コード例 #1
0
ファイル: gapfile.py プロジェクト: demis001/NGSCoverage
    def plotPrimers(self):
        """ Plot Primer Sets """
        if self.primerfile is None:
            sys.stderr.write(
                "You cannot plot the primers without specifying the primer file location\n"
            )
            sys.exit(-1)

        primer = Primer(self.primerfile)
        primergenes = primer.unique_genes()
        # Filter out the primer genes not in the names
        genelist = set()
        for gene in primergenes:
            for name in self.names:
                # If the gene is in any of the names then
                # add it to the genelist and break the loop
                if gene in name:
                    genelist.add(gene)
                    break

        if len(genelist) == 0:
            raise ValueError(
                "None of the genes in %s were found to match any of the identifiers names in %s"
                % (str(primergenes), str(self.names)))

        genecount = 0
        labelf = 'Forward Primer'
        labelr = 'Reverse Primer'
        yaxislabels = []
        for gene in genelist:
            genecount -= 1
            primer_regions = primer.get_merged_primer_regions(gene)
            for region in primer_regions:
                if region.direction == 'R':
                    marker = '<'
                    self.ax.plot((region.start, region.end),
                                 (genecount, genecount),
                                 color=self.linestyle['Primer']['color'],
                                 lw=self.linestyle['Primer']['width'],
                                 label=labelr,
                                 marker=marker)
                    labelr = ''
                else:
                    marker = '>'
                    self.ax.plot((region.start, region.end),
                                 (genecount, genecount),
                                 color=self.linestyle['Primer']['color'],
                                 lw=self.linestyle['Primer']['width'],
                                 label=labelf,
                                 marker=marker)
                    labelf = ''
                self.xmax = region.end
            yaxislabels.insert(0, (genecount, gene))
        self.yaxislabels = yaxislabels + [(0, '')] + self.yaxislabels
コード例 #2
0
def ref_coverage( reffile, primerfile, pattern ):
    '''
        >>> from pprint import pprint
        >>> ref_match_pattern = '(?P<name>(?P<accession>.*?)_(?P<gene>.*?)_(?P<virus>.*))'
        >>> reffile = 'Examples/Ref/H1N1_boston.fasta'
        >>> primerfile = 'Examples/Primer/sH1N1.fasta' 
        >>> rc = ref_coverage( reffile, primerfile, ref_match_pattern )
        >>> isinstance( rc, dict )
        True
    '''
    ref = refs( reffile, pattern )
    primer = Primer( primerfile )

    genes = {}
    count = 0

    # Labels for legend
    labelf = 'Forward Primer'
    labelr = 'Reverse Primer'
    # Ensure iteration in sorted order to ensure consistent iteration everywhere
    for gene in sorted( ref.keys() ):
        logging.debug( "Creating Line2D for %s" % gene )
        regions = primer.get_merged_primer_regions( gene )
        reflen = ref.get( gene, False )
        if not regions:
            raise ValueError( "%s had no regions for gene %s. You may need to refine the match pattern." % (primerfile, gene) )

        # Create a line for the reference segment
        refline = Line2D( [0, reflen], [count, count], linewidth=5, color='green', alpha=0.5 )
        logging.debug( "Reference Line: (0,%s), (%s,%s)" % (reflen, count, count) )
        primerlines = []
        for region in regions:
            primerlines.append( Line2D( [region.start, region.end], [count, count], linewidth=2, color='black' ) )
            if region.direction == 'R':
                primerlines[-1].set_marker( '<' )
                primerlines[-1].set_label( labelr )
                # Set reverse label to None so that only 1 line gets an actual label
                #  otherwise the legend tries to use all of them making it way to big
                labelr = ''
            else:
                primerlines[-1].set_marker( '>' )
                primerlines[-1].set_label( labelf )
                # Same principal as above
                labelf = ''
            logging.debug( "Primer Line: (%s,%s), (%s,%s)" % (region.start, region.end, count, count) )
        genes[gene] = {'Reference': refline, 'Primers': primerlines}
        count += 1

    # Now create just one labeled refrence line for the legend
    first = genes[genes.keys()[0]]
    first['Reference'].set_label( 'Reference' )

    return genes
コード例 #3
0
ファイル: gapfile.py プロジェクト: VDBWRAIR/NGSCoverage
    def plotPrimers( self ):
        """ Plot Primer Sets """
        if self.primerfile is None:
            sys.stderr.write( "You cannot plot the primers without specifying the primer file location\n" )
            sys.exit( -1 )

        primer = Primer( self.primerfile )
        primergenes = primer.unique_genes()
        # Filter out the primer genes not in the names
        genelist = set()
        for gene in primergenes:
            for name in self.names:
                # If the gene is in any of the names then
                # add it to the genelist and break the loop
                if gene in name:
                    genelist.add( gene )
                    break

        if len( genelist ) == 0:
            raise ValueError( "None of the genes in %s were found to match any of the identifiers names in %s" % (str( primergenes ), str( self.names )) )

        genecount = 0
        labelf='Forward Primer'
        labelr='Reverse Primer'
        yaxislabels = []
        for gene in genelist:
            genecount -= 1
            primer_regions = primer.get_merged_primer_regions( gene )
            for region in primer_regions:
                if region.direction == 'R':
                    marker = '<'
                    self.ax.plot( (region.start, region.end), (genecount, genecount), color=self.linestyle['Primer']['color'], lw=self.linestyle['Primer']['width'], label=labelr, marker=marker )
                    labelr = ''
                else:
                    marker = '>'
                    self.ax.plot( (region.start, region.end), (genecount, genecount), color=self.linestyle['Primer']['color'], lw=self.linestyle['Primer']['width'], label=labelf, marker=marker )
                    labelf = ''
                self.xmax = region.end
            yaxislabels.insert( 0, (genecount, gene) )
        self.yaxislabels = yaxislabels + [(0, '')] + self.yaxislabels