Struct(pname=None, ofwhat=checkStatusConsensusResponse.typecode.ofwhat, pyclass=checkStatusConsensusResponse.typecode.pyclass)
response = self.binding.Receive(typecode)
return response
# op: getResultsConsensus
def getResultsConsensus(self, request, **kw):
if isinstance(request, getResultsConsensusRequest) is False:
raise TypeError, "%s incorrect request type" % (request.__class__)
# no input wsaction
self.binding.Send(None, None, request, soapaction="urn:ConsensusWS.wsdl#getResultsConsensus", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
# no output wsaction
typecode = Struct(pname=None, ofwhat=getResultsConsensusResponse.typecode.ofwhat, pyclass=getResultsConsensusResponse.typecode.pyclass)
response = self.binding.Receive(typecode)
return response
# op: cancelConsensus
def cancelConsensus(self, request, **kw):
if isinstance(request, cancelConsensusRequest) is False:
raise TypeError, "%s incorrect request type" % (request.__class__)
# no input wsaction
self.binding.Send(None, None, request, soapaction="urn:ConsensusWS.wsdl#cancelConsensus", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
# no output wsaction
typecode = Struct(pname=None, ofwhat=cancelConsensusResponse.typecode.ofwhat, pyclass=cancelConsensusResponse.typecode.pyclass)
response = self.binding.Receive(typecode)
return response
class submitConsensusRequest:
def __init__(self, **kw):
"""Keyword parameters:
SecStructure1 -- part SecStructure1
SecStructure2 -- part SecStructure2
SecStructure3 -- part SecStructure3
SecStructure4 -- part SecStructure4
SecStructure5 -- part SecStructure5
SecStructure6 -- part SecStructure6
"""
self._SecStructure1 = kw.get("SecStructure1")
self._SecStructure2 = kw.get("SecStructure2")
self._SecStructure3 = kw.get("SecStructure3")
self._SecStructure4 = kw.get("SecStructure4")
self._SecStructure5 = kw.get("SecStructure5")
self._SecStructure6 = kw.get("SecStructure6")
submitConsensusRequest.typecode = Struct(pname=("urn:Consensus_Service","submitConsensus"), ofwhat=[ZSI.TC.String(pname="SecStructure1", aname="_SecStructure1", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True), ZSI.TC.String(pname="SecStructure2", aname="_SecStructure2", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True), ZSI.TC.String(pname="SecStructure3", aname="_SecStructure3", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True), ZSI.TC.String(pname="SecStructure4", aname="_SecStructure4", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True), ZSI.TC.String(pname="SecStructure5", aname="_SecStructure5", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True), ZSI.TC.String(pname="SecStructure6", aname="_SecStructure6", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=submitConsensusRequest, encoded="urn:Consensus_Service")
class submitConsensusResponse:
def __init__(self, **kw):
"""Keyword parameters:
JobId -- part JobId
"""
self._JobId = kw.get("JobId")
submitConsensusResponse.typecode = Struct(pname=("urn:Consensus_Service","submitConsensusResponse"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=submitConsensusResponse, encoded="urn:Consensus_Service")
class checkStatusConsensusRequest:
def __init__(self, **kw):
"""Keyword parameters:
JobId -- part JobId
"""
self._JobId = kw.get("JobId")
checkStatusConsensusRequest.typecode = Struct(pname=("urn:Consensus_Service","checkStatusConsensus"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=checkStatusConsensusRequest, encoded="urn:Consensus_Service")
class checkStatusConsensusResponse:
def __init__(self, **kw):
"""Keyword parameters:
Status -- part Status
"""
self._Status = kw.get("Status")
checkStatusConsensusResponse.typecode = Struct(pname=("urn:Consensus_Service","checkStatusConsensusResponse"), ofwhat=[ZSI.TC.String(pname="Status", aname="_Status", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=checkStatusConsensusResponse, encoded="urn:Consensus_Service")
class getResultsConsensusRequest:
def __init__(self, **kw):
"""Keyword parameters:
JobId -- part JobId
"""
self._JobId = kw.get("JobId")
getResultsConsensusRequest.typecode = Struct(pname=("urn:Consensus_Service","getResultsConsensus"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=getResultsConsensusRequest, encoded="urn:Consensus_Service")
class getResultsConsensusResponse:
def __init__(self, **kw):
"""Keyword parameters:
SecConsensus -- part SecConsensus
"""
self._SecConsensus = kw.get("SecConsensus")
getResultsConsensusResponse.typecode = Struct(pname=("urn:Consensus_Service","getResultsConsensusResponse"), ofwhat=[ZSI.TC.String(pname="SecConsensus", aname="_SecConsensus", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=getResultsConsensusResponse, encoded="urn:Consensus_Service")
class cancelConsensusRequest:
def __init__(self, **kw):
"""Keyword parameters:
JobId -- part JobId
"""
self._JobId = kw.get("JobId")
cancelConsensusRequest.typecode = Struct(pname=("urn:Consensus_Service","cancelConsensus"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=cancelConsensusRequest, encoded="urn:Consensus_Service")
class cancelConsensusResponse:
def __init__(self, **kw):
"""Keyword parameters:
Status -- part Status
"""
self._Status = kw.get("Status")
cancelConsensusResponse.typecode = Struct(pname=("urn:Consensus_Service","cancelConsensusResponse"), ofwhat=[ZSI.TC.String(pname="Status", aname="_Status", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=cancelConsensusResponse, encoded="urn:Consensus_Service")
Consensus_Service_client.pyc (binary file)
Consensus_Service_types.py
################################################## # file: Consensus_Service_types.py # # schema types generated by "ZSI.generate.wsdl2python.WriteServiceModule" # /usr/local/bin/wsdl2py http://gbio-pbil.ibcp.fr/ws/ConsensusWS.wsdl # ################################################## import ZSI import ZSI.TCcompound from ZSI.schema import LocalElementDeclaration, ElementDeclaration, TypeDefinition, GTD, GED
control-seq001.Consensus
Secondary consensus
C. Blanchet
Laboratoire de Conformation des Proteines
http://www.ibcp.fr/team_fpgd.html
IBCP - CNRS UPR 412
7, passage du Vercors 69367 Lyon, FRANCE
MPSA code : secondary sequence GOR4 DSC SIMPA CONS
unknown
270 9 HETCSBGI?
namelen 19 ; blocklen 60
10 20 30 40 50 60
| | | | | |
unknown MKKITIYDLAELSGVSASAVSAILNGNWKKRRISAKLAEKVTRIAEEQGYAINRQASMLR
GOR 4 ccceeeeehhhhccchhhhhhhhhhcchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
DSC cccccchhhhhccccccchhhhhhcccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
SIMPA 96 ccceeehhhhhhccchhhhhhhhhccchhhhhhhhhhhhhhhhhhhhcccchhhhhhhhh
Sec. Cons. ccceeehhhhhhccchhhhhhhhhccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
70 80 90 100 110 120
| | | | | |
unknown SKKSHVIGMIIPKYDNRYFGSIAERFEEMARERGLLPIITCTRRRPELEIEAVKAMLSWQ
GOR 4 hhhceeeeeeeccccccccchhhhhhhhhhhhhcccceeccccccchhhhhhhhhhhhhc
DSC ccccceeeeecccccccccchhhhhhhhhhhhccccccchhcccccchhhhhhhhhccce
SIMPA 96 hchhhhheeeccccccchhhhhhhhhhhhhhhccceeeeeccccchhhhhhhhhhhhhhc
Sec. Cons. hchc?eeeeecccccccccchhhhhhhhhhhhcccccee?cccccchhhhhhhhhhhhhc
130 140 150 160 170 180
| | | | | |
unknown VDWVVATGATNPDKISALCQQAGVPTVNLDLPGSLSPSVISDNYGGAKALTHKILANSAR
GOR 4 eeeeeeccccccchhhhhccccccceecccccccccceeeecccccchhhhhhhhhhhhh
DSC eeeeeeccccccchhhhhhhccccceeeecccccccceeeecccccchhhhhhhhhhhhh
SIMPA 96 cceeeeccccchhhhhhhhhhcccceeeeccccccccceecccccchhhhhhhhhhhhhc
Sec. Cons. eeeeeeccccccchhhhhhhccccceeeecccccccceeeecccccchhhhhhhhhhhhh
190 200 210 220 230 240
| | | | | |
unknown RRGELAPLTFIGGRRATITPASVYAASTMRIASWGLACRRRIFWLPAIRKATLRTACRSG
GOR 4 hhcccccceecccccceecccchhhhchhhhhhhceeeccceeccccccchhhhhhhhhc
DSC hhcccccccccccccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhc
SIMPA 96 cccccceeeecccccccccccceecccceeeecccccchhhhhhcccchhhhhhhhhhcc
Sec. Cons. hhcccccceecccccccccccc??hhchhhhhhhc???hhhhhhcccchhhhhhhhhhhc
250 260 270 280 290 300
| | | | | |
unknown LAARRRCCRGYLLTRRYPWKGLCAGCRRWV
GOR 4 cccccccccceeeecccccceeecccccee
DSC cchhhhhhhccccccccccccccccccccc
SIMPA 96 ccccccccccceeccccccccccchhhhhhhhccccchhhhhhccccchhhhhhhhhcC
Sec. Cons. ccccccccccceeccccccccccccccc??control-seq001.Dsc
DSC - Ross D. King First sequence predicted Predicted accuracy = 0.66 Input format = PIR/Fasta/ASCII: Output format = PIR/Fasta/ASCII: Filter level = 1: Singlets are removed: Regions of bad alignment are removed if they have 40 residues with less than 20 percent identity. /**********************************************************/ /**********************************************************/ /**********************************************************/ Unknow MKKITIYDLA ELSGVSASAV SAILNGNWKK RRISAKLAEK VTRIAEEQGY DSC_SECCCCCCCHHHH HCCCCCCCHH HHHHCCCCHH HHHHHHHHHH HHHHHHHHHH PROB_H 3233114678 6421224344 5556421356 7797999999 9999999657 PROB_E 1013443111 1010121333 3432000101 1111000000 0000000000 PROB_C 6864553321 3679765433 2122689653 2202111111 1111111453 Unknow AINRQASMLR SKKSHVIGMI IPKYDNRYFG SIAERFEEMA RERGLLPIIT DSC_SECHHHHHHHHHH CCCCCEEEEE CCCCCCCCCC HHHHHHHHHH HHCCCCCCCH PROB_H 9999999996 4444422110 2211224444 6999999999 9621114447 PROB_E 0000000001 0000146667 3100000000 0000000000 0000111111 PROB_C 1111111113 6666542333 5799886666 4111111111 1489885552 Unknow CTRRRPELEI EAVKAMLSWQ VDWVVATGAT NPDKISALCQ QAGVPTVNLD DSC_SECHCCCCCCHHH HHHHHHCCCE EEEEEECCCC CCCHHHHHHH CCCCCEEEEC PROB_H 5431134679 9999974311 1000011111 1125775565 3111110001 PROB_E 1010010110 0000011345 5799962100 0000113322 1011257774 PROB_C 4669966321 1111125454 4311137899 9985222223 6988743335 Unknow LPGSLSPSVI SDNYGGAKAL THKILANSAR RRGELAPLTF IGGRRATITP DSC_SECCCCCCCCEEE ECCCCCCHHH HHHHHHHHHH HHCCCCCCCC CCCCCCCCCC PROB_H 0111101101 1222114899 7799999997 6542214444 4212221111 PROB_E 1111112576 5211000100 1111000000 0001211111 1101133322 PROB_C 9888897433 4677996111 2200111113 4567685555 5797756677 Unknow ASVYAASTMR IASWGLACRR RIFWLPAIRK ATLRTACRSG LAARRRCCRG DSC_SECCCCCHHHHHH HHHHHHHHHH HHHHHHHHHH HHHHHHHHHC CCHHHHHHHC PROB_H 2311455776 7786555556 7767679979 7777999954 4355899754 PROB_E 3344221111 1110000001 1111100000 0111000000 1112100000 PROB_C 5455434223 2214555553 2232331131 3222111156 5643111356 Unknow YLLTRRYPWK GLCAGCRRWV DSC_SECCCCCCCCCCC CCCCCCCCCC PROB_H 2333221123 2223234323 PROB_E 2331110001 1111010111 PROB_C 6446779986 7776866676 /**********************************************************/ /**********************************************************/ /**********************************************************/ NO. RES DSC_SEC PROB_H PROB_E PROB_C 1 m C 0.255 0.051 0.694 2 k C 0.185 0.021 0.794 3 k C 0.319 0.128 0.553 4 i C 0.302 0.299 0.399 5 t C 0.100 0.400 0.500 6 i C 0.100 0.400 0.500 7 y H 0.416 0.348 0.236 8 d H 0.621 0.113 0.266 9 l H 0.745 0.119 0.136 10 a H 0.790 0.067 0.143 11 e H 0.626 0.096 0.278 12 l C 0.366 0.042 0.592 13 s C 0.189 0.138 0.673 14 g C 0.070 0.040 0.890 15 v C 0.189 0.134 0.677 16 s C 0.239 0.180 0.581 17 a C 0.393 0.150 0.457 18 s C 0.302 0.299 0.399 19 a H 0.443 0.344 0.213 20 v H 0.416 0.348 0.236 21 s H 0.510 0.314 0.176 22 a H 0.524 0.381 0.095 23 i H 0.510 0.314 0.176 24 l H 0.603 0.167 0.230 25 n C 0.366 0.042 0.592 26 g C 0.185 0.021 0.794 27 n C 0.087 0.020 0.893 28 w C 0.255 0.051 0.694 29 k H 0.517 0.046 0.437 30 k H 0.626 0.096 0.278 31 r H 0.745 0.119 0.136 32 r H 0.686 0.149 0.165 33 i H 0.851 0.085 0.064 34 s H 0.686 0.149 0.165 35 a H 0.893 0.032 0.075 36 k H 0.945 0.014 0.041 37 l H 0.877 0.004 0.119 38 a H 0.877 0.004 0.119 39 e H 0.877 0.004 0.119 40 k H 0.877 0.004 0.119 41 v H 0.905 0.015 0.080 42 t H 0.945 0.014 0.041 43 r H 0.893 0.032 0.075 44 i H 0.893 0.032 0.075 45 a H 0.893 0.032 0.075 46 e H 0.905 0.015 0.080 47 e H 0.877 0.004 0.119 48 q H 0.589 0.036 0.375 49 g H 0.517 0.046 0.437 50 y H 0.723 0.020 0.257 51 a H 0.877 0.004 0.119 52 i H 0.905 0.015 0.080 53 n H 0.877 0.004 0.119 54 r H 0.877 0.004 0.119 55 q H 0.905 0.015 0.080 56 a H 0.945 0.014 0.041 57 s H 0.945 0.014 0.041 58 m H 0.893 0.032 0.075 59 l H 0.893 0.032 0.075 60 r H 0.626 0.096 0.278 61 s C 0.366 0.042 0.592 62 k C 0.366 0.042 0.592 63 k C 0.366 0.042 0.592 64 s C 0.366 0.042 0.592 65 h C 0.393 0.150 0.457 66 v E 0.198 0.418 0.384 67 i E 0.163 0.589 0.248 68 g E 0.144 0.648 0.208 69 m E 0.144 0.648 0.208 70 i E 0.026 0.696 0.278 71 i C 0.181 0.348 0.471 72 p C 0.189 0.134 0.677 73 k C 0.070 0.040 0.890 74 y C 0.091 0.027 0.882 75 d C 0.185 0.021 0.794 76 n C 0.185 0.021 0.794 77 r C 0.366 0.042 0.592 78 y C 0.366 0.042 0.592 79 f C 0.366 0.042 0.592 80 g C 0.366 0.042 0.592 81 s H 0.589 0.036 0.375 82 i H 0.905 0.015 0.080 83 a H 0.905 0.015 0.080 84 e H 0.877 0.004 0.119 85 r H 0.877 0.004 0.119 86 f H 0.905 0.015 0.080 87 e H 0.905 0.015 0.080 88 e H 0.877 0.004 0.119 89 m H 0.877 0.004 0.119 90 a H 0.877 0.004 0.119 91 r H 0.877 0.004 0.119 92 e H 0.589 0.036 0.375 93 r C 0.185 0.021 0.794 94 g C 0.070 0.040 0.890 95 l C 0.110 0.069 0.821 96 l C 0.110 0.069 0.821 97 p C 0.393 0.150 0.457 98 i C 0.400 0.100 0.500 99 i C 0.400 0.100 0.500 100 t H 0.662 0.080 0.259 101 c H 0.484 0.118 0.398 102 t C 0.366 0.042 0.592 103 r C 0.255 0.051 0.694 104 r C 0.087 0.020 0.893 105 r C 0.087 0.020 0.893 106 p C 0.255 0.051 0.694 107 e C 0.366 0.042 0.592 108 l H 0.626 0.096 0.278 109 e H 0.745 0.119 0.136 110 i H 0.910 0.036 0.054 111 e H 0.893 0.032 0.075 112 a H 0.893 0.032 0.075 113 v H 0.945 0.014 0.041 114 k H 0.945 0.014 0.041 115 a H 0.945 0.014 0.041 116 m H 0.662 0.080 0.259 117 l C 0.400 0.100 0.500 118 s C 0.302 0.299 0.399 119 w C 0.130 0.429 0.441 120 q E 0.056 0.476 0.468 121 v E 0.070 0.466 0.464 122 d E 0.026 0.696 0.278 123 w E 0.027 0.888 0.085 124 v E 0.027 0.888 0.085 125 v E 0.046 0.867 0.087 126 a E 0.144 0.648 0.208 127 t C 0.145 0.192 0.665 128 g C 0.088 0.085 0.827 129 a C 0.070 0.040 0.890 130 t C 0.091 0.027 0.882 131 n C 0.091 0.027 0.882 132 p C 0.087 0.020 0.893 133 d C 0.185 0.021 0.794 134 k H 0.517 0.046 0.437 135 i H 0.662 0.080 0.259 136 s H 0.686 0.149 0.165 137 a H 0.542 0.301 0.157 138 l H 0.542 0.301 0.157 139 c H 0.603 0.167 0.230 140 q H 0.519 0.156 0.325 141 q C 0.255 0.051 0.694 142 a C 0.070 0.040 0.890 143 g C 0.110 0.069 0.821 144 v C 0.062 0.088 0.850 145 p C 0.086 0.160 0.754 146 t E 0.056 0.476 0.468 147 v E 0.026 0.661 0.313 148 n E 0.026 0.661 0.313 149 l E 0.026 0.661 0.313 150 d C 0.067 0.365 0.568 151 l C 0.032 0.100 0.868 152 p C 0.062 0.121 0.817 153 g C 0.062 0.088 0.850 154 s C 0.062 0.121 0.817 155 l C 0.062 0.121 0.817 156 s C 0.032 0.100 0.868 157 p C 0.086 0.160 0.754 158 s E 0.056 0.476 0.468 159 v E 0.026 0.696 0.278 160 i E 0.094 0.650 0.256 161 s E 0.092 0.511 0.397 162 d C 0.239 0.180 0.581 163 n C 0.207 0.122 0.671 164 y C 0.207 0.122 0.671 165 g C 0.091 0.027 0.882 166 g C 0.087 0.020 0.893 167 a C 0.366 0.042 0.592 168 k H 0.751 0.065 0.184 169 a H 0.893 0.032 0.075 170 l H 0.893 0.032 0.075 171 t H 0.745 0.119 0.136 172 h H 0.686 0.149 0.165 173 k H 0.851 0.085 0.064 174 i H 0.851 0.085 0.064 175 l H 0.910 0.036 0.054 176 a H 0.945 0.014 0.041 177 n H 0.877 0.004 0.119 178 s H 0.877 0.004 0.119 179 a H 0.877 0.004 0.119 180 r H 0.723 0.020 0.257 181 r H 0.589 0.036 0.375 182 r H 0.517 0.046 0.437 183 g C 0.366 0.042 0.592 184 e C 0.210 0.090 0.700 185 l C 0.239 0.180 0.581 186 a C 0.110 0.069 0.821 187 p C 0.393 0.150 0.457 188 l C 0.400 0.100 0.500 189 t C 0.400 0.100 0.500 190 f C 0.400 0.100 0.500 191 i C 0.393 0.150 0.457 192 g C 0.207 0.122 0.671 193 g C 0.087 0.020 0.893 194 r C 0.207 0.122 0.671 195 r C 0.189 0.138 0.673 196 a C 0.194 0.267 0.539 197 t C 0.119 0.260 0.621 198 i C 0.119 0.260 0.621 199 t C 0.059 0.209 0.732 200 p C 0.101 0.175 0.725 201 a C 0.194 0.267 0.539 202 s C 0.275 0.330 0.395 203 v C 0.100 0.400 0.500 204 y C 0.100 0.400 0.500 205 a H 0.422 0.216 0.362 206 a H 0.519 0.156 0.325 207 s H 0.484 0.118 0.398 208 t H 0.662 0.080 0.259 209 m H 0.745 0.119 0.136 210 r H 0.621 0.113 0.266 211 i H 0.686 0.149 0.165 212 a H 0.745 0.119 0.136 213 s H 0.751 0.065 0.184 214 w H 0.589 0.036 0.375 215 g H 0.517 0.046 0.437 216 l H 0.517 0.046 0.437 217 a H 0.517 0.046 0.437 218 c H 0.517 0.046 0.437 219 r H 0.517 0.046 0.437 220 r H 0.626 0.096 0.278 221 r H 0.745 0.119 0.136 222 i H 0.686 0.149 0.165 223 f H 0.621 0.113 0.266 224 w H 0.662 0.080 0.259 225 l H 0.626 0.096 0.278 226 p H 0.723 0.020 0.257 227 a H 0.877 0.004 0.119 228 i H 0.877 0.004 0.119 229 r H 0.723 0.020 0.257 230 k H 0.877 0.004 0.119 231 a H 0.723 0.020 0.257 232 t H 0.662 0.080 0.259 233 l H 0.662 0.080 0.259 234 r H 0.745 0.119 0.136 235 t H 0.945 0.014 0.041 236 a H 0.905 0.015 0.080 237 c H 0.877 0.004 0.119 238 r H 0.877 0.004 0.119 239 s H 0.517 0.046 0.437 240 g C 0.366 0.042 0.592 241 l C 0.400 0.100 0.500 242 a C 0.319 0.128 0.553 243 a H 0.484 0.118 0.398 244 r H 0.519 0.156 0.325 245 r H 0.751 0.065 0.184 246 r H 0.905 0.015 0.080 247 c H 0.877 0.004 0.119 248 c H 0.723 0.020 0.257 249 r H 0.517 0.046 0.437 250 g C 0.366 0.042 0.592 251 y C 0.249 0.234 0.517 252 l C 0.302 0.299 0.399 253 l C 0.302 0.299 0.399 254 t C 0.319 0.128 0.553 255 r C 0.210 0.090 0.700 256 r C 0.207 0.122 0.671 257 y C 0.091 0.027 0.882 258 p C 0.087 0.020 0.893 259 w C 0.185 0.021 0.794 260 k C 0.255 0.051 0.694 261 g C 0.189 0.138 0.673 262 l C 0.189 0.138 0.673 263 c C 0.210 0.090 0.700 264 a C 0.255 0.051 0.694 265 g C 0.185 0.021 0.794 266 c C 0.255 0.051 0.694 267 r C 0.366 0.042 0.592 268 r C 0.255 0.051 0.694 269 w C 0.210 0.090 0.700 270 v C 0.255 0.051 0.694
control-seq001.GorIV
Unknow sequence for GBIO Web Services test ( C Blanchet, 14 jan 2009) 270 SEQ PRD H E C M C 0.000 0.002 0.998 K C 0.000 0.015 0.985 K C 0.000 0.238 0.762 I E 0.000 0.698 0.302 T E 0.000 0.900 0.100 I E 0.002 0.940 0.058 Y E 0.013 0.763 0.224 D E 0.079 0.527 0.394 L H 0.559 0.197 0.244 A H 0.506 0.203 0.292 E H 0.581 0.153 0.265 L H 0.498 0.087 0.415 S C 0.299 0.116 0.585 G C 0.310 0.097 0.593 V C 0.383 0.093 0.525 S H 0.519 0.099 0.381 A H 0.674 0.081 0.245 S H 0.638 0.120 0.242 A H 0.656 0.171 0.173 V H 0.511 0.373 0.116 S H 0.441 0.437 0.122 A H 0.590 0.324 0.086 I H 0.433 0.473 0.093 L H 0.638 0.189 0.173 N H 0.525 0.033 0.441 G C 0.333 0.054 0.613 N C 0.315 0.007 0.678 W H 0.587 0.010 0.403 K H 0.635 0.031 0.334 K H 0.698 0.052 0.250 R H 0.726 0.088 0.187 R H 0.776 0.105 0.119 I H 0.701 0.151 0.148 S H 0.664 0.131 0.204 A H 0.779 0.096 0.125 K H 0.807 0.040 0.153 L H 0.798 0.039 0.164 A H 0.806 0.019 0.176 E H 0.811 0.022 0.167 K H 0.812 0.025 0.163 V H 0.833 0.036 0.130 T H 0.751 0.094 0.155 R H 0.767 0.116 0.117 I H 0.772 0.130 0.098 A H 0.812 0.072 0.115 E H 0.794 0.040 0.166 E H 0.737 0.039 0.224 Q H 0.671 0.026 0.303 G H 0.632 0.043 0.325 Y H 0.667 0.099 0.233 A H 0.593 0.205 0.202 I H 0.677 0.205 0.118 N H 0.715 0.132 0.153 R H 0.762 0.101 0.137 Q H 0.878 0.042 0.079 A H 0.850 0.067 0.084 S H 0.746 0.148 0.107 M H 0.767 0.094 0.139 L H 0.756 0.120 0.123 R H 0.693 0.104 0.203 S H 0.502 0.183 0.315 K H 0.496 0.106 0.398 K H 0.436 0.134 0.430 S C 0.360 0.231 0.410 H E 0.327 0.343 0.331 V E 0.176 0.624 0.201 I E 0.170 0.671 0.158 G E 0.082 0.734 0.183 M E 0.082 0.664 0.254 I E 0.039 0.777 0.184 I E 0.085 0.596 0.319 P C 0.093 0.135 0.772 K C 0.093 0.164 0.742 Y C 0.120 0.132 0.748 D C 0.138 0.094 0.768 N C 0.162 0.064 0.774 R C 0.216 0.139 0.645 Y C 0.230 0.204 0.566 F C 0.242 0.301 0.457 G C 0.255 0.325 0.420 S H 0.304 0.393 0.303 I H 0.590 0.243 0.167 A H 0.818 0.080 0.102 E H 0.821 0.052 0.127 R H 0.879 0.026 0.096 F H 0.934 0.013 0.054 E H 0.953 0.011 0.036 E H 0.962 0.007 0.032 M H 0.965 0.002 0.032 A H 0.949 0.010 0.041 R H 0.948 0.005 0.048 E H 0.887 0.018 0.095 R H 0.442 0.155 0.403 G C 0.104 0.200 0.696 L C 0.151 0.335 0.514 L C 0.114 0.450 0.436 P C 0.149 0.329 0.522 I E 0.166 0.559 0.274 I E 0.145 0.577 0.279 T C 0.174 0.405 0.420 C C 0.181 0.147 0.673 T C 0.206 0.124 0.671 R C 0.235 0.049 0.716 R C 0.131 0.074 0.795 R C 0.042 0.039 0.919 P C 0.293 0.010 0.697 E H 0.544 0.016 0.440 L H 0.591 0.087 0.322 E H 0.732 0.057 0.211 I H 0.877 0.064 0.058 E H 0.697 0.235 0.067 A H 0.795 0.123 0.082 V H 0.790 0.136 0.074 K H 0.857 0.052 0.091 A H 0.654 0.215 0.131 M H 0.481 0.377 0.143 L H 0.511 0.251 0.238 S H 0.502 0.189 0.309 W H 0.539 0.182 0.279 Q C 0.360 0.207 0.432 V E 0.399 0.419 0.182 D E 0.177 0.664 0.159 W E 0.226 0.622 0.152 V E 0.090 0.866 0.045 V E 0.135 0.785 0.080 A E 0.245 0.560 0.195 T C 0.155 0.228 0.617 G C 0.089 0.157 0.754 A C 0.053 0.078 0.869 T C 0.044 0.065 0.891 N C 0.025 0.051 0.924 P C 0.164 0.043 0.793 D C 0.305 0.028 0.666 K H 0.486 0.072 0.442 I H 0.621 0.168 0.211 S H 0.646 0.186 0.168 A H 0.606 0.216 0.177 L H 0.427 0.327 0.246 C C 0.350 0.242 0.409 Q C 0.360 0.124 0.516 Q C 0.278 0.127 0.595 A C 0.072 0.096 0.832 G C 0.021 0.079 0.901 V C 0.031 0.207 0.762 P C 0.036 0.316 0.648 T E 0.041 0.557 0.401 V E 0.059 0.475 0.466 N C 0.067 0.448 0.486 L C 0.060 0.430 0.510 D C 0.041 0.349 0.610 L C 0.033 0.163 0.804 P C 0.033 0.054 0.912 G C 0.028 0.068 0.904 S C 0.016 0.080 0.904 L C 0.024 0.129 0.847 S C 0.031 0.149 0.819 P C 0.099 0.141 0.760 S E 0.088 0.478 0.434 V E 0.111 0.613 0.276 I E 0.157 0.646 0.198 S E 0.253 0.434 0.313 D C 0.249 0.220 0.532 N C 0.261 0.125 0.614 Y C 0.269 0.141 0.590 G C 0.232 0.093 0.675 G C 0.287 0.049 0.664 A C 0.401 0.063 0.536 K H 0.558 0.081 0.361 A H 0.660 0.167 0.174 L H 0.597 0.227 0.177 T H 0.579 0.276 0.145 H H 0.756 0.142 0.103 K H 0.775 0.134 0.091 I H 0.764 0.130 0.106 L H 0.716 0.177 0.107 A H 0.735 0.118 0.147 N H 0.732 0.041 0.227 S H 0.703 0.023 0.274 A H 0.704 0.025 0.271 R H 0.696 0.028 0.277 R H 0.639 0.050 0.312 R H 0.551 0.060 0.389 G C 0.371 0.078 0.551 E C 0.248 0.167 0.586 L C 0.224 0.313 0.463 A C 0.174 0.233 0.593 P C 0.295 0.137 0.568 L C 0.358 0.259 0.383 T E 0.316 0.408 0.276 F E 0.371 0.388 0.241 I C 0.256 0.312 0.432 G C 0.170 0.185 0.645 G C 0.128 0.114 0.758 R C 0.115 0.237 0.648 R C 0.157 0.383 0.460 A C 0.117 0.356 0.526 T E 0.106 0.463 0.430 I E 0.140 0.442 0.417 T C 0.050 0.328 0.622 P C 0.192 0.195 0.613 A C 0.193 0.188 0.619 S C 0.273 0.242 0.484 V H 0.452 0.257 0.291 Y H 0.580 0.153 0.267 A H 0.439 0.224 0.337 A H 0.443 0.172 0.385 S C 0.394 0.168 0.439 T H 0.471 0.273 0.257 M H 0.531 0.289 0.180 R H 0.108 0.818 0.074 I H 0.305 0.623 0.072 A H 0.420 0.451 0.129 S H 0.484 0.233 0.283 W H 0.640 0.086 0.274 G C 0.407 0.114 0.479 L E 0.176 0.626 0.198 A E 0.307 0.435 0.258 C E 0.409 0.200 0.391 R C 0.299 0.247 0.454 R C 0.351 0.181 0.468 R C 0.330 0.183 0.487 I E 0.155 0.494 0.351 F E 0.362 0.317 0.321 W C 0.269 0.194 0.537 L C 0.108 0.318 0.574 P C 0.273 0.103 0.623 A C 0.474 0.225 0.301 I C 0.465 0.132 0.403 R C 0.148 0.430 0.421 K C 0.384 0.189 0.427 A H 0.314 0.415 0.270 T H 0.251 0.454 0.295 L H 0.495 0.319 0.186 R H 0.522 0.285 0.193 T H 0.720 0.134 0.146 A H 0.737 0.111 0.152 C H 0.682 0.064 0.253 R H 0.766 0.042 0.192 S H 0.490 0.137 0.373 G C 0.197 0.337 0.467 L C 0.498 0.110 0.393 A C 0.523 0.105 0.372 A C 0.414 0.130 0.456 R C 0.397 0.095 0.508 R C 0.324 0.155 0.521 R C 0.496 0.237 0.267 C C 0.306 0.366 0.328 C C 0.225 0.292 0.483 R C 0.184 0.212 0.604 G C 0.062 0.294 0.644 Y E 0.024 0.701 0.274 L E 0.028 0.762 0.211 L E 0.023 0.677 0.301 T E 0.021 0.588 0.391 R C 0.008 0.331 0.660 R C 0.023 0.299 0.678 Y C 0.030 0.428 0.542 P C 0.037 0.257 0.706 W C 0.068 0.248 0.684 K C 0.039 0.465 0.497 G E 0.005 0.801 0.194 L E 0.006 0.818 0.175 C E 0.006 0.641 0.353 A C 0.004 0.388 0.607 G C 0.001 0.418 0.582 C C 0.001 0.085 0.914 R C 0.000 0.128 0.872 R C 0.000 0.342 0.658 W E 0.000 0.888 0.112 V E 0.000 0.984 0.016
control-seq001.Simpa96
SIMPA96 secondary structure prediction program
H = helix b = strand . = other
Scale indicates prediction strength: 0-weak, 2-medium, 5-strong 9-very strong
secondary structure prediction without homologues
sequence 1
Unknow sequence for GBIO Web Services test ( C Blanchet, 14 jan 2009
10 20 30 40 50 60
sequence MKKITIYDLAELSGVSASAVSAILNGNWKKRRISAKLAEKVTRIAEEQGYAINRQASMLR
prediction ...bbbHHHHHH...HHHHHHHHH...HHHHHHHHHHHHHHHHHHHH....HHHHHHHHH
scale 142122102211233201232221244211222345544454443312430000023443
70 80 90 100 110 120
sequence SKKSHVIGMIIPKYDNRYFGSIAERFEEMARERGLLPIITCTRRRPELEIEAVKAMLSWQ
prediction H.HHHHHbbb.......HHHHHHHHHHHHHHH...bbbbb.....HHHHHHHHHHHHHH.
scale 001010001202345310002455566654422640244212223111233344443201
130 140 150 160 170 180
sequence VDWVVATGATNPDKISALCQQAGVPTVNLDLPGSLSPSVISDNYGGAKALTHKILANSAR
prediction ..bbbb.....HHHHHHHHHH....bbbb.........bb......HHHHHHHHHHHHH.
scale 010230255673024433331476402101467545411114445410223433431110
190 200 210 220 230 240
sequence RRGELAPLTFIGGRRATITPASVYAASTMRIASWGLACRRRIFWLPAIRKATLRTACRSG
prediction ......bbbb............bb....bbbb......HHHHHH....HHHHHHHHHH..
scale 013310034304542110343200122101100133210000001211100122331023
250 260 270 280 290
sequence LAARRRCCRGYLLTRRYPWKGLCAGCRRWVASWGLACRRRIFWLPAIRKATLRTACRSG
prediction ...........bb...........HHHHHHHH.....HHHHHH.....HHHHHHHHH..
scale 21010012331122444222313210221120121000000001211100021121024gbiowstest-secons.py
#!/usr/bin/env python
# ================================================================================
#
# COPYRIGHT NOTICE
#
# Centre National de la Recherche Scientifique
# CNRS
#
# Institut de Biologie et Chimie des Proteines
# IBCP CNRS UMR 5086
# 7 passage du Vercors
# 69007 Lyon, FRANCE
#
# This software/database is covered by copyright of CNRS IBCP
# All rights reserved. Reproduction and usage of this software/database are
# strictly restricted, and need a prior written permission from CNRS IBCP
# (see "Contact" below).
#
# CNRS IBCP do not and cannot warrant the performance or results that
# may be obtained by using this software or data. CNRS IBCP disclaim all
# warranties, express or implied, including warranties of performance,
# merchantability or fitness for any particular purpose.
#
# ================================================================================
#
# Author: Christophe Blanchet
#
# Contact: Christophe.Blanchet@ibcp.fr
#
# First Version Creation Date: 18/11/2008
#
# $Revision: 1.0 $
#
# File Description:
#
#
# Modifications:
# --------------------------------------------------------------------------
# Date Name Description of modification
# ------- ---------- -----------------------------------------------------
#
# ================================================================================
import sys
import time
from Consensus_Service_client import *
secstructs = { '_SecStructure1': 'control-seq001.GorIV'
, '_SecStructure2': 'control-seq001.Dsc'
, '_SecStructure3': 'control-seq001.Simpa96'
# , '_SecStructure4': 'control-seq001.Predator'
, '_SecStructure4': ''
, '_SecStructure5': ''
, '_SecStructure6': ''
}
fn_input = 'benchy_seq001.seq'
fn_control = 'control-seq001.Consensus'
ret = 0
# get a port proxy instance
loc = Consensus_ServiceLocator()
port = loc.getConsensusPort()
###
# submit a new request
# create
req = submitConsensusRequest()
# populate
for cursec in secstructs.keys():
if not secstructs[cursec]:
req.__dict__[cursec] = ''
continue
#print secstructs[cursec]
fp_input = open (secstructs[cursec], 'r')
req.__dict__[cursec] = fp_input.read()
#print req.__dict__[cursec]
# call the remote method
resp = port.submitConsensus(req)
jobid = resp._JobId
#print jobid
if not jobid:
ret = 1
###
# check status
# while status different of 'done' or 'aborted', check again
status = 'init'
req = checkStatusConsensusRequest()
req._JobId = jobid
while status not in ('done','aborted'):
time.sleep(2)
resp = port.checkStatusConsensus(req)
status = resp._Status
print status
if status != 'done':
ret = 1
###
# get results
req = getResultsConsensusRequest()
req._JobId = jobid
resp = port.getResultsConsensus(req)
# write result
#open(fn_control,'w').write(resp._SecConsensus)
#open('result-file.txt','w').write(resp._SecConsensus)
#compare result with ref
resultcontrol = open(fn_control, 'r').read()
if resp._SecConsensus != resultcontrol:
ret = 1
#print "wooohh"
print ret
sys.exit (ret)
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