def manage_analysis(self):
if self.annotation_mode in 'metacv':
print_verbose("For a detailed analysis blastn with XML output is needed")
else:
# test for blastrun with outfmt 5 mode
if is_xml(self.blast_output):
# create a SQLite DB from the xml file
self.parse_to_db(to_string(self.blast_output), self.parsed_db_out)
# test the exit code, because next script need the output as input
if self.exitcode is 0:
# update input
parser_out = absolute_path(update_reads(self.parsed_db_out,
self.parser_name,
'db'))
# raise step_number
self.step_number += 1
# create a new database with taxonomical annotations
self.annotate_db(parser_out, self.annotated_db_out)
# test the exit code, because next script need the output as input
if self.exitcode is 0:
# update input
annotated_output = absolute_path(update_reads(self.annotated_db_out,
self.R_annotate_name,
'db'))
# raise step_number
self.step_number += 1
# subset the taxonomical database for a better and
# faster analysis after the pipline has finished
self.subset_db(annotated_output, self.subseted_db_out, parser_out)
# raise step_number
self.step_number += 1
else:
print_verbose("ERROR: Annotated Database could not be subseted correctly")
# create a pie chart of the blast data with Krona Webtools
if self.krona:
self.krona_report(self.blast_output, self.krona_report_out, parser_out)
return [parser_out, annotated_output]
else:
print_verbose("ERROR: XML file could not be parsed")
# test for blast tabular output
elif is_tabular(self.blast_output) and self.krona is True:
self.krona_report(self.blast_output, self.krona_report_out, '')
return []
else:
print_verbose("ERROR: Blast output file is not in xml or tabular format.\n" +
"Please use outfmt 5 or 6 for Blast run")
return []
def krona_report(self, input, output, parser_output):
# create a dir for output
create_outputdir(output)
# generate path and name for output file
outfile = output + os.sep + self.krona_name + '.html'
# test type of input file
if is_tabular(input):
# print actual informations about the step on stdout
print_step(self.step_number,
'Analysis',
'Create Overview from tabular output',
self.krona_parameter)
newline()
# start the Krona import script for Blast tabular output
# pipe all output for stdout in a logfile
p = subprocess.Popen(shlex.split('perl -l %s %s -o %s %s %s'
% (self.perl_lib,
self.krona_exe,
outfile,
self.krona_parameter,
to_string(input))),
stdout = open_logfile(self.logdir + 'krona.log'),
stderr = open_logfile(self.logdir + 'krona.err.log'))
# wait until process is complete
p.wait()
if p.returncode:
raise KronaException(self.logdir + 'krona.err.log')
else:
# remove unused error logs
remove_empty_logfile(self.logdir + 'krona.err.log')
# print summary of the process after completion
print_verbose('Creation of Krona Pie Chart complete \n')
print_running_time(self.time)
newline()
elif is_xml(input) and is_db(parser_output):
print_step(self.step_number,
'Analysis',
'Create Overview from XML output',
self.krona_parameter)
# convert the values from database to tabular format
extract_tabular(to_string(parser_output), output)
# set the new input
input = update_reads(output, 'extracted_from_DB','tab')
# start the Krona import script for Blast tabular output
# pipe all output for stdout in a logfile
p = subprocess.Popen(shlex.split('perl -l %s %s -o %s %s %s'
% (self.perl_lib,
self.krona_exe,
outfile,
self.krona_parameter,
to_string(input))),
stdout = open_logfile(self.logdir + 'krona.log'),
stderr = open_logfile(self.logdir + 'krona.err.log'))
# wait until process is complete
p.wait()
if p.returncode:
raise KronaException(self.logdir + 'krona.err.log')
else:
# remove unused error logs
remove_empty_logfile(self.logdir + 'krona.err.log')
# print summary of the process after completion
print_verbose('Creation of Krona Pie Chart complete \n')
print_running_time(self.time)
newline()
elif not is_tabular(input) or not is_xml(input):
raise KronaFormatException()
else:
print_verbose('ERROR 25: Krona Report could not be generated, because of unknown reasons')
sys.exit(1)