From d1adc66569a54b6ae7dd9f32db07ff58079f06a6 Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Tue, 12 Dec 2023 16:25:57 +0100
Subject: [PATCH] remove method `_filter_only_common_strains`

The loading part should return all relevant strains to scoring part. It should allow users to specify if they want to filter common strains or not in the scoring part (to be implemented in the class `NPLinker`).
---
 src/nplinker/loader.py | 39 ---------------------------------------
 1 file changed, 39 deletions(-)

diff --git a/src/nplinker/loader.py b/src/nplinker/loader.py
index 521c6ec0..4ceda3ac 100644
--- a/src/nplinker/loader.py
+++ b/src/nplinker/loader.py
@@ -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}?")
 
@@ -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: