Utopia

#!/usr/bin/python
## SERVICE INTERFACE

import utopia
import SOAPpy

class BLAST(utopia.Service):

    def description(self):
        return 'protein_sequence', 'searching', 'UniProt_accession_list', 'BLAST search against the UniProt protein database'

    def invoke(self, source):

        # Ensure input are of correct type (they should be!)
        if type(source) != utopia.Node or source.getNodeClass() != 'source':
            return utopia.Exception('Expected %s but got %s' % (utopia.Node, type(source)))

        # Get source > complex > protein > sequence

        cx = source.getComplex()
        seq = cx.getSequence()

        # Get the ID of the sequence
        ID = ''
        if cx.has_key('utopia name'):
            ID = cx['utopia name']
        else:
           return utopia.Exception("Could not find an ID for the input sequence")

        # Get list of residue nodes
        residues = seq.getResidues()
        # Serialise sequence
        seq_str = utopia.serialize(seq, 'raw')
        # Remove gaps
        seq_str = seq_str.replace('-','')
        # finally, create a fasta sequence from the input
        fastaStr = '>' + ID + '\n' + seq_str +'\n'

        # Get web service proxy
        proxy = SOAPpy.WSDL.Proxy('http://xml.nig.ac.jp/wsdl/Blast.wsdl')

        # BLAST the query sequence
        blastResult = proxy.searchSimple(program='blastp', database='UNIPROT', query=fastaStr)

        # Check to see if we have any valid results, bail if not
        if blastResult.find('No hits found') != -1 or blastResult.find('Sequences producing significant alignments:') == -1:
            return utopia.Exception('No hits were found')

        # Split results up into lines
        lines = blastResult.splitlines()

        # Skip through to the start of the results
        lineCount = 0
        while lines[lineCount].find('Sequences producing significant alignments:') == -1:
            lineCount += 1
        lineCount += 1
        while len(lines[lineCount]) == 0:
            lineCount += 1

        hits = []
        while len(lines[lineCount]) != 0:
            hit = '';
            # parse the hit
            pos = 0;
            while lines[lineCount][pos] != '|':
                pos += 1
            pos += 1
            while lines[lineCount][pos] != '|':
                pos += 1
            pos += 1
            while lines[lineCount][pos] != ' ':
                hit += lines[lineCount][pos];
                pos += 1
            hit += ' '
            # append  the description - we don't filter out the scores
            while lines[lineCount][pos] == ' ':
                pos += 1
            while pos != len(lines[lineCount]):
                hit += lines[lineCount][pos];
                pos += 1
            hits.append(hit)
            lineCount += 1

        return hits

__all__ = ['BLAST']



if __name__ == '__main__':
    import sys
    utopia.init()
    from uniprot_fetch import UniProtFetch
    
    ret = 0

    try:
        input = 'OPSD_HUMAN'
        plugin = UniProtFetch()
        output = plugin.invoke(input)

        if type(output) != utopia.Node:
            ret = 1
            print 'The BLAST service test replies on getting a sequence from UniProt. This step has failed.'
        else:
			input = output
			plugin = BLAST()
			output = plugin.invoke(input)

			if type(output) != list:
				ret = 1
				print 'Service returned something other than a list.'
			elif len(output) == 0:
				ret = 2
				print 'Service returned an empty list. This test should return hundreds.'
        
    except Exception, e:
        ret = 1
        print e

    sys.exit(ret)