def output_maps(self, all_mapping_results, form):
csv_files = CSVFiles()
## Obtain OutputPrinter: out file set to None. CSV file will be asigned later
beauty_nums = True
show_headers = True
if form.get_collapsed_view():
output_printer = OutputFacade.get_collapsed_printer(None, self._verbose, beauty_nums, show_headers)
else:
output_printer = OutputFacade.get_expanded_printer(None, self._verbose, beauty_nums, show_headers)
## Output the different maps
multiple_param = form.get_multiple()
for mapping_results in all_mapping_results:
map_config = mapping_results.get_map_config()
map_id = map_config.get_id()
map_csv_files = MapCSVFiles(map_id)
csv_files.set_map_csv_files(map_id, map_csv_files)
## Map positions
csv_file = self._output_map(mapping_results, output_printer, multiple_param)
map_csv_files.set_mapped(csv_file)
## Enriched
if form.get_show_markers() and mapping_results.get_map_with_markers():
csv_file = self._output_map_with_markers(mapping_results, output_printer, multiple_param)
map_csv_files.set_map_with_markers(csv_file)
if form.get_show_genes() and mapping_results.get_map_with_genes():
annotator = mapping_results.get_annotator()
csv_file = self._output_map_with_genes(mapping_results, output_printer, multiple_param, annotator)
map_csv_files.set_map_with_genes(csv_file)
if form.get_show_anchored() and mapping_results.get_map_with_anchored():
csv_file = self._output_map_with_anchored(mapping_results, output_printer, multiple_param)
map_csv_files.set_map_with_anchored(csv_file)
## Unmapped
if mapping_results.get_unmapped():
csv_file = self._output_unmapped(mapping_results, output_printer)
map_csv_files.set_unmapped(csv_file)
## Unaligned
if mapping_results.get_unaligned():
csv_file = self._output_unaligned(mapping_results, output_printer)
map_csv_files.set_unaligned(csv_file)
return csv_files
## END
def __features_to_map_file(features, maps_path, map_config, map_output_path,
verbose_param):
multiple_param = True
mapMarkers = MapMarkers(maps_path, map_config, verbose=verbose_param)
unaligned = [] # Better this than None
mapMarkers.create_map(features, unaligned,
map_config.get_default_sort_by(), multiple_param)
mapping_results = mapMarkers.get_mapping_results()
sys.stderr.write("Mapped results " +
str(len(mapping_results.get_mapped())) + "\n")
map_output = open(map_output_path, 'w')
try:
outputPrinter = OutputFacade.get_expanded_printer(
map_output,
verbose=verbose_param,
beauty_nums=False,
show_headers=True)
outputPrinter.print_map(mapping_results.get_mapped(), map_config,
multiple_param)
except Exception as e:
raise e
finally:
map_output.close()
return
def __features_to_map_file(features, maps_path, map_config, map_output_path, verbose_param):
multiple_param = True
mapMarkers = MapMarkers(maps_path, map_config, verbose = verbose_param)
unaligned = [] # Better this than None
mapMarkers.create_map(features, unaligned, map_config.get_default_sort_by(), multiple_param)
mapping_results = mapMarkers.get_mapping_results()
sys.stderr.write("Mapped results "+str(len(mapping_results.get_mapped()))+"\n")
map_output = open(map_output_path, 'w')
try:
outputPrinter = OutputFacade.get_expanded_printer(map_output, verbose = verbose_param,
beauty_nums = False, show_headers = True)
outputPrinter.print_map(mapping_results.get_mapped(), map_config, multiple_param)
except Exception as e:
raise e
finally:
map_output.close()
return
datasets_facade = DatasetsFacade(datasets_config, datasets_path, maps_path, verbose = verbose_param)
# GenesAnnotator
if show_genes and load_annot:
## Load annotation config
dsannot_conf_file = __app_path+DATASETS_ANNOTATION_CONF
anntypes_conf_file = __app_path+ANNOTATION_TYPES_CONF
annot_path = paths_config.get_annot_path()
annotator = AnnotatorsFactory.get_annotator(dsannot_conf_file, anntypes_conf_file, annot_path, verbose_param)
else:
annotator = None
# OutputFacade
if collapsed_view:
outputPrinter = OutputFacade.get_collapsed_printer(sys.stdout, verbose = verbose_param, beauty_nums = beauty_nums, show_headers = True)
else:
outputPrinter = OutputFacade.get_expanded_printer(sys.stdout, verbose = verbose_param, beauty_nums = beauty_nums, show_headers = True)
# Temp directory
tmp_files_dir = paths_config.get_tmp_files_path()
########### Create maps
###########
for map_id in maps_ids:
sys.stderr.write("bmap_align: Map "+map_id+"\n")
map_config = maps_config.get_map_config(map_id)
databases_ids = map_config.get_db_list()
sort_by = map_config.check_sort_param(map_config, sort_param, DEFAULT_SORT_PARAM)
## Load annotation config
dsannot_conf_file = __app_path + DATASETS_ANNOTATION_CONF
anntypes_conf_file = __app_path + ANNOTATION_TYPES_CONF
annot_path = paths_config.get_annot_path()
annotator = AnnotatorsFactory.get_annotator(dsannot_conf_file,
anntypes_conf_file,
annot_path, verbose_param)
else:
annotator = None
# OutputFacade
if collapsed_view:
outputPrinter = OutputFacade.get_collapsed_printer(
sys.stdout,
verbose=verbose_param,
beauty_nums=beauty_nums,
show_headers=True)
else:
outputPrinter = OutputFacade.get_expanded_printer(
sys.stdout,
verbose=verbose_param,
beauty_nums=beauty_nums,
show_headers=True)
# Temp directory
tmp_files_dir = paths_config.get_tmp_files_path()
########### Create maps
###########
for map_id in maps_ids:
def output_maps(self, all_mapping_results, form):
csv_files = CSVFiles()
## Obtain OutputPrinter: out file set to None. CSV file will be asigned later
beauty_nums = True
show_headers = True
if form.get_collapsed_view():
output_printer = OutputFacade.get_collapsed_printer(
None, self._verbose, beauty_nums, show_headers)
else:
output_printer = OutputFacade.get_expanded_printer(
None, self._verbose, beauty_nums, show_headers)
## Output the different maps
multiple_param = form.get_multiple()
for mapping_results in all_mapping_results:
map_config = mapping_results.get_map_config()
map_id = map_config.get_id()
map_csv_files = MapCSVFiles(map_id)
csv_files.set_map_csv_files(map_id, map_csv_files)
## Map positions
csv_file = self._output_map(mapping_results, output_printer,
multiple_param)
map_csv_files.set_mapped(csv_file)
## Enriched
if form.get_show_markers(
) and mapping_results.get_map_with_markers():
csv_file = self._output_map_with_markers(
mapping_results, output_printer, multiple_param)
map_csv_files.set_map_with_markers(csv_file)
if form.get_show_genes() and mapping_results.get_map_with_genes():
annotator = mapping_results.get_annotator()
csv_file = self._output_map_with_genes(mapping_results,
output_printer,
multiple_param,
annotator)
map_csv_files.set_map_with_genes(csv_file)
if form.get_show_anchored(
) and mapping_results.get_map_with_anchored():
csv_file = self._output_map_with_anchored(
mapping_results, output_printer, multiple_param)
map_csv_files.set_map_with_anchored(csv_file)
## Unmapped
if mapping_results.get_unmapped():
csv_file = self._output_unmapped(mapping_results,
output_printer)
map_csv_files.set_unmapped(csv_file)
## Unaligned
if mapping_results.get_unaligned():
csv_file = self._output_unaligned(mapping_results,
output_printer)
map_csv_files.set_unaligned(csv_file)
return csv_files
## END
sys.stderr.write("\nWorking with map:"+map_id+"\n")
map_config = maps_config.get_map_config(map_id)
sys.stdout.write(">>"+map_config.get_name()+"\n")
databases_ids = map_config.get_db_list()
# Perform alignments
alignment_results = facade.perform_alignment(query_fasta_path, databases_ids, databases_config, search_type, aligner_list, \
threshold_id, threshold_cov, n_threads)
aligned = alignment_results.get_aligned()
########## Output
alignments_printer = OutputFacade.get_alignments_printer(search_type, databases_config)
alignments_printer.output_results(aligned, databases_ids)
except m2pException as m2pe:
sys.stderr.write("\nThere was an error.\n")
sys.stderr.write(m2pe.msg+"\n")
#traceback.print_exc(file=sys.stderr)
except Exception as e:
#traceback.print_exc(file=sys.stderr)
sys.stderr.write("\nThere was an error.\n")
sys.stderr.write(str(e)+"\n")
sys.stderr.write('If you can not solve it please contact [email protected] ('+\
'laboratory of computational biology at EEAD).\n')
finally:
pass