def phamerated_phage_report(self):
phage_phams, seq_length = find_phams_of_a_phage(self.db, self.name)
for gene_name, pham_no in phage_phams:
gene_number = utils.get_gene_number(gene_name)
gene_id = self.name +'_' + str(gene_number)
gene = GeneReport(gene_number, self.name, self.is_phamerated, is_all=True)
self.genes[gene_number] = (gene, pham_no)
return self.phage_report(seq_length)
def phamerated_phage_report(self):
phage_phams, seq_length = find_phams_of_a_phage(self.db, self.name)
for gene_name, pham_no in phage_phams:
gene_number = utils.get_gene_number(gene_name)
gene_id = self.name + '_' + str(gene_number)
gene = GeneReport(gene_number,
self.name,
self.is_phamerated,
is_all=True)
self.genes[gene_number] = (gene, pham_no)
return self.phage_report(seq_length)
def make_report(self):
if self.is_phamerated:
print 'before phams found'
phams = self.phage.get_phams()
seq_length = self.phage.length()
print 'after phams found'
for gene_name, pham_no in phams:
if self.gui:
if self.event.is_set():
print 'stopped in make_report'
sys.exit(0)
gene_number = utils.get_gene_number(gene_name)
# gene_id = self.name +'_' + str(gene_number)
gene = genes.Gene(gene_number,
self.name,
self.is_phamerated,
self.config,
self.db,
is_all=True)
self.genes[gene_number] = (gene, pham_no)
return self.phage_report(seq_length)
else:
if self.gui:
print 'in unphamerated pham'
if self.event.is_set():
sys.exit(0)
self.gui.update('Finished Making Unphamerated Genes.', .02)
for gene_number in self.genes:
if self.gui:
if self.event.is_set():
sys.exit(0)
gene = self.genes[gene_number][0]
pham_no = self.genes[gene_number][1]
if pham_no == None:
pass
else:
if pham_no not in self.unphamerated_genes:
self.unphamerated_genes[pham_no] = []
self.unphamerated_genes[pham_no].append(gene)
return self.phage_report(seq_length)
def phage_report(self, seq_length):
phams_done = []
pham_genes = {}
self.total_phams = len(set(self.genes.values()))
for gene_number in self.genes:
if self.gui and self.event.is_set():
sys.exit(0)
self.current_pham[0] += 1
gene = self.genes[gene_number][0]
pham_no = self.genes[gene_number][1]
self.current_pham[1] = pham_no
if pham_no not in phams_done and pham_no is not None:
if not self.is_phamerated:
unphamerated_genes = self.unphamerated_genes[pham_no]
else:
unphamerated_genes = None
if self.gui:
if self.event.is_set():
sys.exit(0)
self.gui.update(
'Aligning and Graphing Pham %s (Gene %s) \n' %
(pham_no, gene_number) + 'Pham %d of %d' %
(self.current_pham[0], self.total_phams),
(float(self.current_pham[0]) / self.total_phams) - .05)
pham = gene.make_report(genes=unphamerated_genes)
for gene_record in pham.phage_gene:
gene_num = utils.get_gene_number(gene_record.id)
suggested_start = pham.suggest_start_site_coord(
gene_record.id)
gene_record.annotations[
'suggested_start'] = suggested_start
pham_genes[gene_num] = gene_record, gene.pham_no
phams_done.append(pham_no)
if self.gui:
if self.event.is_set():
sys.exit(0)
self.gui.update('Making Final Report', .97)
self.make_pham_genome(pham_genes, seq_length)
self.make_suggested_starts_page(pham_genes)
return self.make_phage_report(pham_genes, seq_length)
def phage_report(self, seq_length):
phams_done = []
pham_genes = {}
self.total_phams = len(set(self.genes.values()))
for gene_number in self.genes:
if self.gui and self.event.is_set():
sys.exit(0)
self.current_pham[0] += 1
gene = self.genes[gene_number][0]
pham_no = self.genes[gene_number][1]
self.current_pham[1] = pham_no
if pham_no not in phams_done and pham_no is not None:
if not self.is_phamerated:
unphamerated_genes = self.unphamerated_genes[pham_no]
else:
unphamerated_genes = None
if self.gui:
if self.event.is_set():
sys.exit(0)
self.gui.update('Aligning and Graphing Pham %s (Gene %s) \n' % (pham_no, gene_number) +
'Pham %d of %d' % (self.current_pham[0], self.total_phams)
, (float(self.current_pham[0])/ self.total_phams) - .05 )
pham = gene.make_report(genes=unphamerated_genes)
for gene_record in pham.phage_gene:
gene_num = utils.get_gene_number(gene_record.id)
suggested_start = pham.suggest_start_site_coord(gene_record.id)
gene_record.annotations['suggested_start'] = suggested_start
pham_genes[gene_num] = gene_record, gene.pham_no
phams_done.append(pham_no)
if self.gui:
if self.event.is_set():
sys.exit(0)
self.gui.update('Making Final Report', .97)
self.make_pham_genome(pham_genes, seq_length)
self.make_suggested_starts_page(pham_genes)
return self.make_phage_report(pham_genes, seq_length)
def make_report(self):
if self.is_phamerated:
print 'before phams found'
phams = self.phage.get_phams()
seq_length = self.phage.length()
print 'after phams found'
for gene_name, pham_no in phams:
if self.gui:
if self.event.is_set():
print 'stopped in make_report'
sys.exit(0)
gene_number = utils.get_gene_number(gene_name)
# gene_id = self.name +'_' + str(gene_number)
gene = genes.Gene(gene_number, self.name, self.is_phamerated, self.config, self.db, is_all=True)
self.genes[gene_number] = (gene, pham_no)
return self.phage_report(seq_length)
else:
if self.gui:
print 'in unphamerated pham'
if self.event.is_set():
sys.exit(0)
self.gui.update('Finished Making Unphamerated Genes.', .02)
for gene_number in self.genes:
if self.gui:
if self.event.is_set():
sys.exit(0)
gene = self.genes[gene_number][0]
pham_no = self.genes[gene_number][1]
if pham_no == None:
pass
else:
if pham_no not in self.unphamerated_genes:
self.unphamerated_genes[pham_no] = []
self.unphamerated_genes[pham_no].append(gene)
return self.phage_report(seq_length)
