Multalin functionnal test

>CCPA_BACME GLUCOSE-RESISTANCE AMYLASE REGULATOR (CATABOLITE CONTROL PROTEIN).
MNVTIYDVAREASVSMATVSRVVNGNPNVKPSTRKKVLETIERLGYRPNAVARGLASKKT
TTVGVIIPDISNIFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNMLGKQVDGI
IFMSGNVTEEHVEELKKSPVPVVLAASIESTNQIPSVTIDYEQAAFDAVQSLIDSGHKNI
AFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIVEGDYTYDSGIEAVEKLLEEDEKP
TAIFVGTDEMALGVIHGAQDRGLNVPNDLEIIGFDNTRLSTMVRPQLTSVVQPMYDIGAV
AMRLLTKYMNKETVDSSIVQLPHRIEFRQSTK
>CCPA_BACSU GLUCOSE-RESISTANCE AMYLASE REGULATOR (CATABOLITE CONTROL PROTEIN).
MSNITIYDVAREANVSMATVSRVVNGNPNVKPTTRKKVLEAIERLGYRPNAVARGLASKK
TTTVGVIIPDISSIFYSELARGIEDIATMYKYNIILSNSDQNMEKELHLLNTMLGKQVDG
IVFMGGNITDEHVAEFKRSPVPIVLAASVEEQEETPSVAIDYEQAIYDAVKLLVDKGHTD
IAFVSGPMAEPINRSKKLQGYKRALEEANLPFNEQFVAEGDYTYDSGLEALQHLMSLDKK
PTAILSATDEMALGIIHAAQDQGLSIPEDLDIIGFDNTRLSLMVRPQLSTVVQPTYDIGA
VAMRLLTKLMNKEPVEEHIVELPHRIELRKSTKS
>CCPA_STRMU PROBABLE CATABOLITE CONTROL PROTEIN A.
MNTDDTITIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARGLA
SKKTTTVGVVIPNIANAYFSILAKGIDDIATMYKYNIVLASSDEDDDKEVNVINTLFAKQ
VDGIIFMGHHLTEKIRAEFSRARTPVVLSGTVDLEHQLPSVNIDHSKAAQDAVALLAKHH
DKIAFVSGPLIDDINGKVRLAGYKEGLKKKGLPFKEGLVFEAQYKYQEGYQLAQRVINSG
ATAAYVAEDELAAGLLNGLFAAGRKVPEDFEIITSNDSTIALYTRPNMTSISQPIYDLGA
VAMRMLTKIMNKEELEEKEIVLNHGIKKRGTTK
>DEGA_BACSU DEGRADATION ACTIVATOR.
MKTTIYDVAKAAGVSITTVSRVINNTGRISDKTRQKVMNVMNEMAYTPNVHAAALTGKRT
NMIALVAPDISNPFYGELAKSIEERADELGFQMLICSTDYDPKKETKYFSVLKQKKVDGI
IFATGIESHDSMSALEEIASEQIPIAMISQDKPLLPMDIVVIDDVRGGYEAAKHLLSLGH
TNIACIIGDGSTTGEKNRIKGFRQAMEEAGVPIDESLIIQTRFSLESGKEEAGKLLDRNA
PTAIFAFNDVLACAAIQAARIRGIKVPDDLSIIGFDNTILAEMAAPPLTTVAQPIKEMGA
ERHRTAGRSNRGKRKAKQKIVLPPELVVRHSTSPLNT
>FRUR_ECOLI FRUCTOSE REPRESSOR.
MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPNAVAAGLRAGR
TRSIGLVIPDLENTSYTRIANYLERQARQRGYQLLIACSEDQPDNEMRCIEHLLQRQVDA
IIVSTSLPPEHPFYQRWANDPFPIVALDRALDREHFTSVVGADQDDAEMLAEELRKFPAE
TVLYLGALPELSVSFLREQGFRTAWKDDPREVHFLYANSYEREAAAQLFEKWLETHPMPQ
ALFTTSFALLQGVMDVTLRRDGKLPSDLAIATFGDNELLDFLQCPVLAVAQRHRDVAERV
LEIVLASLDEPRKPKPGLTRIKRNLYRRGVLSRS
>RBTR_KLEAE RIBITOL (RBT) OPERON REPRESSOR.
MKKITIYDLAELSGVSASAVSAILNGNWKKRRISAKLAEKVTRIAEEQGYAINRQASMLR
SKKSHVIGMIIPKYDNRYFGSIAERFEEMARERGLLPIITCTRRRPELEIEAVKAMLSWQ
VDWVVATGATNPDKISALCQQAGVPTVNLDLPGSLSPSVISDNYGGAKALTHKILANSAR
RRGELAPLTFIGGRRATITPASVYAASTMRIASWGLACRRRIFWLPAIRKATLRTACRSG
LAARRRCCRGYLLTRRYPWKGLCAGCRRWV

Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Symbol comparison table: blosum62
Gap weight: 12
Gap length weight: 2
Consensus levels: high=90% low=50%
Consensus symbols:
 ! is anyone of IV
 $ is anyone of LM
 % is anyone of FY
 # is anyone of NDQEBZ

 MSF:    346    Check:   0         ..
 Name: CCPA_BACME     Len:   346  Check: 6548  Weight:  0.42
 Name: CCPA_BACSU     Len:   346  Check: 7212  Weight:  0.42
 Name: CCPA_STRMU     Len:   346  Check: 4395  Weight:  0.82
 Name: DEGA_BACSU     Len:   346  Check: 6161  Weight:  1.17
 Name: FRUR_ECOLI     Len:   346  Check: 3223  Weight:  1.41
 Name: RBTR_KLEAE     Len:   346  Check: 8225  Weight:  1.76
 Name: Consensus      Len:   346  Check: 7673  Weight:  0.00

//

                      1                                                   50
          CCPA_BACME  ....MNVTIY DVAREASVSM ATVSRVVNGN P...NVKPST RKKVLETIER
          CCPA_BACSU  ...MSNITIY DVAREANVSM ATVSRVVNGN P...NVKPTT RKKVLEAIER
          CCPA_STRMU  MNTDDTITIY DVAREAGVSM ATVSRVVNGN K...NVKENT RKKVLEVIDR
          DEGA_BACSU  ....MKTTIY DVAKAAGVSI TTVSRVINNT G...RISDKT RQKVMNVMNE
          FRUR_ECOLI  ......MKLD EIARLAGVSR TTASYVINGK AKQYRVSDKT VEKVMAVVRE
          RBTR_KLEAE  ...MKKITIY DLAELSGVSA SAVSAILNGN WKKRRISAKL AEKVTRIAEE
           Consensus  ......itiy #.ArlagVS. .tvS.!.Ngn .k..r!s.kt .eKV..v..e

                      51                                                 100
          CCPA_BACME  LGYRPNAVAR GLASKKTTTV GVIIPDISNI FYAELARGIE DIATMYKYNI
          CCPA_BACSU  LGYRPNAVAR GLASKKTTTV GVIIPDISSI FYSELARGIE DIATMYKYNI
          CCPA_STRMU  LDYRPNAVAR GLASKKTTTV GVVIPNIANA YFSILAKGID DIATMYKYNI
          DEGA_BACSU  MAYTPNVHAA ALTGKRTNMI ALVAPDISNP FYGELAKSIE ERADELGFQM
          FRUR_ECOLI  HNYHPNAVAA GLRAGRTRSI GLVIPDLENT SYTRIANYLE RQARQRGYQL
          RBTR_KLEAE  QGYAINRQAS MLRSKKSHVI GMIIPKYDNR YFGSIAERFE EMARERGLLP
           Consensus  ..Y.pNavA. gLrskkt..! g.!iPd..N. .%..iA...# ..Ar.rgy..

                      101                                                150
          CCPA_BACME  ILSNSDQNQD KELHLLNNML GKQVDGIIFM SG...NVTEE HVEELKKSPV
          CCPA_BACSU  ILSNSDQNME KELHLLNTML GKQVDGIVFM GG...NITDE HVAEFKRSPV
          CCPA_STRMU  VLASSDEDDD KEVNVINTLF AKQVDGIIFM GH...HLTEK IRAEFSRART
          DEGA_BACSU  LICSTDYDPK KETKYFSVLK QKKVDGIIFA TGIESHDSMS ALEEIASEQI
          FRUR_ECOLI  LIACSEDQPD NEMRCIEHLL QRQVDAIIVS TSL..PPEHP FYQRWANDPF
          RBTR_KLEAE  IITCTRRRPE LEIEAVKAML SWQVDWVVAT GATNPDKISA LCQQAGVPTV
           Consensus  .i.cs...p. .E......$l ..qVD.!!.. g......... ..q.......

                      151                                                200
          CCPA_BACME  PVVLAASIES TNQIPSVTID YEQAAFDAVQ SLIDSGHKNI AFVSGTLEEP
          CCPA_BACSU  PIVLAASVEE QEETPSVAID YEQAIYDAVK LLVDKGHTDI AFVSGPMAEP
          CCPA_STRMU  PVVLSGTVDL EHQLPSVNID HSKAAQDAVA LLA.KHHDKI AFVSGPLIDD
          DEGA_BACSU  PIAMISQDKP LLPMDIVVID DVRGGYEAAK HLLSLGHTNI ACIIGD.GST
          FRUR_ECOLI  PIVALDRALD REHFTSVVGA DQDDAEMLAE ELRKFPAETV LYL.GALPEL
          RBTR_KLEAE  NLDLPGSLSP SVISDNYGGA KALTHKILAN SARRRGELAP LTFIGGRRAT
           Consensus  pivl...... .....sv.ga .......la. .lr..g.... l...G.....

                      201                                                250
          CCPA_BACME  INHAKKVKGY KRALTESGLP VRDSYIVEGD YTYDSGIEAV EKLLEEDEKP
          CCPA_BACSU  INRSKKLQGY KRALEEANLP FNEQFVAEGD YTYDSGLEAL QHLMSLDKKP
          CCPA_STRMU  INGKVRLAGY KEGLKKKGLP FKEGLVFEAQ YKYQEGYQLA QRVI..NSGA
          DEGA_BACSU  TGEKNRIKGF RQAMEEAGVP IDESLIIQTR FSLESGKEEA GKLLDRNA.P
          FRUR_ECOLI  SVSFLREQGF RTAWKDD..P REVHFLYANS YEREAAAQLF EKWLETHPMP
          RBTR_KLEAE  ITPASVYAAS TMRIASWGLA CRRRIFWLPA IRKATLRTAC RSGLAARRRC
           Consensus  i....r..g. ..a....glp .......... y......... .k.l.....p

                      251                                                300
          CCPA_BACME  TAIFVGTDEM ALGVIHGAQD RGLNVPNDLE IIGFDNTRLS TMVRPQLTSV
          CCPA_BACSU  TAILSATDEM ALGIIHAAQD QGLSIPEDLD IIGFDNTRLS LMVRPQLSTV
          CCPA_STRMU  TAAYVAEDEL AAGLLNGLFA AGRKVPEDFE IITSNDSTIA LYTRPNMTSI
          DEGA_BACSU  TAIFAFNDVL ACAAIQAARI RGIKVPDDLS IIGFDNTILA EMAAPPLTTV
          FRUR_ECOLI  QALFTTSFAL LQGVMDVTLR RDGKLPSDLA IATFGDNELL DFLQCPVLAV
          RBTR_KLEAE  CRGYLLTRRY PWKGLCAGCR RWV....... .......... ..........
           Consensus  .a.%.....l ..g...a..r r..k.p.dl. i..f....l. .........v

                      301                                            346
          CCPA_BACME  VQPMYDIGAV AMRLLTKYMN KETVDSSIVQ LPHRIEFRQS TK....
          CCPA_BACSU  VQPTYDIGAV AMRLLTKLMN KEPVEEHIVE LPHRIELRKS TKS...
          CCPA_STRMU  SQPIYDLGAV AMRMLTKIMN KEELEEKEIV LNHGIKKRGT TK....
          DEGA_BACSU  AQPIKEMGAE RHRTAGRSNR GKRKAKQKIV LPPELVVRHS TSPLNT
          FRUR_ECOLI  AQRHRDVAER VLEIVLASLD EPRKPKPGLT RIKRNLYRRG VLSRS.
          RBTR_KLEAE  .......... .......... .......... .......... ......
           Consensus  .q...d.... .......... .......... .......r.. ......

#!/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 Multalin_Service_client import *

fn_input = 'benchy_seqdb001.seq'
fn_control = 'control-seqdb001.Multalin'
ret = 0

# get a port proxy instance
loc = Multalin_ServiceLocator()
port = loc.getMultalinPort()

###
# submit a new request
# create
req = submitMultalinRequest()
fp_input = open (fn_input, 'r')
req._Sequences = fp_input.read()

# call the remote method
resp = port.submitMultalin(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 = checkStatusMultalinRequest()
req._JobId = jobid
while status not in ('done','aborted'):
	time.sleep(2) 
	resp = port.checkStatusMultalin(req)
	status = resp._Status
	#print status
if status != 'done':
	ret = 1

###
# get results
req = getResultsMultalinRequest()
req._JobId = jobid
resp = port.getResultsMultalin(req)

# write result
#open(fn_control,'w').write(resp._Msf)

#compare result with ref
resultcontrol = open(fn_control, 'r').read()
if resp._Msf != resultcontrol:
	ret = 1
	#print "wooohh"

#print ret
sys.exit (ret)

##################################################
# file: Multalin_Service_client.py
# 
# client stubs generated by "ZSI.generate.wsdl2python.WriteServiceModule"
#     /usr/local/bin/wsdl2py http://gbio-pbil.ibcp.fr/ws/MultalinWS.wsdl
# 
##################################################


import urlparse, types
from ZSI.TCcompound import ComplexType, Struct
from ZSI import client
from ZSI.schema import GED, GTD
import ZSI

# Locator
class Multalin_ServiceLocator:
    MultalinPort_address = "http://gbio.ibcp.fr:8090/Multalin_Service"
    def getMultalinPortAddress(self):
        return Multalin_ServiceLocator.MultalinPort_address
    def getMultalinPort(self, url=None, **kw):
        return MultalinBindingSOAP(url or Multalin_ServiceLocator.MultalinPort_address, **kw)

# Methods
class MultalinBindingSOAP:
    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: submitMultalin
    def submitMultalin(self, request, **kw):
        if isinstance(request, submitMultalinRequest) is False:
            raise TypeError, "%s incorrect request type" % (request.__class__)
        # no input wsaction
        self.binding.Send(None, None, request, soapaction="urn:MultalinWS.wsdl#submitMultalin", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
        # no output wsaction
        typecode = Struct(pname=None, ofwhat=submitMultalinResponse.typecode.ofwhat, pyclass=submitMultalinResponse.typecode.pyclass)
        response = self.binding.Receive(typecode)
        return response

    # op: checkStatusMultalin
    def checkStatusMultalin(self, request, **kw):
        if isinstance(request, checkStatusMultalinRequest) is False:
            raise TypeError, "%s incorrect request type" % (request.__class__)
        # no input wsaction
        self.binding.Send(None, None, request, soapaction="urn:MultalinWS.wsdl#checkStatusMultalin", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
        # no output wsaction
        typecode = Struct(pname=None, ofwhat=checkStatusMultalinResponse.typecode.ofwhat, pyclass=checkStatusMultalinResponse.typecode.pyclass)
        response = self.binding.Receive(typecode)
        return response

    # op: getResultsMultalin
    def getResultsMultalin(self, request, **kw):
        if isinstance(request, getResultsMultalinRequest) is False:
            raise TypeError, "%s incorrect request type" % (request.__class__)
        # no input wsaction
        self.binding.Send(None, None, request, soapaction="urn:MultalinWS.wsdl#getResultsMultalin", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
        # no output wsaction
        typecode = Struct(pname=None, ofwhat=getResultsMultalinResponse.typecode.ofwhat, pyclass=getResultsMultalinResponse.typecode.pyclass)
        response = self.binding.Receive(typecode)
        return response

    # op: cancelMultalin
    def cancelMultalin(self, request, **kw):
        if isinstance(request, cancelMultalinRequest) is False:
            raise TypeError, "%s incorrect request type" % (request.__class__)
        # no input wsaction
        self.binding.Send(None, None, request, soapaction="urn:MultalinWS.wsdl#cancelMultalin", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
        # no output wsaction
        typecode = Struct(pname=None, ofwhat=cancelMultalinResponse.typecode.ofwhat, pyclass=cancelMultalinResponse.typecode.pyclass)
        response = self.binding.Receive(typecode)
        return response

class submitMultalinRequest:
    def __init__(self, **kw):
        """Keyword parameters:
        Sequences -- part Sequences
        """
        self._Sequences =  kw.get("Sequences")
submitMultalinRequest.typecode = Struct(pname=("urn:Multalin_Service","submitMultalin"), ofwhat=[ZSI.TC.String(pname="Sequences", aname="_Sequences", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=submitMultalinRequest, encoded="urn:Multalin_Service")

class submitMultalinResponse:
    def __init__(self, **kw):
        """Keyword parameters:
        JobId -- part JobId
        """
        self._JobId =  kw.get("JobId")
submitMultalinResponse.typecode = Struct(pname=("urn:Multalin_Service","submitMultalinResponse"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=submitMultalinResponse, encoded="urn:Multalin_Service")

class checkStatusMultalinRequest:
    def __init__(self, **kw):
        """Keyword parameters:
        JobId -- part JobId
        """
        self._JobId =  kw.get("JobId")
checkStatusMultalinRequest.typecode = Struct(pname=("urn:Multalin_Service","checkStatusMultalin"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=checkStatusMultalinRequest, encoded="urn:Multalin_Service")

class checkStatusMultalinResponse:
    def __init__(self, **kw):
        """Keyword parameters:
        Status -- part Status
        """
        self._Status =  kw.get("Status")
checkStatusMultalinResponse.typecode = Struct(pname=("urn:Multalin_Service","checkStatusMultalinResponse"), ofwhat=[ZSI.TC.String(pname="Status", aname="_Status", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=checkStatusMultalinResponse, encoded="urn:Multalin_Service")

class getResultsMultalinRequest:
    def __init__(self, **kw):
        """Keyword parameters:
        JobId -- part JobId
        """
        self._JobId =  kw.get("JobId")
getResultsMultalinRequest.typecode = Struct(pname=("urn:Multalin_Service","getResultsMultalin"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=getResultsMultalinRequest, encoded="urn:Multalin_Service")

class getResultsMultalinResponse:
    def __init__(self, **kw):
        """Keyword parameters:
        Clu -- part Clu
        Cl2 -- part Cl2
        Msf -- part Msf
        Logout -- part Logout
        """
        self._Clu =  kw.get("Clu")
        self._Cl2 =  kw.get("Cl2")
        self._Msf =  kw.get("Msf")
        self._Logout =  kw.get("Logout")
getResultsMultalinResponse.typecode = Struct(pname=("urn:Multalin_Service","getResultsMultalinResponse"), ofwhat=[ZSI.TC.String(pname="Clu", aname="_Clu", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True), ZSI.TC.String(pname="Cl2", aname="_Cl2", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True), ZSI.TC.String(pname="Msf", aname="_Msf", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True), ZSI.TC.String(pname="Logout", aname="_Logout", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=getResultsMultalinResponse, encoded="urn:Multalin_Service")

class cancelMultalinRequest:
    def __init__(self, **kw):
        """Keyword parameters:
        JobId -- part JobId
        """
        self._JobId =  kw.get("JobId")
cancelMultalinRequest.typecode = Struct(pname=("urn:Multalin_Service","cancelMultalin"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=cancelMultalinRequest, encoded="urn:Multalin_Service")

class cancelMultalinResponse:
    def __init__(self, **kw):
        """Keyword parameters:
        Status -- part Status
        """
        self._Status =  kw.get("Status")
cancelMultalinResponse.typecode = Struct(pname=("urn:Multalin_Service","cancelMultalinResponse"), ofwhat=[ZSI.TC.String(pname="Status", aname="_Status", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=cancelMultalinResponse, encoded="urn:Multalin_Service")

##################################################
# file: Multalin_Service_types.py
#
# schema types generated by "ZSI.generate.wsdl2python.WriteServiceModule"
#    /usr/local/bin/wsdl2py http://gbio-pbil.ibcp.fr/ws/MultalinWS.wsdl
#
##################################################

import ZSI
import ZSI.TCcompound
from ZSI.schema import LocalElementDeclaration, ElementDeclaration, TypeDefinition, GTD, GED