def main():
args = get_arguments()
config = utils.get_config()
print config["count"]
phamgene.check_protein_db(config["count"])
# --Phamerated and only one gene
if args.gene_number != -1 and args.phage is not None and args.unphamed is False:
gene = report.GeneReport(args.phage, args.gene_number, True)
print gene
gene.get_pham()
gene.make_report()
final_file, s = gene.merge_report()
# --Unphameratored Phage with only one gene
elif args.given_start > -1 and args.phage is not None and args.unphamed is True:
# given start and stop coordinates and orientation
one_or_all = 'One'
given_start = args.given_start
given_stop = args.given_stop
given_orientation = args.given_orientation
gene_name = args.phage + '_' + str(args.gene_number)
gene = report.GeneReport(args.phage,
args.gene_number,
fasta_file=args.fasta)
gene.make_unpham_gene(given_start, given_stop, given_orientation)
print gene
gene.make_report()
final_file, s = gene.merge_report()
# --Phameratored or Unphameratored Phages with all genes
elif args.pham_no == -1 and args.phage is not None and args.unphamed is False:
phage = report.PhageReport(args.phage, gui=None)
final_file, short_final = phage.final_report()
elif args.pham_no == -1 and args.phage is not None and args.unphamed is True:
phage = report.UnPhamPhageReport(args.phage,
fasta_file=args.fasta,
profile_file=args.profile,
gui=None)
final_file, short_final = phage.final_report()
elif args.phage is None:
pham = report.PhamReport(args.pham_no)
if args.save_json is True:
final_file, short_final = pham.final_report(save_json=True)
else:
final_file, short_final = pham.final_report()
def starterate(self, button):
db = self.db_connect()
phamgene.check_protein_db(self.config_info['count'])
phage_name = self.find_phage_in_db(db, str(self.info['phage']))
print 'uiStarterate.starterate new phage, name is ', self.info['phage']
print 'uiStarterate.starterate phamerated is ', self.info['phamerated']
print 'uiStarterate.starterate self.info.all is ', self.info['all']
if phage_name == None and self.info["phamerated"] and not self.info["pham"]:
self.phameratored_exception(self.info["phage"])
return
elif self.info["phamerated"]:
self.info["phage"] = phage_name
self.progress_label = Gtk.Label('Starterator is starting')
self.progress_bar = Gtk.ProgressBar()
self.box.pack_start(self.progress_label, False, False, 0)
self.box.pack_start(self.progress_bar, False, False, 0)
self.show_all()
self.starterate_thread = StarteratorThread(self, db, self.config_info, self.info)
self.starterate_thread.start()
def starterate(self, button):
db = self.db_connect()
phamgene.check_protein_db(self.config_info['count'])
phage_name = self.find_phage_in_db(db, str(self.info['phage']))
print 'uiStarterate.starterate new phage, name is ', self.info['phage']
print 'uiStarterate.starterate phamerated is ', self.info['phamerated']
print 'uiStarterate.starterate self.info.all is ', self.info['all']
if phage_name == None and self.info[
"phamerated"] and not self.info["pham"]:
self.phameratored_exception(self.info["phage"])
return
elif self.info["phamerated"]:
self.info["phage"] = phage_name
self.progress_label = Gtk.Label('Starterator is starting')
self.progress_bar = Gtk.ProgressBar()
self.box.pack_start(self.progress_label, False, False, 0)
self.box.pack_start(self.progress_bar, False, False, 0)
self.show_all()
self.starterate_thread = StarteratorThread(self, db, self.config_info,
self.info)
self.starterate_thread.start()
def main():
args = get_arguments()
config = utils.get_config()
print config["count"]
phamgene.check_protein_db(config["count"])
# --Phamerated and only one gene
if args.gene_number != -1 and args.phage != None and args.unphamed == False:
gene = report.GeneReport(args.phage, args.gene_number, True)
print gene
gene.get_pham()
gene.make_report()
final_file, s = gene.merge_report()
# --Unphameratored Phage with only one gene
elif args.given_start > -1 and args.phage != None and args.unphamed == True:
# given start and stop coordinates and orientation
one_or_all = 'One'
given_start = args.given_start
given_stop = args.given_stop
given_orientation = args.given_orientation
gene_name = args.phage + '_' + str(args.gene_number)
gene = report.GeneReport(args.phage, args.gene_number, fasta_file=args.fasta)
gene.make_unpham_gene(given_start, given_stop, given_orientation)
print gene
gene.make_report()
final_file, s = gene.merge_report()
# --Phameratored or Unphameratored Phages with all genes
elif args.pham_no == -1 and args.phage != None and args.unphamed == False:
phage = report.PhageReport(args.phage, gui=None)
final_file, short_final = phage.final_report()
elif args.pham_no == -1 and args.phage != None and args.unphamed == True:
phage = report.UnPhamPhageReport(args.phage, fasta_file=args.fasta, profile_file=args.profile, gui=None)
final_file, short_final = phage.final_report()
elif args.phage == None:
pham = report.PhamReport(args.pham_no)
final_file, short_final = pham.final_report()