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add option to include pathway name in output map files
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@semiller10
semiller10 committed Sep 19, 2024
1 parent dea23c7 commit 7e38e09
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Showing 2 changed files with 136 additions and 20 deletions.
139 changes: 120 additions & 19 deletions anvio/keggmapping.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,10 @@ class Mapper:
available_pathway_numbers : List[str]
ID numbers of all pathways set up with PNG and KGML files in the KEGG data directory.
pathway_names : Dict[str, str]
The names of all KEGG pathways, including those without files in the KEGG data directory.
Keys are pathway ID numbers and values are pathway names.
rn_constructor : anvio.reactionnetwork.Constructor
Used for loading reaction networks from anvi'o databases.
Expand All @@ -83,6 +87,9 @@ class Mapper:
overwrite_output : bool
If True, methods in this class overwrite existing output files.
name_files : bool
Include the pathway name along with the number in output map file names.
run : anvio.terminal.Run
This object prints run information to the terminal.
Expand All @@ -93,6 +100,7 @@ def __init__(
self,
kegg_dir: str = None,
overwrite_output: bool = FORCE_OVERWRITE,
name_files: bool = False,
run: terminal.Run = terminal.Run(),
progress: terminal.Progress = terminal.Progress(),
quiet: bool = QUIET
Expand All @@ -108,6 +116,9 @@ def __init__(
overwrite_output : bool, anvio.FORCE_OVERWRITE
If True, methods in this class overwrite existing output files.
name_files : bool, False
Include the pathway name along with the number in output map file names.
run : anvio.terminal.Run, anvio.terminal.Run()
This object prints run information to the terminal.
Expand Down Expand Up @@ -139,11 +150,19 @@ def __init__(
available_pathway_numbers.append(row.Index[-5:])
self.available_pathway_numbers = available_pathway_numbers

pathway_names: Dict[str, str] = {}
for pathway_number, pathway_name in pd.read_csv(
self.kegg_context.kegg_pathway_list_file, sep='\t', header=None
).itertuples(index=False):
pathway_names[pathway_number[3:]] = pathway_name
self.pathway_names = pathway_names

self.rn_constructor = rn.Constructor(kegg_dir=self.kegg_context.kegg_data_dir)

self.xml_ops = kgml.XMLOps()
self.drawer = kgml.Drawer(kegg_dir=self.kegg_context.kegg_data_dir)

self.name_files = name_files
self.overwrite_output = overwrite_output
self.run = run
self.progress = progress
Expand Down Expand Up @@ -750,9 +769,13 @@ def map_contigs_databases_kos(
color_hexcode=color_hexcode,
draw_maps_lacking_kos=True
)
paths_to_remove.append(
os.path.join(output_dir, project_name, f'kos_{pathway_number}.pdf')
)
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
paths_to_remove.append(os.path.join(
output_dir, project_name, f'kos_{pathway_number}{pathway_name}.pdf'
))
self.progress = progress
self.run = run

Expand All @@ -761,7 +784,11 @@ def map_contigs_databases_kos(
filesnpaths.gen_output_directory(grid_dir, progress=self.progress, run=self.run)
for pathway_number in pathway_numbers:
self.progress.update(pathway_number)
unified_map_path = os.path.join(output_dir, f'kos_{pathway_number}.pdf')
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
unified_map_path = os.path.join(output_dir, f'kos_{pathway_number}{pathway_name}.pdf')
if not os.path.exists(unified_map_path):
continue
in_paths = [unified_map_path]
Expand All @@ -773,15 +800,23 @@ def map_contigs_databases_kos(
landscape = True if input_aspect_ratio > 1 else False

for project_name in draw_grid_project_names:
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
individual_map_path = os.path.join(
output_dir, project_name, f'kos_{pathway_number}.pdf'
output_dir, project_name, f'kos_{pathway_number}{pathway_name}.pdf'
)
if not os.path.exists(individual_map_path):
break
in_paths.append(os.path.join(output_dir, project_name, f'kos_{pathway_number}.pdf'))
in_paths.append(individual_map_path)
labels.append(project_name)
else:
out_path = os.path.join(grid_dir, f'kos_{pathway_number}.pdf')
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
out_path = os.path.join(grid_dir, f'kos_{pathway_number}{pathway_name}.pdf')
self.make_grid(in_paths, out_path, labels=labels, landscape=landscape)
drawn['grid'][pathway_number] = True
self.progress.end()
Expand Down Expand Up @@ -1245,9 +1280,13 @@ def map_pan_database_kos(
color_hexcode=color_hexcode,
draw_maps_lacking_kos=True
)
paths_to_remove.append(
os.path.join(output_dir, genome_name, f'kos_{pathway_number}.pdf')
)
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
paths_to_remove.append(os.path.join(
output_dir, genome_name, f'kos_{pathway_number}{pathway_name}.pdf'
))
self.progress = progress
self.run = run

Expand All @@ -1256,7 +1295,11 @@ def map_pan_database_kos(
filesnpaths.gen_output_directory(grid_dir, progress=self.progress, run=self.run)
for pathway_number in pathway_numbers:
self.progress.update(pathway_number)
unified_map_path = os.path.join(output_dir, f'kos_{pathway_number}.pdf')
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
unified_map_path = os.path.join(output_dir, f'kos_{pathway_number}{pathway_name}.pdf')
if not os.path.exists(unified_map_path):
continue
in_paths = [unified_map_path]
Expand All @@ -1268,15 +1311,23 @@ def map_pan_database_kos(
landscape = True if input_aspect_ratio > 1 else False

for genome_name in draw_grid_genome_names:
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
individual_map_path = os.path.join(
output_dir, genome_name, f'kos_{pathway_number}.pdf'
output_dir, genome_name, f'kos_{pathway_number}{pathway_name}.pdf'
)
if not os.path.exists(individual_map_path):
break
in_paths.append(os.path.join(output_dir, genome_name, f'kos_{pathway_number}.pdf'))
in_paths.append(individual_map_path)
labels.append(genome_name)
else:
out_path = os.path.join(grid_dir, f'kos_{pathway_number}.pdf')
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
out_path = os.path.join(grid_dir, f'kos_{pathway_number}{pathway_name}.pdf')
self.make_grid(in_paths, out_path, labels=labels, landscape=landscape)
drawn['grid'][pathway_number] = True
self.progress.end()
Expand Down Expand Up @@ -1547,7 +1598,8 @@ def _find_maps(self, output_dir: str, prefix: str, patterns: List[str] = None) -
created if it does not exist.
prefix : str
Output filenames are formatted as <prefix>_<pathway_number>.pdf.
Output filenames are formatted as <prefix>_<pathway_number>.pdf or
<prefix>_<pathway_number>_<pathway_name>.pdf.
patterns : List[str], None
Regex patterns of pathway numbers, which are five digits.
Expand All @@ -1559,7 +1611,11 @@ def _find_maps(self, output_dir: str, prefix: str, patterns: List[str] = None) -

if not self.overwrite_output:
for pathway_number in pathway_numbers:
out_path = os.path.join(output_dir, f'{prefix}_{pathway_number}.pdf')
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
out_path = os.path.join(output_dir, f'{prefix}_{pathway_number}{pathway_name}.pdf')
if os.path.exists(out_path):
raise ConfigError(
f"Output files would be overwritten in the output directory, {output_dir}. "
Expand Down Expand Up @@ -1705,7 +1761,11 @@ def _draw_map_kos_single_color(
)

# Draw the map.
out_path = os.path.join(output_dir, f'kos_{pathway_number}.pdf')
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
out_path = os.path.join(output_dir, f'kos_{pathway_number}{pathway_name}.pdf')
if os.path.exists(out_path) and self.overwrite_output:
os.remove(out_path)
else:
Expand Down Expand Up @@ -1826,7 +1886,11 @@ def _draw_map_kos_original_color(
)

# Draw the map.
out_path = os.path.join(output_dir, f'kos_{pathway_number}.pdf')
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
out_path = os.path.join(output_dir, f'kos_{pathway_number}{pathway_name}.pdf')
if os.path.exists(out_path) and self.overwrite_output:
os.remove(out_path)
else:
Expand Down Expand Up @@ -1991,7 +2055,11 @@ def _draw_map_kos_membership(
)

# Draw the map.
out_path = os.path.join(output_dir, f'kos_{pathway_number}.pdf')
if self.name_files:
pathway_name = '_' + self._get_filename_pathway_name(pathway_number)
else:
pathway_name = ''
out_path = os.path.join(output_dir, f'kos_{pathway_number}{pathway_name}.pdf')
if os.path.exists(out_path) and self.overwrite_output:
os.remove(out_path)
else:
Expand Down Expand Up @@ -2036,6 +2104,39 @@ def _get_pathway(self, pathway_number: str) -> kgml.Pathway:

return pathway

def _get_filename_pathway_name(self, pathway_number: str) -> str:
"""
Format the pathway name corresponding to the number to include in file paths.
Replace all non-alphanumeric characters except parentheses, brackets, and curly braces with
underscores. Replace multiple consecutive underscores with a single underscore. Strip
leading and trailing underscores.
Parameters
==========
pathway_number : str
Numeric ID of a pathway map.
Returns
=======
str
Altered version of the pathway name.
"""
try:
pathway_name = self.pathway_names[pathway_number]
except KeyError:
raise ConfigError(
f"The pathway number, '{pathway_number}', is not recognized in the table of KEGG "
"pathway names set up in the KEGG data directory, which can be found here: "
f"'{self.kegg_context.kegg_pathway_list_file}'."
)

altered = re.sub(r'[^a-zA-Z0-9()\[\]\{\}]', '_', pathway_name)
altered = re.sub(r'_+', '_', altered)
altered = altered.strip('_')

return altered

def _draw_colorbar(
self,
colors: Iterable,
Expand Down
17 changes: 16 additions & 1 deletion bin/anvi-draw-kegg-pathways
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,11 @@ def main() -> None:
check_kegg_data(args)
consolidate_contigs_dbs(args)

mapper = Mapper(kegg_dir=args.kegg_dir, overwrite_output=args.overwrite_output_destinations)
mapper = Mapper(
kegg_dir=args.kegg_dir,
overwrite_output=args.overwrite_output_destinations,
name_files=args.name_files
)

performed = False
if (
Expand Down Expand Up @@ -113,6 +117,17 @@ def get_args() -> Namespace:
groupOUT = parser.add_argument_group("OUTPUT", "Output files")
groupOUT.add_argument(*A('output-dir'), **K('output-dir'))
groupOUT.add_argument(*A('overwrite-output-destinations'), **K('overwrite-output-destinations'))
groupOUT.add_argument(
'--name-files', action='store_true', default=False, help=
"Include the pathway name along with the number in output map file names. For example, in "
"drawing KO presence/absence data, the 'Glycolysis / Gluconeogenesis' map would be saved "
"by default to a file named 'kos_00010.pdf', but with this flag would be saved to a file "
"named 'kos_00010_Glycolysis_Gluconeogenesis.pdf'. Likewise, the file name for "
"'Glycosylphosphatidylinositol (GPI)-anchor biosynthesis' would be "
"'kos_00563_Glycosylphosphatidylinositol_(GPI)_anchor_biosynthesis.pdf', and the file "
"name for 'Biosynthesis of 12-, 14- and 16-membered macrolides' would be "
"'kos_00522_Biosynthesis_of_12_14_and_16_membered_macrolides.pdf' with this flag."
)
groupOUT.add_argument(
'--draw-individual-files', nargs='*', help=
"Draw pathway maps for individual contigs databases if multiple databases are provided, or "
Expand Down

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