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remove filtering of common strains during loading #200

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Jan 24, 2024
Merged

remove filtering of common strains during loading #200

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39 changes: 0 additions & 39 deletions src/nplinker/loader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -198,13 +198,6 @@ def load(self):
if not self._load_genomics():
return False

# Restrict strain list to only relevant strains (those that are present
# in both genomic and metabolomic data)
# TODO add a config file option for this?
self._filter_only_common_strains()

# if we don't have at least *some* strains here it probably means missing mappings
# or a complete failure to parse things, so bail out
if len(self.strains) == 0:
raise Exception(f"Failed to find *ANY* strains, missing {STRAIN_MAPPINGS_FILENAME}?")

Expand Down Expand Up @@ -566,38 +559,6 @@ def _load_class_info(self):
self.chem_classes = chem_classes
return True

def _filter_only_common_strains(self):
"""Filter strain population to only strains present in both genomic and molecular data."""
# TODO: Maybe there should be an option to specify which strains are used, both so we can
# selectively exclude strains, and include strains that are missing from either side.
bgc_strains = {x.strain for x in self.bgcs}
spectrum_strains = set().union(*[x.strains for x in self.spectra])
common_strains = bgc_strains.intersection(spectrum_strains)
logger.debug(
"Filtering strains: genomics count {}, metabolomics count: {}".format(
len(bgc_strains), len(spectrum_strains)
)
)
logger.debug(f"Common strains found: {len(common_strains)}")

# write out a list of the common strains to the dataset folder (might be useful for
# anyone wanting to do additional filtering)
cs_path = os.path.join(self._root, "common_strains.csv")
logger.info(f"Writing common strain labels to {cs_path}")
with open(cs_path, "w") as cs:
cs.write("# strain label\n")
for strain in self.strains:
cs.write(f"{strain.id}\n")

# filter the master list of strains down to include only the common set
self.strains.filter(common_strains)

for gcf in self.gcfs:
gcf.strains.filter(common_strains)
for spec in self.spectra:
spec.strains.filter(common_strains)
logger.info("Strains filtered down to total of {}".format(len(self.strains)))


def find_via_glob(path, file_type, optional=False):
try:
Expand Down
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