def make_reports(self):
pham_counter = 0
total_no = len(self._phams.keys())
pham_items = self._phams.items()
pham_items.sort(
key=lambda item: (item[1][0].start_codon_location, item[0]))
sorted_keys = [item[0] for item in pham_items]
for pham_no in sorted_keys:
if pham_no is not None:
pham_counter += 1
gene_name = self._phams[pham_no][0].gene_id
self.update_gui(
"Aligning and Graphing %s \nPham %s (%d of %d)" %
(gene_name, pham_no, pham_counter, total_no),
(float(pham_counter) / total_no))
gene_report = GeneReport(self.base_name, self.phage_)
pham_no = gene_report.get_pham(pham_no)
pham = gene_report.make_report(whole=True)
print pham_no
genes = self._phams[pham_no]
for gene in genes:
print gene.gene_id
phage_gene = pham.genes[gene.gene_id]
gene_no = phamgene.get_gene_number(gene.gene_id)
self.phage_genes[gene_no] = {
'suggested_start':
phage_gene.suggested_start["most_called"],
'gene':
pham.genes[gene.gene_id],
'pham_no':
pham_no
}
def make_reports(self):
self.phage_genes = {}
pham_counter = 0
total_no = len(self._phams)
for pham_no in self._phams:
genes = self._phams[pham_no]
if pham_no is not None:
self.update_gui(
"Aligning and Graphing Pham %s \n Pham %d of %d" %
(pham_no, pham_counter, total_no),
float(pham_counter) / total_no)
gene_report = GeneReport(self.base_name,
self.name,
whole_phage=True)
pham_no = gene_report.get_pham(pham_no, genes)
pham = gene_report.make_report(True)
for gene in genes:
phage_gene = pham.genes[gene.gene_id]
gene_no = phamgene.get_gene_number(gene.gene_id)
self.phage_genes[gene_no] = {
'suggested_start':
phage_gene.suggested_start["most_called"],
'gene':
gene,
'pham_no':
pham_no
}
else:
for gene in genes:
self.phage_genes[gene.gene_id] = {
'pham_no': None,
"gene": gene,
"suggested_start": None
}
pham_counter += 1
def make_pham_genome(phage_genes, phage_name, length, file_path):
file_name = os.path.join(file_path, '%sPhamsGraph.pdf' % phage_name)
if check_file(file_name):
return
pham_colors = phams.get_pham_colors()
gd_diagram = GenomeDiagram.Diagram(phage_name)
gd_track = gd_diagram.new_track(1, name=phage_name, greytrack=1)
gd_pham_set = gd_track.new_set()
print "making genome page"
for gene_id in sorted(phage_genes.iterkeys()):
phage_gene = phage_genes[gene_id]
pham_no = phage_gene["pham_no"]
gene = phage_gene["gene"]
print pham_no, gene.gene_id
if pham_no is None:
pham_no = "None"
pham_color = 'Black'
else:
pham_color = colors.HexColor(pham_colors[str(pham_no)])
if gene.orientation == 'F':
gene_location = FeatureLocation(gene.start, gene.stop)
strand = 1
else:
strand = -1
gene_location = FeatureLocation(gene.stop, gene.start)
gene_feature = SeqFeature(gene_location, strand=strand)
gene_number = phamgene.get_gene_number(gene.gene_id)
# label the gene with the gene number
gd_pham_set.add_feature(gene_feature,
name=str(gene_number),
label=True,
label_size=6,
label_angle=75)
# label gene with pham color and name
gd_pham_set.add_feature(gene_feature,
color=pham_color,
name=str(pham_no),
label=True,
label_position='middle')
print type(length), length
gd_diagram.draw(format='linear',
orientation='portrait',
pagesize=reportlab.lib.pagesizes.letter,
fragments=8,
start=0,
end=length)
gd_diagram.write(file_name, "PDF")
def make_reports(self):
self.phage_genes = {}
pham_counter = 0
total_no = len(self._phams.keys())
for pham_no in self._phams.keys():
if pham_no is not None:
pham_counter += 1
self.update_gui("Aligning and Graphing Pham %s \n Pham %d of %d"
% (pham_no, pham_counter, total_no), (float(pham_counter)/total_no))
gene_report = GeneReport(self.base_name, self.phage_)
pham_no = gene_report.get_pham(pham_no)
pham = gene_report.make_report(whole=True)
print pham_no
genes = self._phams[pham_no]
for gene in genes:
print gene.gene_id
phage_gene = pham.genes[gene.gene_id]
gene_no = phamgene.get_gene_number(gene.gene_id)
self.phage_genes[gene_no] = {'suggested_start': phage_gene.suggested_start["most_called"],
'gene': gene,
'pham_no': pham_no}
def make_reports(self):
self.phage_genes = {}
pham_counter = 0
total_no = len(self._phams)
for pham_no in self._phams:
genes = self._phams[pham_no]
if pham_no is not None:
self.update_gui("Aligning and Graphing Pham %s \n Pham %d of %d"
% (pham_no, pham_counter, total_no), float(pham_counter)/total_no)
gene_report = GeneReport(self.base_name, self.name, whole_phage=True)
pham_no = gene_report.get_pham(pham_no, genes)
pham = gene_report.make_report(True)
for gene in genes:
phage_gene = pham.genes[gene.gene_id]
gene_no = phamgene.get_gene_number(gene.gene_id)
self.phage_genes[gene_no] = {'suggested_start': phage_gene.suggested_start["most_called"],
'gene': gene,
'pham_no': pham_no}
else:
for gene in genes:
self.phage_genes[gene.gene_id] = {'pham_no': None,
"gene": gene,
"suggested_start": None}
pham_counter += 1
def make_pham_genome(phage_genes, phage_name, length, file_path):
file_name = os.path.join(file_path,'%sPhamsGraph.pdf' % (phage_name))
if check_file(file_name):
return
pham_colors = phams.get_pham_colors()
gd_diagram = GenomeDiagram.Diagram(phage_name)
gd_track = gd_diagram.new_track(1, name=phage_name, greytrack=1)
gd_pham_set = gd_track.new_set()
print "making genome page"
for gene_id in sorted(phage_genes.iterkeys()):
phage_gene = phage_genes[gene_id]
pham_no = phage_gene["pham_no"]
gene = phage_gene["gene"]
print pham_no, gene.gene_id
if pham_no == None:
pham_no = "None"
pham_color = 'Black'
else:
pham_color = colors.HexColor(pham_colors[str(pham_no)])
if gene.orientation == 'F':
gene_location = FeatureLocation(gene.start, gene.stop)
strand = 1
else:
strand = -1
gene_location = FeatureLocation(gene.stop, gene.start)
gene_feature = SeqFeature(gene_location, strand=strand)
gene_number = phamgene.get_gene_number(gene.gene_id)
# label the gene with the gene number
gd_pham_set.add_feature(gene_feature, name=str(gene_number), label=True,
label_size=6, label_angle=75)
# label gene with pham color and name
gd_pham_set.add_feature(gene_feature, color=pham_color, name=str(pham_no), label=True, label_position='middle')
print type(length), length
gd_diagram.draw(format='linear', orientation='portrait', pagesize=letter, fragments=8, start=0, end=length)
gd_diagram.write(file_name, "PDF")
