Functional test
This is a test of the CONSENSUS of protein secondary structure prediction (CNRS IBCP) service.
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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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