def run_parser():
padding = 300
directory_and_file = entry.get()
file_name = directory_and_file.split(
'/')[-2] + '/' + directory_and_file.split('/')[-1]
file_type = check_file_type(file_name)
username = entry_name.get()
dictionary = {}
nm = ''
parser_details = ''
#primer_list = [name.split('.')[0] for name in os.listdir('primers')]
primer_list = os.listdir('primers')
primer_applied = False
if file_type == 'gbk':
print 'Running parser'
gbk_reader = GbkParser(file_name, padding, args.trim_flanking)
dictionary = gbk_reader.run()
parser_details = gbk_reader.get_version
elif file_type == 'lrg':
print 'Running parser'
lrg_reader = LrgParser(file_name, padding, args.trim_flanking)
dictionary = lrg_reader.run()
parser_details = lrg_reader.get_version
if dictionary['genename'] + '.csv' in primer_list:
primer_applied = True
primer_label = primer()
primer_details = 'Primer Labels: ' + primer_label.get_version
dictionary = primer_label.run(dictionary, os.getcwd())
parser_details = '{0} {1} {2}'.format(file_type.upper(), 'Parser:',
parser_details)
os.chdir("output")
for transcript in dictionary['transcripts']:
print 'transcript: %d' % transcript
input_reader = Reader()
writer = LatexWriter()
reader_details = 'Reader: ' + input_reader.get_version
writer_details = 'Writer: ' + writer.get_version
xml_gui_details = 'Control: ' + get_version()
if primer_applied:
list_of_versions = [parser_details, reader_details, \
writer_details, xml_gui_details, primer_details]
else:
list_of_versions = [parser_details, reader_details, \
writer_details, xml_gui_details]
lrg_num = file_name.split('.')[0].split('/')[1].replace(
'_', '\_') + 't' + str(transcript)
input_list, nm = input_reader.run(dictionary, transcript,
args.write_as_latex,
list_of_versions, args.print_clashes,
file_type, lrg_num, username)
if file_type == 'gbk':
filename = dictionary['genename'] + '_' + nm
else:
filename = dictionary['genename'] + '_' + file_name.split(
'.')[0].split('/')[1] + 't' + str(transcript)
if args.write_as_latex:
latex_file, pdf_file = writer.run(input_list, filename,
args.write_as_latex)
call(["pdflatex", "-interaction=batchmode", latex_file])
clean_up(os.getcwd(), pdf_file)
move_files(latex_file)
else:
latex_file = writer.run(input_list, filename, args.write_as_latex)
# quick step to allow for non-overlapping writes
print str(transcript) + ' has been printed'
print "Process has completed successfully"
root.quit()
