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
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
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