genewise.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

###############################################################################
#
# Copyright 2012-2024 EMBL - European Bioinformatics Institute
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Python Client Automatically generated with:
# https://github.com/ebi-jdispatcher/webservice-clients-generator
#
# Genewise (REST) web service Python client using xmltramp2.
#
# For further information see:
# https://www.ebi.ac.uk/Tools/webservices/
#
###############################################################################

from __future__ import print_function

import os
import sys
import time
import requests
import platform
from xmltramp2 import xmltramp
from optparse import OptionParser

try:
    from urllib.parse import urlparse, urlencode
    from urllib.request import urlopen, Request
    from urllib.error import HTTPError
    from urllib.request import __version__ as urllib_version
except ImportError:
    from urlparse import urlparse
    from urllib import urlencode
    from urllib2 import urlopen, Request, HTTPError
    from urllib2 import __version__ as urllib_version


# Debug print
def printDebugMessage(functionName, message, level):
    if (level <= debugLevel):
        print(u'[' + functionName + u'] ' + message, file=sys.stderr)


# User-agent for request (see RFC2616).
def getUserAgent():
    printDebugMessage(u'getUserAgent', u'Begin', 11)
    # Agent string for urllib2 library.
    urllib_agent = u'Python-urllib/%s' % urllib_version
    clientRevision = version
    # Prepend client specific agent string.
    try:
        pythonversion = platform.python_version()
        pythonsys = platform.system()
    except ValueError:
        pythonversion, pythonsys = "Unknown", "Unknown"
    user_agent = u'EBI-Sample-Client/%s (%s; Python %s; %s) %s' % (
        clientRevision, os.path.basename(__file__),
        pythonversion, pythonsys, urllib_agent)
    printDebugMessage(u'getUserAgent', u'user_agent: ' + user_agent, 12)
    printDebugMessage(u'getUserAgent', u'End', 11)
    return user_agent


# Wrapper for a REST (HTTP GET) request
def restRequest(url):
    printDebugMessage(u'restRequest', u'Begin', 11)
    printDebugMessage(u'restRequest', u'url: ' + url, 11)
    try:
        # Set the User-agent.
        user_agent = getUserAgent()
        http_headers = {u'User-Agent': user_agent}
        req = Request(url, None, http_headers)
        # Make the request (HTTP GET).
        reqH = urlopen(req)
        resp = reqH.read()
        contenttype = reqH.info()

        if (len(resp) > 0 and contenttype != u"image/png;charset=UTF-8"
                and contenttype != u"image/jpeg;charset=UTF-8"
                and contenttype != u"application/gzip;charset=UTF-8"):
            try:
                result = unicode(resp, u'utf-8')
            except UnicodeDecodeError:
                result = resp
        else:
            result = resp
        reqH.close()
    # Errors are indicated by HTTP status codes.
    except HTTPError as ex:
        result = requests.get(url).content
    printDebugMessage(u'restRequest', u'End', 11)
    return result


# Get input parameters list
def serviceGetParameters():
    printDebugMessage(u'serviceGetParameters', u'Begin', 1)
    requestUrl = baseUrl + u'/parameters'
    printDebugMessage(u'serviceGetParameters', u'requestUrl: ' + requestUrl, 2)
    xmlDoc = restRequest(requestUrl)
    doc = xmltramp.parse(xmlDoc)
    printDebugMessage(u'serviceGetParameters', u'End', 1)
    return doc[u'id':]

# Get list of parameters for error handling
def getListOfParameters():
    printDebugMessage(u'getListOfParameters', u'Begin', 1)
    return [str(x) for x in serviceGetParameters()]


# Print list of parameters
def printGetParameters():
    printDebugMessage(u'printGetParameters', u'Begin', 1)
    idList = serviceGetParameters()
    for id_ in idList:
        print(id_)
    printDebugMessage(u'printGetParameters', u'End', 1)


# Get input parameter information
def serviceGetParameterDetails(paramName):
    printDebugMessage(u'serviceGetParameterDetails', u'Begin', 1)
    printDebugMessage(u'serviceGetParameterDetails', u'paramName: ' + paramName, 2)
    requestUrl = baseUrl + u'/parameterdetails/' + paramName
    printDebugMessage(u'serviceGetParameterDetails', u'requestUrl: ' + requestUrl, 2)
    xmlDoc = restRequest(requestUrl)
    doc = xmltramp.parse(xmlDoc)
    printDebugMessage(u'serviceGetParameterDetails', u'End', 1)
    return doc


# Print description of a parameter
def printGetParameterDetails(paramName):
    printDebugMessage(u'printGetParameterDetails', u'Begin', 1)
    doc = serviceGetParameterDetails(paramName)
    print(unicode(doc.name) + u"\t" + unicode(doc.type))
    print(doc.description)
    if hasattr(doc, 'values'):
        for value in doc.values:
            print(value.value)
            if unicode(value.defaultValue) == u'true':
                print(u'default')
            print(u"\t" + unicode(value.label))
            if hasattr(value, u'properties'):
                for wsProperty in value.properties:
                    print(u"\t" + unicode(wsProperty.key) + u"\t" + unicode(wsProperty.value))
    printDebugMessage(u'printGetParameterDetails', u'End', 1)


# Submit job
def serviceRun(email, title, params):
    printDebugMessage(u'serviceRun', u'Begin', 1)
    # Insert e-mail and title into params
    params[u'email'] = email
    if title:
        params[u'title'] = title
    requestUrl = baseUrl + u'/run/'
    printDebugMessage(u'serviceRun', u'requestUrl: ' + requestUrl, 2)

    # Get the data for the other options
    requestData = urlencode(params)

    printDebugMessage(u'serviceRun', u'requestData: ' + requestData, 2)
    # Errors are indicated by HTTP status codes.
    try:
        # Set the HTTP User-agent.
        user_agent = getUserAgent()
        http_headers = {u'User-Agent': user_agent}
        req = Request(requestUrl, None, http_headers)
        # Make the submission (HTTP POST).
        reqH = urlopen(req, requestData.encode(encoding=u'utf_8', errors=u'strict'))
        jobId = unicode(reqH.read(), u'utf-8')
        reqH.close()
    except HTTPError as ex:
        print(xmltramp.parse(unicode(ex.read(), u'utf-8'))[0][0])
        quit()
    printDebugMessage(u'serviceRun', u'jobId: ' + jobId, 2)
    printDebugMessage(u'serviceRun', u'End', 1)
    return jobId


# Get job status
def serviceGetStatus(jobId):
    printDebugMessage(u'serviceGetStatus', u'Begin', 1)
    printDebugMessage(u'serviceGetStatus', u'jobId: ' + jobId, 2)
    requestUrl = baseUrl + u'/status/' + jobId
    printDebugMessage(u'serviceGetStatus', u'requestUrl: ' + requestUrl, 2)
    status = restRequest(requestUrl)
    printDebugMessage(u'serviceGetStatus', u'status: ' + status, 2)
    printDebugMessage(u'serviceGetStatus', u'End', 1)
    return status


# Print the status of a job
def printGetStatus(jobId):
    printDebugMessage(u'printGetStatus', u'Begin', 1)
    status = serviceGetStatus(jobId)
    if outputLevel > 0:
        print("Getting status for job %s" % jobId)
    print(status)
    if outputLevel > 0 and status == "FINISHED":
        print("To get results: python %s --polljob --jobid %s"
              "" % (os.path.basename(__file__), jobId))
    printDebugMessage(u'printGetStatus', u'End', 1)


# Get available result types for job
def serviceGetResultTypes(jobId):
    printDebugMessage(u'serviceGetResultTypes', u'Begin', 1)
    printDebugMessage(u'serviceGetResultTypes', u'jobId: ' + jobId, 2)
    requestUrl = baseUrl + u'/resulttypes/' + jobId
    printDebugMessage(u'serviceGetResultTypes', u'requestUrl: ' + requestUrl, 2)
    xmlDoc = restRequest(requestUrl)
    doc = xmltramp.parse(xmlDoc)
    printDebugMessage(u'serviceGetResultTypes', u'End', 1)
    return doc[u'type':]


# Print list of available result types for a job.
def printGetResultTypes(jobId):
    printDebugMessage(u'printGetResultTypes', u'Begin', 1)
    if outputLevel > 0:
        print("Getting result types for job %s" % jobId)

    resultTypeList = serviceGetResultTypes(jobId)
    if outputLevel > 0:
        print("Available result types:")
    for resultType in resultTypeList:
        print(resultType[u'identifier'])
        if hasattr(resultType, u'label'):
            print(u"\t", resultType[u'label'])
        if hasattr(resultType, u'description'):
            print(u"\t", resultType[u'description'])
        if hasattr(resultType, u'mediaType'):
            print(u"\t", resultType[u'mediaType'])
        if hasattr(resultType, u'fileSuffix'):
            print(u"\t", resultType[u'fileSuffix'])
    if outputLevel > 0:
        print("To get results:\n  python %s --polljob --jobid %s\n"
              "  python %s --polljob --outformat <type> --jobid %s"
              "" % (os.path.basename(__file__), jobId,
                    os.path.basename(__file__), jobId))
    printDebugMessage(u'printGetResultTypes', u'End', 1)


# Get result
def serviceGetResult(jobId, type_):
    printDebugMessage(u'serviceGetResult', u'Begin', 1)
    printDebugMessage(u'serviceGetResult', u'jobId: ' + jobId, 2)
    printDebugMessage(u'serviceGetResult', u'type_: ' + type_, 2)
    requestUrl = baseUrl + u'/result/' + jobId + u'/' + type_
    result = restRequest(requestUrl)
    printDebugMessage(u'serviceGetResult', u'End', 1)
    return result


# Client-side poll
def clientPoll(jobId):
    printDebugMessage(u'clientPoll', u'Begin', 1)
    result = u'QUEUED'
    while result == u'RUNNING' or result == u'QUEUED':
        result = serviceGetStatus(jobId)
        if outputLevel > 0:
            print(result)
        if result == u'RUNNING' or result == u'QUEUED':
            time.sleep(pollFreq)
    printDebugMessage(u'clientPoll', u'End', 1)


# Get result for a jobid
# Allows more than one output file written when 'outformat' is defined.
def getResult(jobId):
    printDebugMessage(u'getResult', u'Begin', 1)
    printDebugMessage(u'getResult', u'jobId: ' + jobId, 1)
    if outputLevel > 1:
        print("Getting results for job %s" % jobId)
    # Check status and wait if necessary
    clientPoll(jobId)
    # Get available result types
    resultTypes = serviceGetResultTypes(jobId)

    for resultType in resultTypes:
        # Derive the filename for the result
        if options.outfile:
            filename = (options.outfile + u'.' + unicode(resultType[u'identifier']) +
                        u'.' + unicode(resultType[u'fileSuffix']))
        else:
            filename = (jobId + u'.' + unicode(resultType[u'identifier']) +
                        u'.' + unicode(resultType[u'fileSuffix']))
        # Write a result file

        outformat_parm = str(options.outformat).split(',')
        for outformat_type in outformat_parm:
            outformat_type = outformat_type.replace(' ', '')

            if outformat_type == 'None':
                outformat_type = None

            if not outformat_type or outformat_type == unicode(resultType[u'identifier']):
                if outputLevel > 1:
                    print("Getting %s" % unicode(resultType[u'identifier']))
                # Get the result
                result = serviceGetResult(jobId, unicode(resultType[u'identifier']))
                if (unicode(resultType[u'mediaType']) == u"image/png"
                        or unicode(resultType[u'mediaType']) == u"image/jpeg"
                        or unicode(resultType[u'mediaType']) == u"application/gzip"):
                    fmode = 'wb'
                else:
                    fmode = 'w'

                try:
                    fh = open(filename, fmode)
                    fh.write(result)
                    fh.close()
                except TypeError:
                    fh.close()
                    fh = open(filename, "wb")
                    fh.write(result)
                    fh.close()
                if outputLevel > 0:
                    print("Creating result file: " + filename)
    printDebugMessage(u'getResult', u'End', 1)


# Read a file
def readFile(filename):
    printDebugMessage(u'readFile', u'Begin', 1)
    fh = open(filename, 'r')
    data = fh.read()
    fh.close()
    printDebugMessage(u'readFile', u'End', 1)
    return data


def print_usage():
    print("""\
EMBL-EBI Genewise Python Client:

Pairwise sequence alignment with Genewise.

[Required (for job submission)]
  --email               E-mail address.
  --asequence           The protein sequence can be entered directly into this form.
                        The sequence can be in GCG, FASTA, EMBL (Nucleotide only),
                        GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein
                        only) format. A partially formatted sequence is not
                        accepted. Adding a return to the end of the sequence may
                        help certain applications understand the input. Note that
                        directly using data from word processors may yield
                        unpredictable results as hidden/control characters may be
                        present. There is a limit of 1MB for the sequence entry.
  --bsequence           The DNA sequence to be compared can be entered directly into
                        the form. The sequence must be in a recognised format eg.
                        GCG, FASTA, EMBL, GenBank. Partially formatted sequences are
                        not accepted. Adding a return to the end of the sequence may
                        help certain applications understand the input. Note that
                        directly using data from word processors may yield
                        unpredictable results as hidden/control characters may be
                        present. There is a limit of 1MB for the sequence entry.

[Optional]
  --para                Show parameters in the output alignmment, as in genewise.
  --pretty              Show pretty ASCII alignment viewing, as in genewise.
  --genes               Show gene structure, as in genewise.
  --trans               Show protein translation, breaking at frameshifts.
  --cdna                Show cDNA, as in genewise.
  --embl                EMBL feature table format with CDS key.
  --ace                 Show Ace file gene structure, as in genewise.
  --gff                 Show Gene Feature Format file, as in genewise.
  --diana               Show EMBL FT format suitable for diana.
  --init                Model in local/global mode. You should only put the model in
                        global mode if you expect your protein homolog to have
                        homology from start to end to the gene in the DNA sequence.
  --splice              Using splice model or GT/AG? Use the full blown model for
                        splice sites, or a simplistic GT/AG. Generally if you are
                        using a DNA sequence which is from human or worm, then leave
                        this on. If you are using a very different (eg plant)
                        species, switch it off.
  --random              The probability of the model has to compared to an
                        alternative model (in fact to all alternative models which
                        are possible) to allow proper Bayesian inference. This
                        causes considerable difficulty in these algorithms because
                        from a algorithmical point of view we would probably like to
                        use an alternative model which is a single state, like the
                        random model in profile-HMMs, where we can simply 'log-odd'
                        the scored model, whereas from a biological point of view we
                        probably want to use a full gene predicting alternative
                        model. In addition we need to account for the fact that the
                        protein HMM or protein homolog probably does not extend over
                        all the gene sequence, nor in fact does the gene have to be
                        the only gene in the DNA sequence. This means that there are
                        very good splice sites/poly-pyrimidine tracts outside of the
                        'matched' alignment can severely de-rail the alignment.
  --alg                 The solutions is different in the genewise21:93 compared to
                        the genewise 6:23 algorithms. (1) In 6:23 we force the
                        external match portions of the homology model to be
                        identical to the alternative model, thus cancelling each
                        other out. This is a pretty gross approximation and is sort
                        of equivalent to the intron tie'ing. It makes things
                        algorithmically easier... However this means a) 6:23 is
                        nowhere near a probabilistic model and b) you really have to
                        used a tied intron model in 6:23 otherwise very bad edge
                        effects (final introns being ridiculously long) occur. (2)
                        In 21:93 we have a full probabilistic model on each side of
                        the homology segment. This is not reported in the -pretty
                        output but you can see it in the -alb output if you like. Do
                        not trust the gene model outside of the homology segment
                        however. By having these external gene model parts we can
                        use all the gene model features safe in the knowledge that
                        if the homology segments do not justify the match then the
                        external part of the model will soak up the additional
                        intron/py-tract/splice site biases.

[General]
  -h, --help            Show this help message and exit.
  --asyncjob            Forces to make an asynchronous query.
  --title               Title for job.
  --status              Get job status.
  --resultTypes         Get available result types for job.
  --polljob             Poll for the status of a job.
  --pollFreq            Poll frequency in seconds (default 3s).
  --jobid               JobId that was returned when an asynchronous job was submitted.
  --outfile             File name for results (default is JobId; for STDOUT).
  --outformat           Result format(s) to retrieve. It accepts comma-separated values.
  --params              List input parameters.
  --paramDetail         Display details for input parameter.
  --verbose             Increase output.
  --version             Prints out the version of the Client and exit.
  --quiet               Decrease output.
  --baseUrl             Base URL. Defaults to:
                        https://www.ebi.ac.uk/Tools/services/rest/genewise

Synchronous job:
  The results/errors are returned as soon as the job is finished.
  Usage: python genewise.py --email <your@email.com> [options...] <SeqFile|SeqID(s)>
  Returns: results as an attachment

Asynchronous job:
  Use this if you want to retrieve the results at a later time. The results
  are stored for up to 24 hours.
  Usage: python genewise.py --asyncjob --email <your@email.com> [options...] <SeqFile|SeqID(s)>
  Returns: jobid

Check status of Asynchronous job:
  Usage: python genewise.py --status --jobid <jobId>

Retrieve job data:
  Use the jobid to query for the status of the job. If the job is finished,
  it also returns the results/errors.
  Usage: python genewise.py --polljob --jobid <jobId> [--outfile string]
  Returns: string indicating the status of the job and if applicable, results
  as an attachment.

Further information:
  https://www.ebi.ac.uk/Tools/webservices and
    https://github.com/ebi-jdispatcher/webservice-clients

Support/Feedback:
  https://www.ebi.ac.uk/support/""")


# allow unicode(str) to be used in python 3
try:
    unicode('')
except NameError:
    unicode = str

# Base URL for service
baseUrl = u'https://www.ebi.ac.uk/Tools/services/rest/genewise'
version = u'2024-07-11 07:51'

# Set interval for checking status
pollFreq = 3
# Output level
outputLevel = 1
# Debug level
debugLevel = 0
# Number of option arguments.
numOpts = len(sys.argv)

# Process command-line options
parser = OptionParser(add_help_option=False)

# Tool specific options (Try to print all the commands automatically)
parser.add_option('--para', action='store_true', help=('Show parameters in the output alignmment, as in genewise.'))
parser.add_option('--pretty', action='store_true', help=('Show pretty ASCII alignment viewing, as in genewise.'))
parser.add_option('--genes', action='store_true', help=('Show gene structure, as in genewise'))
parser.add_option('--trans', action='store_true', help=('Show protein translation, breaking at frameshifts.'))
parser.add_option('--cdna', action='store_true', help=('Show cDNA, as in genewise.'))
parser.add_option('--embl', action='store_true', help=('EMBL feature table format with CDS key.'))
parser.add_option('--ace', action='store_true', help=('Show Ace file gene structure, as in genewise.'))
parser.add_option('--gff', action='store_true', help=('Show Gene Feature Format file, as in genewise.'))
parser.add_option('--diana', action='store_true', help=('Show EMBL FT format suitable for diana.'))
parser.add_option('--init', type=str, help=('Model in local/global mode. You should only put the model in global'
                  'mode if you expect your protein homolog to have homology from start to'
                  'end to the gene in the DNA sequence.'))
parser.add_option('--splice', type=str, help=('Using splice model or GT/AG? Use the full blown model for splice'
                  'sites, or a simplistic GT/AG. Generally if you are using a DNA'
                  'sequence which is from human or worm, then leave this on. If you are'
                  'using a very different (eg plant) species, switch it off.'))
parser.add_option('--random', type=str, help=('The probability of the model has to compared to an alternative model'
                  '(in fact to all alternative models which are possible) to allow proper'
                  'Bayesian inference. This causes considerable difficulty in these'
                  'algorithms because from a algorithmical point of view we would'
                  'probably like to use an alternative model which is a single state,'
                  'like the random model in profile-HMMs, where we can simply log-odd the'
                  'scored model, whereas from a biological point of view we probably want'
                  'to use a full gene predicting alternative model. In addition we need'
                  'to account for the fact that the protein HMM or protein homolog'
                  'probably does not extend over all the gene sequence, nor in fact does'
                  'the gene have to be the only gene in the DNA sequence. This means that'
                  'there are very good splice sites/poly-pyrimidine tracts outside of the'
                  'matched alignment can severely de-rail the alignment.'))
parser.add_option('--alg', type=str, help=('The solutions is different in the genewise21:93 compared to the'
                  'genewise 6:23 algorithms. (1) In 6:23 we force the external match'
                  'portions of the homology model to be identical to the alternative'
                  'model, thus cancelling each other out. This is a pretty gross'
                  'approximation and is sort of equivalent to the intron tieing. It makes'
                  'things algorithmically easier... However this means a) 6:23 is nowhere'
                  'near a probabilistic model and b) you really have to used a tied'
                  'intron model in 6:23 otherwise very bad edge effects (final introns'
                  'being ridiculously long) occur. (2) In 21:93 we have a full'
                  'probabilistic model on each side of the homology segment. This is not'
                  'reported in the -pretty output but you can see it in the -alb output'
                  'if you like. Do not trust the gene model outside of the homology'
                  'segment however. By having these external gene model parts we can use'
                  'all the gene model features safe in the knowledge that if the homology'
                  'segments do not justify the match then the external part of the model'
                  'will soak up the additional intron/py-tract/splice site biases.'))
parser.add_option('--asequence', type=str, help=('The protein sequence can be entered directly into this form. The'
                  'sequence can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR,'
                  'NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format. A'
                  'partially formatted sequence is not accepted. Adding a return to the'
                  'end of the sequence may help certain applications understand the'
                  'input. Note that directly using data from word processors may yield'
                  'unpredictable results as hidden/control characters may be present.'
                  'There is a limit of 1MB for the sequence entry.'))
parser.add_option('--bsequence', type=str, help=('The DNA sequence to be compared can be entered directly into the form.'
                  'The sequence must be in a recognised format eg. GCG, FASTA, EMBL,'
                  'GenBank. Partially formatted sequences are not accepted. Adding a'
                  'return to the end of the sequence may help certain applications'
                  'understand the input. Note that directly using data from word'
                  'processors may yield unpredictable results as hidden/control'
                  'characters may be present. There is a limit of 1MB for the sequence'
                  'entry.'))
# General options
parser.add_option('-h', '--help', action='store_true', help='Show this help message and exit.')
parser.add_option('--email', help='E-mail address.')
parser.add_option('--title', help='Job title.')
parser.add_option('--outfile', help='File name for results.')
parser.add_option('--outformat', help='Output format for results.')
parser.add_option('--asyncjob', action='store_true', help='Asynchronous mode.')
parser.add_option('--jobid', help='Job identifier.')
parser.add_option('--polljob', action="store_true", help='Get job result.')
parser.add_option('--pollFreq', type='int', default=3, help='Poll frequency in seconds (default 3s).')
parser.add_option('--status', action="store_true", help='Get job status.')
parser.add_option('--resultTypes', action='store_true', help='Get result types.')
parser.add_option('--params', action='store_true', help='List input parameters.')
parser.add_option('--paramDetail', help='Get details for parameter.', choices=getListOfParameters())
parser.add_option('--quiet', action='store_true', help='Decrease output level.')
parser.add_option('--verbose', action='store_true', help='Increase output level.')
parser.add_option('--version', action='store_true', help='Prints out the version of the Client and exit.')
parser.add_option('--debugLevel', type='int', default=debugLevel, help='Debugging level.')
parser.add_option('--baseUrl', default=baseUrl, help='Base URL for service.')

(options, args) = parser.parse_args()

# Increase output level
if options.verbose:
    outputLevel += 1

# Decrease output level
if options.quiet:
    outputLevel -= 1

# Debug level
if options.debugLevel:
    debugLevel = options.debugLevel

if options.pollFreq:
    pollFreq = options.pollFreq

if options.baseUrl:
    baseUrl = options.baseUrl

# No options... print help.
if numOpts < 2:
    print_usage()
elif options.help:
    print_usage()
# List parameters
elif options.params:
    printGetParameters()
# Get parameter details
elif options.paramDetail:
    printGetParameterDetails(options.paramDetail)
# Print Client version
elif options.version:
    print("Revision: %s" % version)
    sys.exit()
# Submit job
elif options.email and not options.jobid:
    params = {}
    if len(args) == 1 and "true" not in args and "false" not in args:
        if os.path.exists(args[0]):  # Read file into content
            params[u'sequence'] = readFile(args[0])
        else:  # Argument is a sequence id
            params[u'sequence'] = args[0]
    elif len(args) == 2 and "true" not in args and "false" not in args:
        if os.path.exists(args[0]) and os.path.exists(args[1]):  # Read file into content
            params[u'asequence'] = readFile(args[0])
            params[u'bsequence'] = readFile(args[1])
        else:  # Argument is a sequence id
            params[u'asequence'] = args[0]
            params[u'bsequence'] = args[0]
    elif hasattr(options, "sequence") or (hasattr(options, "asequence") and hasattr(options, "bsequence")):  # Specified via option
        if hasattr(options, "sequence"):
            if os.path.exists(options.sequence):  # Read file into content
                params[u'sequence'] = readFile(options.sequence)
            else:  # Argument is a sequence id
                params[u'sequence'] = options.sequence
        elif hasattr(options, "asequence") and hasattr(options, "bsequence"):
            if os.path.exists(options.asequence) and os.path.exists(options.bsequence):  # Read file into content
                params[u'asequence'] = readFile(options.asequence)
                params[u'bsequence'] = readFile(options.bsequence)
            else:  # Argument is a sequence id
                params[u'asequence'] = options.asequence
                params[u'bsequence'] = options.bsequence

    # Pass default values and fix bools (without default value)

    if not options.para:
        params['para'] = 'true'
    if options.para:
        params['para'] = options.para
    

    if not options.pretty:
        params['pretty'] = 'true'
    if options.pretty:
        params['pretty'] = options.pretty
    

    if not options.genes:
        params['genes'] = 'true'
    if options.genes:
        params['genes'] = options.genes
    

    if not options.trans:
        params['trans'] = 'true'
    if options.trans:
        params['trans'] = options.trans
    

    if not options.cdna:
        params['cdna'] = 'true'
    if options.cdna:
        params['cdna'] = options.cdna
    

    if not options.embl:
        params['embl'] = 'true'
    if options.embl:
        params['embl'] = options.embl
    

    if not options.ace:
        params['ace'] = 'true'
    if options.ace:
        params['ace'] = options.ace
    

    if not options.gff:
        params['gff'] = 'true'
    if options.gff:
        params['gff'] = options.gff
    

    if not options.diana:
        params['diana'] = 'true'
    if options.diana:
        params['diana'] = options.diana
    

    if not options.init:
        params['init'] = 'local'
    if options.init:
        params['init'] = options.init
    

    if not options.splice:
        params['splice'] = 'flat'
    if options.splice:
        params['splice'] = options.splice
    

    if not options.random:
        params['random'] = 'syn'
    if options.random:
        params['random'] = options.random
    

    if not options.alg:
        params['alg'] = '623'
    if options.alg:
        params['alg'] = options.alg
    


    # Submit the job
    jobId = serviceRun(options.email, options.title, params)
    if options.asyncjob: # Async mode
        print(jobId)
        if outputLevel > 0:
            print("To check status: python %s --status --jobid %s"
                  "" % (os.path.basename(__file__), jobId))
    else:
        # Sync mode
        if outputLevel > 0:
            print("JobId: " + jobId, file=sys.stderr)
        else:
            print(jobId)
        time.sleep(pollFreq)
        getResult(jobId)
# Get job status
elif options.jobid and options.status:
    printGetStatus(options.jobid)

elif options.jobid and (options.resultTypes or options.polljob):
    status = serviceGetStatus(options.jobid)
    if status == 'QUEUED' or status == 'RUNNING':
        print("Error: Job status is %s. "
              "To get result types the job must be finished." % status)
        quit()
    # List result types for job
    if options.resultTypes:
        printGetResultTypes(options.jobid)
    # Get results for job
    elif options.polljob:
        getResult(options.jobid)
else:
    # Checks for 'email' parameter
    if not options.email:
        print('\nParameter "--email" is missing in your command. It is required!\n')

    print(u'Error: unrecognised argument combination', file=sys.stderr)
    print_usage()