def run_parser(filepath, request):
print >>sys.stderr, 'Parsing started with {}'.format(filepath)
base_file_path = os.getcwd()
try:
padding = 300
file_type = check_file_type(filepath)
if file_type == 'file error':
error = 'This file is not the correct input type, please try an LRG or GB file'
document_list = created_documents.objects.order_by('-created_on')
return render(request, 'web_interface/app_homepage.html', {'form': UploadForm(),
'document_list': document_list,
'error_message': error})
dictionary = {}
if file_type == 'gbk':
gbk_reader = GbkParser(filepath, padding, True)
dictionary = gbk_reader.run()
parser_details = gbk_reader.get_version
elif file_type == 'lrg':
lrg_reader = LrgParser(filepath, padding, True)
dictionary = lrg_reader.run()
parser_details = lrg_reader.get_version
parser_details = '{0} {1} {2}'.format(file_type.upper(), 'Parser:', parser_details)
os.chdir('web_interface')
os.chdir('output')
for transcript in dictionary['transcripts']:
input_reader = Reader()
writer = LatexWriter()
reader_details = 'Reader: ' + input_reader.get_version
writer_details = 'Writer: ' + writer.get_version
xml_gui_details = 'Control: {}'.format(get_version)
list_of_versions = [parser_details, reader_details, writer_details, xml_gui_details]
input_list, nm = input_reader.run(dictionary, transcript, True, list_of_versions, True, file_type, 'web user')
transcript_accession = dictionary['transcripts'][transcript]['NM_number']
file_name = transcript_accession
latex_file, pdf_file = writer.run(input_list, file_name)
call(["pdflatex", "-interaction=batchmode", latex_file])
save_as_model = created_documents(transcript=transcript_accession,
location=pdf_file,
gene=dictionary['genename'],
created_on=datetime.now())
save_as_model.save()
delete_all_but_most_recent()
except:
os.chdir(base_file_path)
os.chdir(base_file_path)
clean_up(os.path.join('web_interface', 'output'))
clean_up(os.path.join('web_interface', 'input'))
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()
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()