ClustalW WS: test of bioinformatics availability

#!/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 Clustalw_Service_client import *

fn_input = 'benchy_seqdb001.seq'
fn_aliref = 'benchy_seqdb001_clustalw.ref'
ret = 0

# get a port proxy instance
loc = Clustalw_ServiceLocator()
port = loc.getClustalwPort()

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

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

###
# get results
req = getResultsClustalwRequest()
req._JobId = jobid
resp = port.getResultsClustalw(req)
aliref = open(fn_aliref, 'r').read()
#open('alioutput.ali','w').write(resp._Alignement)
if resp._Alignement != aliref:
	ret = 1
	#print "wooohh"

#print ret
sys.exit (ret)

>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

CLUSTAL 2.0.5 multiple sequence alignment


CCPA_BACME      -MN----VTIYDVAREASVSMATVSRVVNGNP---NVKPSTRKKVLETIERLGYRPNAVA
CCPA_BACSU      MSN----ITIYDVAREANVSMATVSRVVNGNP---NVKPTTRKKVLEAIERLGYRPNAVA
CCPA_STRMU      -MNTDDTITIYDVAREAGVSMATVSRVVNGNK---NVKENTRKKVLEVIDRLDYRPNAVA
DEGA_BACSU      -MK----TTIYDVAKAAGVSITTVSRVINNTG---RISDKTRQKVMNVMNEMAYTPNVHA
FRUR_ECOLI      -------MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPNAVA
RBTR_KLEAE      -MKK---ITIYDLAELSGVSASAVSAILNGNWKKRRISAKLAEKVTRIAEEQGYAINRQA
                        .: ::*. :.** ::.* ::*..    .:. .  :**     .  *  *  *

CCPA_BACME      RGLASKKTTTVGVIIPDISNIFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNM
CCPA_BACSU      RGLASKKTTTVGVIIPDISSIFYSELARGIEDIATMYKYNIILSNSDQNMEKELHLLNTM
CCPA_STRMU      RGLASKKTTTVGVVIPNIANAYFSILAKGIDDIATMYKYNIVLASSDEDDDKEVNVINTL
DEGA_BACSU      AALTGKRTNMIALVAPDISNPFYGELAKSIEERADELGFQMLICSTDYDPKKETKYFSVL
FRUR_ECOLI      AGLRAGRTRSIGLVIPDLENTSYTRIANYLERQARQRGYQLLIACSEDQPDNEMRCIEHL
RBTR_KLEAE      SMLRSKKSHVIGMIIPKYDNRYFGSIAERFEEMARERGLLPIITCTRRRPELEIEAVKAM
                  * . ::  :.:: *.  .  :  :*. ::  *       ::  :    . * . .. :

CCPA_BACME      LGKQVDGIIFMS---GNVTEEHVEELKKSPVPVVLAASIESTNQIPSVTIDYEQAAFDAV
CCPA_BACSU      LGKQVDGIVFMG---GNITDEHVAEFKRSPVPIVLAASVEEQEETPSVAIDYEQAIYDAV
CCPA_STRMU      FAKQVDGIIFMG---HHLTEKIRAEFSRARTPVVLSGTVDLEHQLPSVNIDHSKAAQDAV
DEGA_BACSU      KQKKVDGIIFATGIESHDSMSALEEIASEQIPIAMISQDKPLLPMDIVVIDDVRGGYEAA
FRUR_ECOLI      LQRQVDAIIVSTS--LPPEHPFYQRWANDPFPIVALDRALDREHFTSVVGADQDDAEMLA
RBTR_KLEAE      LSWQVDWVVATG---ATNPDKISALCQQAGVPTVNLDLPGSLS--PSVISDNYGGAKALT
                   :** ::                      * .             *           .

CCPA_BACME      QSLIDSGHKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIVEGDYTYDSGIEA
CCPA_BACSU      KLLVDKGHTDIAFVSGPMAEPINRSKKLQGYKRALEEANLPFNEQFVAEGDYTYDSGLEA
CCPA_STRMU      ALLAKH-HDKIAFVSGPLIDDINGKVRLAGYKEGLKKKGLPFKEGLVFEAQYKYQEGYQL
DEGA_BACSU      KHLLSLGHTNIACIIG-DGSTTGEKNRIKGFRQAMEEAGVPIDESLIIQTRFSLESGKEE
FRUR_ECOLI      EELRKFPAETVLYLGALPELSVS-FLREQGFRTAWKDD--PREVHFLYANSYEREAAAQL
RBTR_KLEAE      HKILANSARRRGELAP---------LTFIGGRRATITPASVYAASTMRIASWGLACRRR-
                  :          :               * : .            :    :      . 

CCPA_BACME      VEKLLEEDEKPTAIFVGTDEMALGVIHGAQDRGLNVPNDLEIIGFDNTRLSTMVRPQLTS
CCPA_BACSU      LQHLMSLDKKPTAILSATDEMALGIIHAAQDQGLSIPEDLDIIGFDNTRLSLMVRPQLST
CCPA_STRMU      AQRVINSG--ATAAYVAEDELAAGLLNGLFAAGRKVPEDFEIITSNDSTIALYTRPNMTS
DEGA_BACSU      AGKLLDRN-APTAIFAFNDVLACAAIQAARIRGIKVPDDLSIIGFDNTILAEMAAPPLTT
FRUR_ECOLI      FEKWLETHPMPQALFTTSFALLQGVMDVTLRRDGKLPSDLAIATFGDNELLDFLQCPVLA
RBTR_KLEAE      --------------IFWLPAIRKATLRTACRSGLAARR-------------RCCRGYLLT
                                    :  . :      .                        : :

CCPA_BACME      VVQPMYDIGAVAMRLLTKYMNKETVDSSIVQLPHRIEFRQSTK----
CCPA_BACSU      VVQPTYDIGAVAMRLLTKLMNKEPVEEHIVELPHRIELRKSTKS---
CCPA_STRMU      ISQPIYDLGAVAMRMLTKIMNKEELEEKEIVLNHGIKKRGTTK----
DEGA_BACSU      VAQPIKEMGAERHRTAGRSNRGKRKAKQKIVLPPELVVRHSTSPLNT
FRUR_ECOLI      VAQRHRDVAERVLEIVLASLDEPRKPKPGLTRIKRNLYRRGVLSRS-
RBTR_KLEAE      RRYPWKGLCAGCRRWV-------------------------------
                       :     .

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


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

# Locator
class Clustalw_ServiceLocator:
    ClustalwPort_address = "http://gbio.ibcp.fr:8090/Clustalw_Service"
    def getClustalwPortAddress(self):
        return Clustalw_ServiceLocator.ClustalwPort_address
    def getClustalwPort(self, url=None, **kw):
        return ClustalwBindingSOAP(url or Clustalw_ServiceLocator.ClustalwPort_address, **kw)

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

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

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

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

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

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

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

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

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

class getResultsClustalwResponse:
    def __init__(self, **kw):
        """Keyword parameters:
        Alignement -- part Alignement
        Logout -- part Logout
        """
        self._Alignement =  kw.get("Alignement")
        self._Logout =  kw.get("Logout")
getResultsClustalwResponse.typecode = Struct(pname=("urn:Clustalw_Service","getResultsClustalwResponse"), ofwhat=[ZSI.TC.String(pname="Alignement", aname="_Alignement", 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=getResultsClustalwResponse, encoded="urn:Clustalw_Service")

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

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

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

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